Using ChemFinder - CambridgeSoft

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CS ChemFinder 8.0
for Windows
User’s Guide
a stand alone application within
ChemOffice, an integrated suite including
Chem3D for molecular modeling and analysis,
ChemFinder for searching and information integration,
ChemInfo for chemical and reference databases, and
E-Notebook for electronic journal and information.

License Information
ChemOffice, ChemDraw, Chem3D, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,
ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright © 1986-2003
by CambridgeSoft Corporation (CS) with all rights reserved worldwide. MOPAC 2000 is Copyright © 1993-2003
by Fujitsu Limited with all rights reserved. Information in this document is subject to change without notice and
does not represent a commitment on the part of CS. Both these materials and the right to use them are owned exclusively
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used only as provided for in said agreement.
ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder, and ChemInfo are not supplied with copy protection.
Please do not duplicate any of the copyrighted materials except for your personal backups without written permission
from CS. To do so would be in violation of federal and international law, and may result in criminal as well
as civil penalties. You may use ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder and ChemInfo on
any computer owned by you; however, extra copies may not be made for that purpose. Consult the CS License
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ChemOffice, ChemDraw, Chem3D, ChemFinder, ChemInfo and ChemACX are registered trademarks of
CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
The Merck Index is a registered trademark of Merck & Co., Inc. ©2001 All rights reserved.
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Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered trademarks of Apple
Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer, Inc.
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Copyright © 1986-2003 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All Rights Reserved.
Printed in the United States of America.
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and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (“Software”) in accordance
with the terms of this Agreement. This licensed copy of the Software may only be used on a single computer,
except as provided below. You may physically transfer the Software from one computer to another for your own use,
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on your computer (other than a network server), you may also use the Software on a portable or home computer,
provided that you use the software on only one computer at a time. You may not (a) electronically transfer the
Software from one computer to another, (b) distribute copies of the Software to others, or (c) modify or translate the
Software without the prior written consent of CambridgeSoft, (d) place the software on a server so that it is accessi-

le via a public network such as the Internet, (e) sublicense, rent, lease or lend any portion of the Software or
Documentation, or (f ) modify or adapt the Software or merge it into another program. The Software may be placed
on a file or disk server connected to a network, provided that a license has been purchased for every computer with
access to that server. You may make only those copies of the Software which are necessary to install and use it as permitted
by this agreement, or are for purposes of backup and archival records; all copies shall bear CambridgeSoft’s
copyright and proprietary notices. You may not make copies of any accompanying written materials.
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Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term
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This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts, United States of
America.

Databases Desktop Applications Software
Tips Enterprise Solutions
Includes
A Guide to CambridgeSoft Manuals
ChemDraw
Chem3D
ChemFinder
E-Notebook Desktop
ChemDraw/Excel
ChemFinder/Office
CombiChem/Excel
ChemSAR/Excel
MOPAC, MM2
CS Gaussian, GAMESS Interface
Purchase/Excel
ChemOffice WebServer
Oracle Cartridge
E-Notebook Enterprise
Document Manager
Registration System
Formulations & Mixtures
Inventory Manager
Discovery LIMS
BioAssay HTS
BioSAR Browser
ChemDraw/Excel
The Merck Index
ChemACX
ChemSCX
ChemMSDX
ChemINDEX
ChemRXN
NCI & AIDS
Structure Drawing Tips
Searching Tips
Importing SD Files
Manuals
Chemical Structure
Drawing Standard
ChemDraw
ChemOffice
Chem3D, ChemFinder
& E-Notebook
ChemOffice
Enterprise Solutions
And Databases

Contents
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . 1
What’s New in ChemFinder 8? . . . . . . . . . . . . . 1
About This User’s Guide . . . . . . . . . . . . . . . . . . 1
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Additional Information. . . . . . . . . . . . . . . . . . . . 2
Quick Reference Card . . . . . . . . . . . . . . . . . 2
Help System . . . . . . . . . . . . . . . . . . . . . . . . . 2
CambridgeSoft Web Pages. . . . . . . . . . . . . . 2
Installation and System Requirements . . . . . . . . 3
Site License Network Installation
Instructions . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 1: ChemFinder Basics . . . . . . . . . 5
Using ChemFinder . . . . . . . . . . . . . . . . . . . . . . . 5
Creating a Form . . . . . . . . . . . . . . . . . . . . . . 5
Creating or Opening a Database. . . . . . . . . . 5
Using the Database Management Scheme . . 6
The Database Model. . . . . . . . . . . . . . . . . . . 6
Understanding Forms and Databases . . . . . . 7
Browsing, Editing, Sorting . . . . . . . . . . . . . . 7
Searching for Compounds . . . . . . . . . . . . . . 7
Selecting the Drawing Mode . . . . . . . . . 8
Searching for Reactions . . . . . . . . . . . . . . . . 9
The ChemFinder Window . . . . . . . . . . . . . . . . . 9
The Status Bar . . . . . . . . . . . . . . . . . . . . . . 12
Opening ChemFinder . . . . . . . . . . . . . . . . . . . . 12
Opening a Blank Form . . . . . . . . . . . . . . . . . . . 13
Creating a Database Connection . . . . . . . . . . . 14
Using the Database Wizard . . . . . . . . . . . . . . . 14
Closing ChemFinder. . . . . . . . . . . . . . . . . . . . . 17
Chapter 2: Tutorials . . . . . . . . . . . . . . . . . 19
Tutorial 1: Searching a Database . . . . . . . . . . . 19
Opening the Demo Database . . . . . . . . . . . 19
Substructure Searching . . . . . . . . . . . . . . . 20
Text Searching . . . . . . . . . . . . . . . . . . . . . . 23
Formula Searching . . . . . . . . . . . . . . . . 23
Name Searching . . . . . . . . . . . . . . . . . . 23
Numerical Searching . . . . . . . . . . . . . . . . . 23
Combined Searching. . . . . . . . . . . . . . . . . . 24
Tutorial 2: Reaction Queries . . . . . . . . . . . . . . 24
Opening A Specific Database . . . . . . . . . . 24
Searching for Reactants . . . . . . . . . . . . . . . 25
Searching for Products . . . . . . . . . . . . . . . . 26
Searching by Reaction Type . . . . . . . . . . . 26
Refining a Search . . . . . . . . . . . . . . . . . . . . 27
Tutorial 3: Using Forms. . . . . . . . . . . . . . . . . . 27
Creating Data Boxes. . . . . . . . . . . . . . . . . . 28
Editing Data Boxes. . . . . . . . . . . . . . . . . . . 29
Deleting Data Boxes. . . . . . . . . . . . . . . . . . 30
Creating and Saving a Form. . . . . . . . . . . . 30
Tutorial 4: Opening a Database . . . . . . . . . . . . 31
Connecting a Database to a Form . . . . . . . 31
Assigning Fields to Data Boxes . . . . . . . . . 32
Tutorial 5: Creating Your Own Database . . . . 33
Assigning Fields. . . . . . . . . . . . . . . . . . . . . 33
Adding Records . . . . . . . . . . . . . . . . . . . . . 34
Tutorial 6: Working with Subforms. . . . . . . . . 36
Creating a Subform . . . . . . . . . . . . . . . . . . 36
Linking the Subform . . . . . . . . . . . . . . . . . 37
Chapter 3: Creating and Editing Forms . 39
Selecting a Database . . . . . . . . . . . . . . . . . . . . 39
Opening an Existing Chemical Database. . 39
Selecting the Data to Display. . . . . . . . . . . 40
Opening a Secured MS Access Database. . 41
Creating a Database . . . . . . . . . . . . . . . . . . 41
Creating Forms Automatically. . . . . . . . . . . . . 42
Saving a Form . . . . . . . . . . . . . . . . . . . . . . 43
Creating Forms Manually . . . . . . . . . . . . . . . . 44
Using the Form Tools. . . . . . . . . . . . . . . . . 44
Creating a New Form . . . . . . . . . . . . . . . . . 44
Using the Grid . . . . . . . . . . . . . . . . . . . . . . 44
Creating Boxes . . . . . . . . . . . . . . . . . . . . . . 44
Creating Frames . . . . . . . . . . . . . . . . . . . . . 45
Creating Boxes with Frames . . . . . . . . . . . 45
Automatic Labels . . . . . . . . . . . . . . . . . 46
Adding Plain Text . . . . . . . . . . . . . . . . . . . 46
Adding a Button . . . . . . . . . . . . . . . . . . . . . 47
Adding Pictures . . . . . . . . . . . . . . . . . . . . . 47
ChemFinder 8 Contents • i

Administrator
Setting Box Properties . . . . . . . . . . . . . . . . . . . 48
Setting Data Box Styles . . . . . . . . . . . . . . . 48
Viewing Structures . . . . . . . . . . . . . . . . . . . 49
Viewing Structures in Chem3D Format 50
Setting Fixed and Live Data . . . . . . . . . . . . 50
Adding a Data Box Menu . . . . . . . . . . . . . . 51
Adding Scroll Bars . . . . . . . . . . . . . . . . . . . 51
Hiding Data Boxes . . . . . . . . . . . . . . . . . . . 52
Customizing Text . . . . . . . . . . . . . . . . . . . . 52
Customizing Fonts . . . . . . . . . . . . . . . . 52
Customizing Numbers. . . . . . . . . . . . . . 53
Setting Color . . . . . . . . . . . . . . . . . . . . . . . . 54
Creating and Editing Tabs . . . . . . . . . . . . . . . . 54
Editing Forms . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Selecting Objects on a Form . . . . . . . . . . . . 55
Moving Objects. . . . . . . . . . . . . . . . . . . . . . 55
Resizing Objects . . . . . . . . . . . . . . . . . . . . . 56
Deleting Objects . . . . . . . . . . . . . . . . . . . . . 56
Reversing and Restoring Changes . . . . . . . 56
Ordering Objects. . . . . . . . . . . . . . . . . . . . . 57
Aligning and Distributing Objects . . . . . . . 57
Changing the Layout of an Existing Form . . . . 58
Securing Forms. . . . . . . . . . . . . . . . . . . . . . . . . 59
Setting Security Options . . . . . . . . . . . . . . . 59
Disabling Security. . . . . . . . . . . . . . . . . . . . 63
Overriding Security. . . . . . . . . . . . . . . . . . . 63
Chapter 4: Working with Data . . . . . . . . 65
Opening Databases . . . . . . . . . . . . . . . . . . . . . . 65
Read-Only Access. . . . . . . . . . . . . . . . . . . . 65
Multi-user Access . . . . . . . . . . . . . . . . . . . . 66
Secured Access . . . . . . . . . . . . . . . . . . . . . . 66
Browsing Databases . . . . . . . . . . . . . . . . . . . . . 67
The Data Table . . . . . . . . . . . . . . . . . . . . . . 67
Creating a Database . . . . . . . . . . . . . . . . . . . . . 68
Creating Tables . . . . . . . . . . . . . . . . . . . . . . 69
Deleting Tables . . . . . . . . . . . . . . . . . . . . . . 70
Attaching Tables from Other Applications. 70
Attaching Files from a File-Based
Database . . . . . . . . . . . . . . . . . . . . . . . 70
Attaching Files from a Non File-Based
Database . . . . . . . . . . . . . . . . . . . . . . . 71
Creating Fields . . . . . . . . . . . . . . . . . . . . . . 72
Deleting Fields . . . . . . . . . . . . . . . . . . . . . . 73
Adding Multiple Structures. . . . . . . . . . . . . 73
Adding Structures to Non-Chemical
Databases . . . . . . . . . . . . . . . . . . . . . . . . . 74
Backing up Databases. . . . . . . . . . . . . . . . . 75
Moving Databases . . . . . . . . . . . . . . . . . . . 75
Creating a Portal Database . . . . . . . . . . . . . . . . 76
Entering Data into a Database . . . . . . . . . . . . . 76
Clearing the Form. . . . . . . . . . . . . . . . . . . . 76
Adding New Data . . . . . . . . . . . . . . . . . . . . 76
Committing the New Data . . . . . . . . . . . . . 77
Duplicating Records . . . . . . . . . . . . . . . . . . 77
Undoing Data Entry . . . . . . . . . . . . . . . . . . 77
Editing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Editing Data . . . . . . . . . . . . . . . . . . . . . . . . 78
Sorting Data . . . . . . . . . . . . . . . . . . . . . . . . 78
Sorting Fields . . . . . . . . . . . . . . . . . . . . 78
Sorting from the Data Table . . . . . . . . . 78
Sorting in Reverse Order . . . . . . . . . . . 78
Sorting Languages Other Than English 79
Resetting the Database . . . . . . . . . . . . . 79
Editing Structures . . . . . . . . . . . . . . . . . . . . 79
Working with Structures Using
ChemDraw . . . . . . . . . . . . . . . . . . . . . 80
Viewing Models using Chem3D. . . . . . 81
Styled Text . . . . . . . . . . . . . . . . . . . . . . . . . 81
Undoing Changes . . . . . . . . . . . . . . . . . . . . 82
Redoing Changes . . . . . . . . . . . . . . . . . . . . 82
Deleting Data . . . . . . . . . . . . . . . . . . . . . . . 82
Changing the Database Scheme . . . . . . . . . . . . 82
Chapter 5: Searching . . . . . . . . . . . . . . . . 83
Beginning a Search. . . . . . . . . . . . . . . . . . . . . . 83
Clearing the Form. . . . . . . . . . . . . . . . . . . . 83
Entering and Submitting a Query . . . . . . . . 83
Stopping a Query . . . . . . . . . . . . . . . . . . . . 84
Viewing Results . . . . . . . . . . . . . . . . . . . . . . . . 84
Viewing Forms in Table View . . . . . . . . . . 84
Viewing Continuous Forms . . . . . . . . . . . . 84
Switching Views. . . . . . . . . . . . . . . . . . . . . 84
Viewing Chemical Markers . . . . . . . . . . . . 84
Refining a Search . . . . . . . . . . . . . . . . . . . . . . . 85
Restoring a Previous List . . . . . . . . . . . . . . . . . 85
Resetting the Database . . . . . . . . . . . . . . . . . . . 85
Text Searching . . . . . . . . . . . . . . . . . . . . . . . . . 86
Numerical Searching . . . . . . . . . . . . . . . . . . . . 86
Date Searching . . . . . . . . . . . . . . . . . . . . . . . . . 86
ii • Contents CambridgeSoft

Molecular Formula Searching . . . . . . . . . . . . . 87
Find List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Structure Searching . . . . . . . . . . . . . . . . . . . . . 88
Entering a Structural Query . . . . . . . . . . . . 88
Types of Structural Searches . . . . . . . . . . . 89
Substructure Searching . . . . . . . . . . . . . 89
Fragment Searching . . . . . . . . . . . . . . . 89
Exact Full Structure Searching . . . . . . . 90
Identity Searching . . . . . . . . . . . . . . . . . 90
Similarity Searching . . . . . . . . . . . . . . . 90
Stereochemistry . . . . . . . . . . . . . . . . . . 91
3D Properties . . . . . . . . . . . . . . . . . . . . 91
Using the Current Molecule as a Query . . . 91
Finding the Current Molecule. . . . . . . . . . . 91
Reaction Searching. . . . . . . . . . . . . . . . . . . . . . 92
Entering a Reaction Query . . . . . . . . . . . . . 92
Reaction Centers. . . . . . . . . . . . . . . . . . . . . 92
Atom-to-Atom Mapping. . . . . . . . . . . . . . . 93
Searching for Reactants . . . . . . . . . . . . . . . 94
Searching for Products . . . . . . . . . . . . . . . . 94
Searching for Intermediates . . . . . . . . . . . . 94
SQL Searching . . . . . . . . . . . . . . . . . . . . . . . . . 95
Combined Searching . . . . . . . . . . . . . . . . . . . . 95
Managing Search Results . . . . . . . . . . . . . . . . . 95
Saving a Hit List . . . . . . . . . . . . . . . . . . . . . 96
Restoring a Hit List. . . . . . . . . . . . . . . . . . . 96
Search Examples. . . . . . . . . . . . . . . . . . . . . 97
Working with Multiple Hit Lists . . . . . 97
Using Atom Lists . . . . . . . . . . . . . . . . . 98
Atom Types and Bond Types . . . . . . . . 98
Searching Fullerenes. . . . . . . . . . . . . . . 98
Searching Link Nodes and
Multivalent Rs (MVRs) . . . . . . . . . . . 98
Searching More Than One
Substructure . . . . . . . . . . . . . . . . . . . . 99
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Page Layout . . . . . . . . . . . . . . . . . . . . . . . 100
Forms . . . . . . . . . . . . . . . . . . . . . . . . . 100
Tables . . . . . . . . . . . . . . . . . . . . . . . . . 101
Print Preview . . . . . . . . . . . . . . . . . . . . . . 101
Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Chapter 6: Relational Data and
Subforms . . . . . . . . . . . . . . . . . . . . . . . . 103
Accessing Relational Data Using Subforms . 103
Creating a Subform . . . . . . . . . . . . . . . . . . . . 103
Changing the Layout of an Existing Subform 105
Working with Subforms. . . . . . . . . . . . . . . . . 106
Searching a Subform . . . . . . . . . . . . . . . . 106
Viewing Subform Data in a Table . . . . . . 106
Using Scripts in Subforms . . . . . . . . . . . . 106
Chapter 7: Importing and
Exporting Data . . . . . . . . . . . . . . . . . . . 109
Supported File Formats . . . . . . . . . . . . . . . . . 109
Saving Structures . . . . . . . . . . . . . . . . . . . . . . 109
Reading a Structure . . . . . . . . . . . . . . . . . . . . 109
Drag and Drop . . . . . . . . . . . . . . . . . . . . . 110
Importing Structures . . . . . . . . . . . . . . . . . . . 110
Importing Individual Structure Files . . . . 110
Importing Structure Data and Reaction
Data Files. . . . . . . . . . . . . . . . . . . . . . . . 111
Adding Data to an Existing Database . . . 112
Merge Options . . . . . . . . . . . . . . . . . . 113
Changing the Data Field Definitions . . . . 114
Using Log Files . . . . . . . . . . . . . . . . . . . . 115
Importing from a Specified Location . . . . 116
Exporting Data Files . . . . . . . . . . . . . . . . . . . 117
Exporting an ASCII File . . . . . . . . . . . . . 118
Chapter 8: Customizing ChemFinder . . 119
Setting Preferences. . . . . . . . . . . . . . . . . . . . . 119
Display Preferences . . . . . . . . . . . . . . . . . 119
Structure Display . . . . . . . . . . . . . . . . 119
Using Keyboard Shortcuts . . . . . . . . . 120
Scaling Structures. . . . . . . . . . . . . . . . 120
Framing Pictures. . . . . . . . . . . . . . . . . 121
Grid Spacing. . . . . . . . . . . . . . . . . . . . 121
Color Preferences . . . . . . . . . . . . . . . . . . . 121
Search Type Preferences . . . . . . . . . . . . . 121
Search Details Preferences. . . . . . . . . . . . 122
General Preferences . . . . . . . . . . . . . . . . . 125
Structure Registration Options . . . . . . 125
ChemFinder Opening Options . . . . . . 125
Setting the Recent File List Size . . . . 126
Customizing Toolbars . . . . . . . . . . . . . . . . . . 126
Using the Periodic Table . . . . . . . . . . . . . . . . 127
ChemFinder Automation Language (CAL) . . 128
Getting CAL Help . . . . . . . . . . . . . . . . . . 129
Writing a Script . . . . . . . . . . . . . . . . . . . . 129
ChemFinder 8 Contents • iii

Administrator
Debugging a Script . . . . . . . . . . . . . . . . . . 129
Executing a Script on a Form . . . . . . . . . . . . . 130
Communicating with Other Applications. . . . 130
Using Scripts. . . . . . . . . . . . . . . . . . . . . . . 130
Using Visual Basic . . . . . . . . . . . . . . . . . . 132
Using Microsoft Access with ChemFinder. . .
132
Chapter 9: Accessing the CambridgeSoft
Web Site. . . . . . . . . . . . . . . . . . . . . . . . . 135
Finding Chemical Suppliers on
ChemStore.com . . . . . . . . . . . . . . . . . . . . . . 135
Finding Information on ChemFinder.com . . . 135
Finding ACX Structures and Numbers. . . . . . 136
ACX Structures. . . . . . . . . . . . . . . . . . . . . 136
ACX Numbers . . . . . . . . . . . . . . . . . . . . . 136
Browsing ChemStore.com . . . . . . . . . . . . . . . 136
Browsing CambridgeSoft.com . . . . . . . . . . . 137
Accessing the Online ChemFinder
User’s Guide . . . . . . . . . . . . . . . . . . . . . . . . 137
Accessing CambridgeSoft Technical Support 137
Registering Online . . . . . . . . . . . . . . . . . . . . . 138
Using the ChemOffice SDK . . . . . . . . . . . . . . 138
Appendix A: Structural Query Features . 1
General Properties . . . . . . . . . . . . . . . . . . . . . . . 1
Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Substituents . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Charges and Radicals . . . . . . . . . . . . . . . . . . 2
Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Stereochemistry. . . . . . . . . . . . . . . . . . . . . . . 3
Relative Tetrahedral Stereochemistry . . . 3
MDL File Formats. . . . . . . . . . . . . . . . . . 4
Normalization . . . . . . . . . . . . . . . . . . . . . . . . 4
Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . . 5
Special Atom Types . . . . . . . . . . . . . . . . . . . 5
Atom Lists. . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Atom Not-Lists . . . . . . . . . . . . . . . . . . . . . . . 5
Substituents: Exactly. . . . . . . . . . . . . . . . . . . 5
Substituents: Up To . . . . . . . . . . . . . . . . . . . 6
Substituents: Free Sites. . . . . . . . . . . . . . . . . 6
Implicit Hydrogens. . . . . . . . . . . . . . . . . . . . 7
Unsaturation . . . . . . . . . . . . . . . . . . . . . . . . . 7
Bond Properties . . . . . . . . . . . . . . . . . . . . . . . . . 7
Special Bond Types . . . . . . . . . . . . . . . . . . . 7
Topology. . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Reaction Center . . . . . . . . . . . . . . . . . . . . . . 8
Appendix B: Formula Input Rules . . . . . . 9
Rules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Appendix C: Similarity Rules . . . . . . . . . 11
Complete Structure Similarity . . . . . . . . . . . . . 11
Substructure Similarity. . . . . . . . . . . . . . . . . . . 12
Appendix D:
CAL Commands . . . . . . . . . . . . . . . . . . . 13
CAL Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Menu Commands . . . . . . . . . . . . . . . . . . . . . . . 13
Box Creation Commands . . . . . . . . . . . . . . . . . 14
Box Manipulation Commands . . . . . . . . . . . . . 15
Program Execution Commands . . . . . . . . . . . . 16
General Commands . . . . . . . . . . . . . . . . . . . . . 17
File Commands. . . . . . . . . . . . . . . . . . . . . . . . . 18
Database Commands . . . . . . . . . . . . . . . . . . . . 18
Variable Commands. . . . . . . . . . . . . . . . . . . . . 19
Environment Variables. . . . . . . . . . . . . . . . . . . 20
Script-Only Commands . . . . . . . . . . . . . . . . . . 21
Appendix E: Technical Support. . . . . . . . 23
Serial Numbers. . . . . . . . . . . . . . . . . . . . . . . . . 23
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . 23
Performance . . . . . . . . . . . . . . . . . . . . . . . . 24
System Crashes. . . . . . . . . . . . . . . . . . . . . . 24
Index
iv • Contents CambridgeSoft

Introduction
About ChemFinder
ChemFinder is a database management system for
anyone who works with chemical information. It
provides a place to store chemical structures,
physical properties, notes, and tables of data. It takes
the place of that box of index cards you’ve been
using to jot notes about interesting molecules and
reactions, but does it much better! With
ChemFinder, you can search through data efficiently
and quickly, and you can organize the data instantly.
ChemFinder is integrated with the following
CambridgeSoft products:
• ChemDraw
• Chem3D
• ChemDraw/Excel
• FrameMaker
What’s New in
ChemFinder 8?
ChemFinder 8.0 includes the following new
features:
• In-place structure editing—using the
ChemDraw ActiveX® control. Structure
display is vastly improved. See “Viewing
Structures” on page 49.
• 3D Searching—search databases of 3D
structures, using new spatial query features. See
“3D Properties” on page 91.
• 3D display of structures—using the Chem3D
ActiveX control. View, rotate, analyze structure
models in ChemFinder forms. See “Viewing
Structures” on page 49.
• Relative Stereochemistry—more flexibility in
stereo representation and searching. See
“Search Details Preferences” on page 122.
• New structure search features—link nodes,
multi-valent R-groups, and more. See
“Searching Link Nodes and Multivalent Rs
(MVRs)” on page 98.
• Triggers—scripts automatically executed on
user-generated events.
• Multi-box text styling—set fonts and styles
over many boxes simultaneously.
• Find Text—search for strings within large
memo fields. See “Creating Fields” on page 72.
• Drag and Drop—structure, graphic, and form
files can now be dragged into ChemFinder. See
“Drag and Drop” on page 110.
About This User’s Guide
This User’s Manual contains information for the
ChemFinder application for Windows. It assumes
that you are familiar with the basics of your
Windows operating system. If you are not, please
refer to your system manual before using the
applications. Some of the material describes tasks
that must be performed in conjuction with other
integrated CambridgeSoft products. The material on
the Addins describes tasks that must be performed in
conjuction with Microsoft Excel or Word. If you are
ChemFinder 8 Introduction
What’s New in ChemFinder 8?
• 1

Administrator
not familiar with these products, please consult the
relevant User’s Manual for more detailed
information.
The chapters in this guide are organized by task.
They are intended to help you familiarize yourself
with ChemFinder and start using it as quickly and
efficiently as possible. New users should read the
Basics chapter to get an overview of the product
and how it works. Chapter 2, Tutorials,
demonstrates most of the features of the application.
Perform the tutorials in the order they are presented.
Experienced users can skip to Chapter 3 and the
subsequent chapters, which provide more detailed
information.
Conventions
The following notations are used throughout this
user’s guide:
Ultra
The Ultra symbol indicates that a feature is
available in the Ultra version only.
Pro
The Pro symbol indicates that a feature is
available in both the Pro and Ultra versions.
Features that are available in the Standard version
are not indicated by a symbol.
NOTE: Notes such as this are used to highlight
information supplemental to the main text.
Shortcut key sequences are indicated with a + sign,
for example: “Use the command: Ctrl+F to enter a
query.
A bold font is used to indicate that you are to take a
particular action, for example: “From the Help
Menu, choose Contents.”
Additional Information
Additional sources of ChemFinder information are:
• The Quick Reference Cards.
• The Help system
• CambridgeSoft Web Pages.
http://www.cambridgesoft.com/support
Quick Reference Card
The ChemFinder Quick Reference Card is located in
the back of the manual. The card provides
summaries of ChemFinder commands and features.
Because many of the instructions require knowledge
of the interface elements, use the Quick Reference
card as you perform the tutorials in Chapter 2:
Tutorials.
Help System
ChemFinder provides the following types of Help:
• ChemFinder Help—A compiled HTML
reference guide.
• ToolTips—Short descriptions of user interface
objects displayed by pointing.
• Status Bar—The lower left corner of the GUI
displays useful information as you work.
CambridgeSoft Web Pages
The following table contains the addresses of
ChemFinder-related web pages.
For
information
about …
Technical
Support
Access …
http://www.cambridgesoft.com/
support/
2 • Introduction
Conventions
CambridgeSoft

For
information
about …
ChemDraw
Plugin
Software
Developer’s kit
ActiveX
control
Purchasing
CambridgeSoft
products and
chemicals
Access …
http://www.cambridgesoft.com/
support/documentation/chemdra
wplugin/
http://sdk.cambridgesoft.com/
http://sdk.cambridgesoft.com/
http://chemstore.cambridgesoft.
com/
Installation and System
Requirements
Before installation, see the “ReadMeFirst” and any
other ReadMe documents on the installation CD-
ROM.
Microsoft Windows
Requirements
• Windows 98, Me, NT4 (SP-6 or higher), 2000,
or XP
• Microsoft ® Office add-ins require Office 2000
or XP.
• Plugins/ActiveX ® controls support Netscape ®
6.2 or greater, Mozilla 1.x, and
Microsoft ® Internet Explorer 5.x and 6.
Site License Network
Installation Instructions
If you have purchased a site license, please see the
following web site for network installation
instructions:
http://www.cambridgesoft.com/support/sl/
ChemFinder 8 Introduction
Installation and System Requirements
• 3

Administrator
4 • Introduction
Installation and System Requirements
CambridgeSoft

Chapter 1: ChemFinder Basics
ChemFinder Overview
ChemFinder is a database management system that
allows storage, retrieval, and searching of molecular
structures, text, and numerical data. Use it to keep
track of what you find in your routine literature
scans. Make a database to keep the figures that go in
your thesis or your next paper. Use it as a reference,
together with one of the CD-ROM databases
provided. Use it as your corporate database system,
available to anyone on your network. Use it as a
registration system or front-end search engine for
your big mainframe database. Use it as a custom
viewer for your Oracle data, with or without
chemical structures.
You can draw structures in ChemDraw to store in
your ChemFinder database and view Chem3D
models from ChemFinder.
ChemFinder provides two associated directories:
• Samples—contains sample database files.
• System—contains files required by
ChemFinder.
Using ChemFinder
The general steps for using ChemFinder are as
follows:
• Create a form
• Create or open a database
• Add or manipulate data
• Perform a search
Creating a Form
You can open a new form and create data boxes on
the form to display your data. The adjustable grid
allows you to create a neatly-organized collection of
data boxes.
You can customize boxes in the following ways:
• Style or label in various ways
• Distinguish with your choice of font and color
• Include pictures
ChemFinder provides complete set of form editing
capabilities, including the following:
• A tool palette to choose a box style while
drawing
• Boxes may be selected, moved, resized, or
restyled either singly or in groups
• Ability to cut and paste
• Multiple-level undo
• Creating tabs
For more information see “Chapter 3: Creating and
Editing Forms.”
Creating or Opening a
Database
When a form contains a single box, you can begin
entering or browsing data. A data source, typically
the name of a field that stores data within a database,
may be associated with each data box.
To attach a data source to a data box:
• Point to the box and press the right mouse
button.
ChemFinder 8 Chapter 1: ChemFinder Basics • 5
Using ChemFinder

Administrator
A shortcut menu appears containing an option
to display the Data Source dialog box,
providing the following options: one tab allows
you to create or select a database, and displays
a tree diagram of the database layout; another
tab allows you to select, create, or modify fields
within the database.
When opening an existing database, you open the
database, choose a field, return to the form, and the
specified type of data of the first record pops into
your form box. You’re ready to browse, clicking
buttons to move from record to record.
ChemFinder allows you to work with multiple data
tables so that you can have a true relational database.
Through subforms, you can interactively display
and search multiple data tables.
Using the Database
Management Scheme
ChemFinder maintains a table of chemical
information (structure, formula, molecular weight)
and relies on Microsoft’s Data Access Objects
(DAO) and Open Database Connectivity (ODBC) to
connect to an external database system for managing
the rest of the data. Systems with DAO or ODBC
drivers include Access, FoxPro, dBASE, Btrieve,
Paradox, SQL Server, Oracle, and others. If you
have any of these systems, you can trust your data to
it, and manage it either from within ChemFinder or
from within the external database system itself. In
ChemFinder 8, you can use the CS Oracle Cartridge
to manage all chemical and relational data directly
in Oracle, without using DAO or ODBC.
If you don’t have a database system, ChemFinder
comes with the Microsoft Jet database engine, the
same Microsoft-developed engine used by Access
and Visual Basic. The sample databases provided
with the program are in Jet format, so if you happen
to have Access or Visual Basic, you can use those
programs to view (or edit) all the data in these
databases except for the structural information.
The Database Model
A database is a collection of information. In
ChemFinder the information is organized into
increasing levels of complexity.
NOTE: At the simplest level is the data item itself,
for example the word “pyrrole.”
The data item is stored within a field, such as
“Molname.” A field contains information of a
specific type. For example, a field can contain
numeric, text, or structure information.
A record is a set of related data items, one per field,
representing a single entry in the database. On a
form, you see a single record at a time.
6•Chapter 1: ChemFinder Basics CambridgeSoft
Using ChemFinder

A collection of records is a table. A table is defined
by a set of fields, generally set up once and rarely
modified, and a set of records which grows as entries
are added.
In spreadsheet terminology:
• A data item is found in a cell.
• A field corresponds to a column.
• A record corresponds to a row.
• A table corresponds to a worksheet.
A database is a storehouse for tables–possibly one,
possibly more than one. A database containing only
one table is known as a simple (or flat or flat-file)
database.
Databases containing multiple tables are called
relational. Relational databases are discussed further
in “Chapter 6: Relational Data and Subforms” on
page 103.
A form displays data from a single table, but may
contain subforms that display data from other tables.
If the tables have a field in common, then any record
retrieved in the form calls up the related records in
the subform.
Understanding Forms and
Databases
There is an important distinction between forms and
databases. Databases are where data is actually
stored. A form is used only to display the
information stored in the database. No data is stored
in a form. The form acts like a window, letting you
select which fields and tables you want to view.
You may want to have more than one form accessing
the same database. For example, you may want to
create one sample form for working with structural
data and a more complicated one to include
literature or lab data. By switching between forms,
you can look at just those fields you want to see. For
more information, see “Chapter 6: Relational Data
and Subforms” on page 103.
Browsing, Editing, Sorting
You can create, modify, or delete boxes on the
ChemFinder form while browsing. For example,
you can create a simple form showing structure and
basic data, and when you come to a compound of
interest, create a couple of temporary boxes to see
additional data.
To edit data, you modify the data directly on the
form. You can also add new records. You access
ChemDraw from within ChemFinder to create or
edit chemical structures.Changes are automatically
validated and stored in the database when you move
to a different record.
To sort data, you right-click a data box and choose
sort, or double-click a header in the data table view.
Searching for Compounds
Molecules can be searched by full structure,
substructure, Tanimoto similarity, formula, or
molecular weight. Text and numeric data can be
ChemFinder 8 Chapter 1: ChemFinder Basics • 7
Using ChemFinder

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searched by exact match, substring, or range, with
Boolean operators. Queries are flexible and entered
directly on the form.
Selecting the Drawing Mode
ChemFinder 8 allows you to choose between two
drawing modes: “ChemFinder style”—the mode
used in earlier versions of ChemFinder, and
“ChemDraw style”, which makes use of the
ChemDraw ActiveX control. You use the Box
Properties dialog box to switch between modes.
To change the drawing mode:
1. Right click on the frame of any window.
2. Select Properties… from the right-click menu.
The Box Properties dialog box appears.
3. From the drop-down menu in the “Box Style”
section of the Box Properties dialog box, select
the desired style and click OK.
If you select ChemFinder style, you draw queries in
ChemDraw, which you activate by clicking Edit
Structure... on the right-click menu from the
Structure window of the ChemFinder query form.
NOTE: To return the structure to ChemFinder, you
must go to the File menu and select Close and
Return to... or completely close ChemDraw. The
method used in previous versions of ChemFinder
(clicking in the ChemFinder query form) will not
return a structure in ChemFinder 8.
If you select ChemDraw style, the ChemDraw Main
Tools Palette will appear when you click in the
Structure window of the ChemFinder query form,
and you use it to draw queries directly in the
window.
Substructure queries can include the following
query features:
• Variable bond types
• Query atom types
• Atom type lists
• 3D Properties
If the query contains stereochemistry, you can
choose whether it must be matched in the search.
Hits are displayed with the query substructure
highlighted in red.
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Using ChemFinder

Formula queries can include ranges of elements,
element counts of zero, and other variability. An
intelligent query processor allows formulas to be
entered in free format, with repeated elements,
subgroup counts, and without case sensitivity.
Molecular weight queries can be ranges, with target
precision automatically determined based on the
number of significant digits in the query. Data
queries can include wild card characters, arithmetic
and Boolean operators, or raw SQL.
Searching for Reactions
You can search and store molecular transformations,
find the products of a reaction, or find the reactants
that combine to create a product. Search reactions by
substructure to find bond-forming transformations,
bond-order changes, or cyclization reactions. Find
information on your planned synthesis routes.
Automatic atom-to-atom mapping speeds the
creation of accurate reactions and queries. The fate
of individual atoms is tracked from reactants to
products, and reaction centers are automatically
perceived. You can create or adjust atom-to-atom
mapping and reaction center information manually
for complicated transformations.
The ChemFinder
Window
The ChemFinder window consists of menus,
commands, and toolbars and the form window. The
central part of the form window contains the work
space where you create and view structures and data.
The toolbars contain icons that change the way the
pointer behaves or that perform actions
corresponding to menu commands.
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The ChemFinder Window

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The components of the ChemFinder window are
shown below.
.
Main
menu
Form
toolbar
Structure
box
Shortcut
menu
Data
table
Status
bar
Title bar
Br
Read-only
indicator
Main toolbar
Add
indicator
Record
toolbar
Query
indicator
Current
record
Search toolbar
Current
list size
10•Chapter 1: ChemFinder Basics CambridgeSoft
The ChemFinder Window
Text toolbar
Main
form
Framed
data box
Subform
Table
header
Total
database size

Screen
Element
Description
Current list size Displays the number of records
through which you are
browsing. Might be less than the
total database size if you have
recently performed a search.
Current record Displays the position within the
current hit list of the record you
are viewing.
Data box Displays data corresponding to a
specific field of the current
record.
Data table Displays many records at once
in a rows-and-columns view.
Form toolbar Contains icons representing the
form-creation tools available in
ChemFinder. Click a tool icon to
select it. The selected tool
determines what action is
carried out when you drag in a
form window.
Framed data box Displays data in a Data Box
surrounded by a labeled frame.
Main form Displays data contained in one
record of the database.
Main toolbar Contains icons representing
general-purpose menu
commands such as copying,
saving, and printing. Click an
icon to perform the command.
Screen
Element
Menu bar Contains all the commands
specific to the ChemFinder
application for manipulating
forms, tables, databases, and
their contents.
New record
indicator
Displays “ADD” if you are in
the process of adding a new
record that had not yet been
committed to the database.
Query indicator Displays “QRY” if you are in the
process of entering a search
query.
Read-only
indicator
Description
Displays “READ” if the
database is read-only and cannot
be modified.
Record toolbar Contains icons for commands in
the Record menu. Click an icon
to perform the command.
Search toolbar Contains icons for commands in
the Search menu. Click an icon
to perform the command.
Shortcut menu Provides options related to the
item on which you have
right-clicked.
Status bar Displays information about the
current state of the ChemFinder
application.
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Screen
Element
Subform Displays records in a table
related to the record shown in
the Main Form.
Table header Displays the name of a field.
Double-clicking on a table
header sorts on that field.
Title bar Contains the name of the
application or document as a
window title. Also, the title bar
can be dragged to move a
window.
Total database
size
The Status Bar
Description
Displays the total number of
records in the current table.
While you move among records, counters in the
lower right corner of the ChemFinder window
change to indicate the current record, the current list
size, and the total size of the database. The lower left
corner of the window displays help for menu items
and other information.
When you first open a form, the current list size
equals the total database size. The total database size
changes only when you add or delete records. If you
search to find a subset of the entries in the database,
then the current list size changes to indicate the
number of hits in the search.
To the left of these counters are three other
indicators that show the general status of the
database. The first displays the word “READ” when
you are using a read-only database, such as one that
is on a CD-ROM.
The second indicator displays the word “ADD”
when you are entering a new record.
The third displays “QRY” when you are entering a
query.
To hide or show the Status Bar:
• From the View menu, deselect or choose Status
Bar.
Opening ChemFinder
To open the ChemFinder application, do one of the
following:
• Double-click the ChemFinder application icon.
• Click Start, point to Programs, point to
ChemOffice 2004, and then choose
ChemFinder.
ChemFinder opens and the ChemFinder dialog
box appears.
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Opening ChemFinder

The ChemFinder dialog box enables you to perform
the following tasks.
• Blank Form—Open a blank form to create
your own form. For more information, see
“Opening a Blank Form” on page 13.
• Database Connection—Allows you to open a
blank form and connect it to a database. You can
create the form manually or choose to create it
automatically. For more information, see
“Creating a Database Connection” on page 14.
• The Database Wizard—Guides you through
the process of setting up a form with a database
connection. For more information, see “Using
the Database Wizard” on page 14.
• Existing tab—Allows you to open an existing
form in your file system.
• Recent tab—Allows you to open a form on the
recently-used file list.
You can choose whether the ChemFinder dialog box
is displayed when Chemfinder opens by doing the
following:
1. From the File menu, choose Preferences.
2. In the Preferences dialog box, click the
General tab.
3. Deselect Show opening dialog.
Subsequent openings of ChemFinder will not
display the ChemFinder dialog box.
To open the ChemFinder dialog box if it is not
displayed:
• From the File menu, choose New.
Opening a Blank Form
You can open a blank form, and then create the form
through which you view data from a database. A
form contains form objects, such as data boxes and
buttons. For more information about form objects,
see “Creating and Editing Tabs” on page 54.
To open a blank form:
• In the ChemFinder dialog box, click Blank
Form, and then click Open.
A blank form, Form1, appears in the
ChemFinder window.
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Opening a Blank Form

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For more information about creating a form and
using the Form tools to customize it, see “Chapter 3:
Creating and Editing Forms.”
Creating a Database
Connection
To open a blank form and connect it to a database:
1. In the ChemFinder dialog box, click Database
Connection, and then click Open.
The Form Properties dialog box appears,
displaying the Database tab, and a form is
created.
2. Take the appropriate action:
If you want to Then click
open an existing
database to associate
with the form
create a new, empty
database to associate
with the form
Open Database and
choose a database from the
Open dialog box.
Create Database, name
the database, select a
location, and then click
Save.
If you want to Then click
use the Database
Wizard to open a
database connection
and design a form
Using the Database
Wizard
You can use the Database Wizard to open or create a
database in which to store information and then
create a form in which to display the data.
To use the Database Wizard:
1. In the Open dialog box, click Database Wizard
and then click Open.
The Welcome dialog box appears.
2. Click Next.
Database Setup Wizard.
For more information, see
“Using the Database
Wizard” as follows.
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Creating a Database Connection

The Relational database dialog box appears.
3. Take the appropriate action:
If you want to Then click
open an existing
database to associate
with the form
open an existing
ODBC data source to
associate with the
form
create a database to
associate with the
form
4. Click Next.
Open Database.
Choose a database from
the Open dialog box. For
more information, see
“Setting Box Properties”
on page 48.
Open ODBC Data
Source.
For more information, see
“Attaching Files from a
Non File-Based Database”
on page 71.
Create New Database.
A database source tree
appears in the Form
Properties dialog box. For
more information, see
“Creating a Database” on
page 68.
If you opened a database containing more than
one table, the Table dialog box appears.
5. Select the table to connect to the form and click
Next.
The Structure Source dialog box appears.
6. Take the appropriate action:
For structures from Click
the same location as the
database
a source outside of the
database
Default location.
MolServer, and in
the MolServer
window, type a path.
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Using the Database Wizard

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7. Click Next.
The Form dialog box appears.
8. To have a Structure box to be created first in the
upper left corner of the form, click Structure in
upper left of form.
9. In Choose Fields to be included section, click
the field names to include.
If you do not select this, the boxes are generated
in the order they appear in the list.
10. Select the form style:
For boxes In the Form style
section, click
surrounded by a
frame
Framed.
labeled above Titled.
labelled to the left Labelled.
not labeled Plain.
11. Choose the number of columns, between one
and four.
12. Choose the size and spacing of the boxes and
grid:
For boxes that are Choose
larger and spaced further
apart
medium, relative to the
Large and Small settings
smaller and spaced closer
together
Large.
Medium.
Small.
13. If your database contains at least two tables,
you can create subforms by clicking Add
subforms.
14. Click Next.
The Subform dialog box appears.
15. Select the sources to link from and to and then
click Add.
16. Click Next.
The final Database Wizard dialog box appears.
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Using the Database Wizard

17. To make changes, click Back until you find the
information to change.
18. Click Finish.
The form you created appears with data (unless
the database is new).
Closing ChemFinder
Closing an application frees up the memory that it
uses so that other applications can have more
memory available to them.
To close the ChemFinder application:
• From the File menu, choose Exit.
If you have forms open that have not been saved, a
message appears asking whether you want to save
them before you close the application.
ChemFinder 8 Chapter 1: ChemFinder Basics • 17
Closing ChemFinder

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18•Chapter 1: ChemFinder Basics CambridgeSoft
Closing ChemFinder

Chapter 2: Tutorials
Overview
The tutorials introduce you to ChemFinder basic
functions. “Tutorial 1: Searching a Database” and
“Tutorial 2: Reaction Queries” illustrate the basics
of searching databases. “Tutorial 3: Using Forms”
through “Tutorial 6: Working with Subforms”
illustrate how to use forms to interact with databases
and how to work with data within a database.
You may want to use the Quick Reference card
while you perform the tutorials.
Perform the tutorials in the sequence they are
presented because each tutorial develops on and
refers to the previous ones.
Tutorial 1: Searching a
Database
ChemFinder helps you organize and find
information. One way to find information is to
browse through the database one record at a time,
like turning the pages in a book. This is a good way
to see some of the information available. However,
because databases can be very big, browsing is often
inefficient.
Searching a database is like using the index of a
book. With an index, you can quickly focus on the
few pages you are interested in. When you search a
database, you find only those few records that have
the information you look for. After you have this
smaller collection (a hit list), you can then browse it
much more efficiently than you could the whole
database.
ChemFinder performs the following types of
searches:
• Text and structure searches, demonstrated in
Tutorial 1.
• Reaction searches, demonstrated in Tutorial 2.
In this tutorial, you will learn how to search
substructures and text in the CS_Demo Database.
This database is included with ChemFinder as a
sample database of approximately 300 organic and
inorganic compounds.
Opening the Demo Database
To open the CS_Demo database:
1. Open ChemFinder and in the Open dialog box,
click the Existing tab.
2. Navigate to the ...\ChemOffice 2004\
ChemFinder\samples folder. (Normally, this is
in C:\Program files.)
ChemFinder 8 Chapter 2: Tutorials • 19
Tutorial 1: Searching a Database
(
3. In the Samples directory, select CS_demo.cfw
4. Click Open.

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The CS_Demo database opens in ChemFinder.
TableFormView 225 dpi
Substructure Searching
To enter a query and search for a substructure:
1. From the Search menu, choose Enter Query, or
from the Search toolbar, click Enter Query
.
The form is cleared to allow you to enter your
search terms. The status indicator in the status
bar is changed to remind you that you are in
query mode and the color of the form may
change.
2. Right-click the Structure box and choose Edit in
ChemDraw.
ChemDraw opens and you can enter your
structure search query.
3. In ChemDraw, draw benzene.
QueryChemDraw 225 dpi
4. From the File menu, select Close and Return
to...
The benzene molecule from ChemDraw
appears.
QueryWindow 225 dpi
To set the correct options for a substructure search:
1. From the Search menu, select Substructure if
it is not already selected.
2. From the Search menu, deselect Similarity if it
is already selected.
NOTE: You can also set search preferences on
the Search tab of the Preferences dialog box.
For more information, see “Chapter 8:
Customizing ChemFinder.”
The Search menu should appear as follows:
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Tutorial 1: Searching a Database

3. From the Search menu, choose Find or click the
Find button .
ChemFinder begins searching. The progress of
the search is indicated by counters in the status
bar at the bottom of the window.
When the search is complete, the number of hits
is displayed in the Current List Size window of
the Status Bar, and the form displays the first
hit.
In this search you get 123 hits of structures that
contain an aromatic six-membered ring. The list
you can browse is limited to the hits found in
the search.
In a substructure search, the matched portion of
each molecule is highlighted in red.
NOTE: If a search gets no hits, an alert appears
and you are returned to the query mode with the
query on display.
There are three methods for browsing the hits:
• In the Form View—Use the Record menu
commands or toolbar to navigate through
records.
• In the Data Table View—Browse the table to
view the records.
• In the Continuous Forms View—view
multiple records in their own forms.
Use Crtl+W or Switch Views from the View menu
to toggle between the different methods.
To use the Record menu or toolbar, do one of the
following:
• From the Record menu, choose First Record,
Previous Record, Next Record, Last Record,
or Go to Record.
• Click the corresponding buttons in the Record
toolbar.
First
Record
Previous
Record
Go To
Record
Next
Record
Last
Record
NOTE: As you change records, counters in the
Status bar indicate the current record, the current
list size, and the total size of the database.
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Tutorial 1: Searching a Database

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To view the database in a table that shows the
records in a list:
From the View menu, point to Data Table, and
then choose In Current Window, or click
Switch to Table .
NOTE: Switch to Table is a toggle. Selecting it
again will return you to the Form view.
The Table view appears and displays all the
records of the current list (in this case, the 123
records that were hit by the search) in a table.
TableListView 225 dpi
You can sort the records for a specific field in Table
View.
To sort records in Table view by the MolWeight
field:
Double-click on the MolWeight table header.
TableListView2 225 dpi
The molecular weight field is sorted in
increasing order.
To change the column widths of your table:
• Position the pointer over a table header divider
and drag to the width you want.
Pointer
To retrieve all the records in your database:
• From the Search menu, choose Retrieve All, or
click Retrieve All .
NOTE: After searching, you do not need to retrieve
all your records before performing another search.
You can perform another search directly.
To use continuous forms to browse your records:
1. On the View menu, point to Continuous
Forms, and then choose In Current Window.
The Continuous Forms view appears.
Adjust the height of any form by dragging the bar
divider on the left to view the forms clearly.
22•Chapter 2: Tutorials CambridgeSoft
Tutorial 1: Searching a Database

Text Searching
In this exercise, you perform a molecular formula
search and then a name search.
Formula Searching
To find compounds in the CS_demo database with
six carbons and one or two nitrogen atoms:
1. In the CS_demo database, from the
Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
2. Click the Formula box and type “C6N1-2”.
NOTE: This entry specifies a molecular
formula having six carbon atoms and one or
two nitrogen atoms.
3. Click Find or press Enter.
The Status Bar indicates that 12 hits were
retrieved from the 285 records in the database.
4. From the View menu, point to Data Table, and
then choose In Current Window.
The Table view appears. Browse to verify that
the molecular formulas are correct.
Name Searching
To find all compounds in the CS_Demo Database
with molecular names starting with “benz:”
1. Click Switch to Table .
The Form view appears.
2. From the Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
3. Click the Molecule Name box, and type
“benz”.
4. Click Find or press Enter.
You get 12 hits with names starting with
“benz”.
5. From the View menu, point to Data Table, and
then choose In Current Window.
The Table view appears. Browse to verify that
the molecular names are correct.
NOTE: Notice that this search gave you “benzene”
but not “bromobenzene.” The query you entered
above is an “anchored substring” and only gives
you strings starting with the indicated substring.
For more information on how to specify text
searches, see “Text Searching” on page 86.
Numerical Searching
To search in the CS_Demo Database for compounds
with molecular weights between 90 and 100:
1. Click Switch to Table .
2. From the Search menu, choose Retrieve All.
3. From the Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
4. Click the Molecular Weight box and type
“90-100”.
ChemFinder 8 Chapter 2: Tutorials • 23
Tutorial 1: Searching a Database

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5. Click Find or press Enter.
You get 11 hits with molecular weights between
90 and 100.
6. From the View menu, point to Data Table, and
then choose In Current Window.
The Table view appears. Browse to verify that
the molecular weights are correct.
NOTE: A molecular weight query is a decimal
value or range. The precision of the search depends
on the number of significant digits entered. For
more information on molecular weight searching,
see , “Chapter 5: Searching” on page 83.
Combined Searching
In some cases, you may want to combine structure
searching with text searching to find a specific class
of compounds. For example, you may want to find
all compounds in the database that have a benzene
substructure and that have a molecular weight
greater than 400.
To perform a combined search:
1. From the Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
2. Right-click the Structure box and choose Edit
Structure.
ChemDraw appears.
3. In ChemDraw, draw benzene.
4. From the file menu, select Close and Return
to...
The benzene molecule appears in the form.
5. Click the Molecular Weight box and type
“>400”.
6. Click Find or press Enter.
You get 8 hits from the 285 records in the
database.
7. From the View menu, point to Data Table, and
then choose In Current Window.
The Table view appears. Browse to verify that
the molecular weights are correct.
Congratulations! You have completed the tutorial on
searching a database using ChemFinder. You may
now close the CS_Demo database.
Tutorial 2: Reaction
Queries
In addition to helping you organize information
about individual substances, ChemFinder also
allows you to store and search chemical reactions.
There are many ways to search reactions, depending
on what sort of information you are interested in. In
this set of exercises, you learn some general
methods to search for different parts of reactions
using a sample from the ISICCR database. This
database is included with ChemFinder as a sample
database of approximately 250 reactions extracted
from the ISI’s ChemPrep database of Current
Chemical Reactions.
Opening A Specific Database
To open the ISICCR database:
1. From the File menu, choose Open.
The Open dialog box appears.
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Tutorial 2: Reaction Queries

2. In the Samples directory, select Isiccr.cfw, and
then click Open.
NOTE: The ISICCR.cfw form is formatted for a
large screen (1024 X 768). If you have a smaller
screen, open ISICCRsm.cfw for an improved view.
O
The ISICCR database opens in ChemFinder.
O
OH
+
O
O
O
TableFormISICCR 275 dpi
Searching for Reactants
Searching for reactants is useful if you have a known
starting material and you are interested in learning
more about what substances it can produce.
For example, to search for Grignard reactions, or
reactants:
1. From the Search menu, choose Enter Query, or
from the Search toolbar, click Enter Query
.
The form clears.
O
OH
O
O
O
2. Right-click in Structure box and choose Edit
Structure.
ChemDraw opens.
3. In ChemDraw, draw the following:
X
This structure represents a carbon atom bonded
to a magnesium atom, which is bonded to any
type of halogen. The arrow at the right indicates
that you are looking for this substructure as a
reactant.
4. From the File menu, select Close and Return
to...
The ChemDraw substructure appears.
5. From the Search menu, select Substructure if
it is not already selected.
6. From the Search menu, deselect Similarity if it
is already selected.
The Search menu should appear as follows:
7. From the Search menu, choose Find or click the
Find button.
ChemFinder 8 Chapter 2: Tutorials • 25
Tutorial 2: Reaction Queries
Mg

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ChemFinder searches. The progress of the search is
indicated by counters in the status bar at the bottom
of the window.
When the search is complete, the number of hits is
displayed in the Current List Size window of the
Status Bar, and the form displays the first hit. In a
substructure search, the matched portion of each
molecule is highlighted in red.
MgXHit 40%
N +
Rxn O
O -
+
Br
You get 3 hits—reactions in which an alkyl
magnesium halide is consumed. Browse the list of
three hits as in previous tutorials.
Searching for Products
In the next exercise, you search for information on a
particular reaction product. Searching for products
of reactions is very common in syntheses, where you
know what you are aiming for but you do not know
how to produce it. In this example, we look for
reactions that close a ring alpha to a carbonyl.
Before you start the search, restore the entire
database:
• From the Search menu, choose Retrieve All.
To perform a reaction product search:
Mg
N +
O
O- Rxn
Rxn
1. From the Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
2. Double-click on the Structure data box.
ChemDraw appears.
3. In ChemDraw, draw the following:
RngRxn Rng O
In this structure, both single bonds have been
marked as having a “Ring” topology. The left
bond has also been marked as having a Reaction
Center property of “Make/Break.” The arrow at
the left indicates that you are looking for this
substructure as a product.
NOTE: Bond properties such as topology can
be assigned from the right-click menu while you
are creating the drawing. For more information
about assigning bond properties, see the
ChemDraw User’s Guide.
4. From the File menu, select Close and Return
to...
The ChemDraw structure is inserted in the
form.
5. Click Find or press Enter.
You get 3 hits containing a product with a
carbonyl ring that was formed during the course
of the reaction.
Searching by Reaction Type
In many cases, you have some idea of both your
starting materials and your products, but are looking
for some information on how to get from one to the
other.
26•Chapter 2: Tutorials CambridgeSoft
Tutorial 2: Reaction Queries
O
HO
H
Cl H
O
OH
O
HO
H
Cl H
Cl
O

For example, to search for reactions that reduce a
carbonyl to an alcohol:
1. Click Enter Query.
The form is cleared.
2. Right-click the Structure box and choose Edit
Structure
3. In ChemDraw, draw the following:.
O
4. From the File menu, select Close and Return
to...
The ChemDraw structure appears.
5. Click Find or press Enter.
Browse through the 23 hits. Each of the
reactions found shows the transformation of a
carbon-oxygen double bond to a carbon-oxygen
single bond.
This hit list includes reductions of aldehydes,
acids, and ketones.
Refining a Search
In this example, you refine the search to get a
smaller hit list. To get only ketone reduction
reactions, you can refine the previous query.
To enter a more specific query:
OH
1. From the Search menu, choose Enter Query.
The form is cleared.
2. Right-click the Structure box and choose Edit
Structure.
ChemDraw appears.
3. In ChemDraw, draw the following with
Reaction Center Bond Properties set to
Change for both reaction centers:
[NOT O,H]
NOTE: [NOT O,H] is an atom label, not an
atom property. Type it exactly as shown (all
uppercase).Type it once, then use right-click
“Repeat Last Label” to reproduce it.
You added the restriction that the atoms
adjacent to the carbon must not be oxygen
atoms or hydrogen atoms. You specified that the
oxygen in the product must be bonded to a
hydrogen and not, for example, a second
carbon.
4. From the File menu, select Close and Return
to...
The ChemDraw substructure appears.
5. Click Find or press Enter.
You get 12 hits. Each reaction shows the
reduction of a ketone to an alcohol.
Congratulations! You have completed the tutorial on
searching for reactions using ChemFinder.You may
now close the ISICCR database.
Tutorial 3: Using Forms
Forms allow you to display your data in a
customized format, to browse and search through
your database, and to interact with other
applications, such as ChemDraw and Chem3D.
ChemFinder 8 Chapter 2: Tutorials • 27
Tutorial 3: Using Forms
O
Rxn
H
[NOT O,H] [NOT O,H]
O
Rxn
[NOT O,H]

Administrator
In this tutorial, you learn to create, edit, and save the
following form:
You create forms using the Form toolbar shown
below:
NOTE: The Form toolbar docks on the left side of
the ChemFinder window by default, but can be
docked anywhere or “torn off”, as shown below.
.
Selection
tool
Frame
Data box Framed box Picture Grid
For detailed information about each tool, see
“Chapter 3: Creating and Editing Forms.”
Creating Data Boxes
Data and structures from a database are displayed in
boxes. You create boxes using the tools in the Form
toolbar. The Form toolbar only appears when you
select Layout mode.
To create a data box:
Text
Button Subform
1. From the Main toolbar, click New .
A new, blank form appears in the ChemFinder
window.
2. If the Form toolbar is not visible, click the
Layout mode tool .
The Form toolbar appears.
3. Click the Data Box tool .
4. In the form window, drag diagonally to create a
box.
5. Draw two more boxes in the same way. You edit
them in later steps
A Frame, a Framed Box, and a Text Box are
different types of boxes and require a label.
To draw a Framed Box:
1. Click the Framed Box tool and drag
diagonally to create a framed box.
A box Labeled “Data” is created.
2. Point to the word “Data”, right-click, and select
Label.
The Box Text or Label dialog box appears.
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Tutorial 3: Using Forms

3. In the Box Text or Label dialog box, type
“Frame box” and click OK.
The label appears above the Framed Box.
4. Click the Frame tool .
5. Place the pointer at the corner of one of the data
boxes and click and drag to create a border
around the data box.
The Enter the Label dialog box appears.
6. In the Enter the Label dialog box, type “Frame”
and click OK.
The label appears above the box.
To place a picture in your form:
1. Click the Picture tool and drag in the
form.
The Open dialog box appears.
2. In the ChemFinder System directory, click
Buttrfly.wmf, then click Open.
The picture appears in the area you dragged in
the form.
Editing Data Boxes
Edit the data boxes using the Selection tool:
1. Click the Selection tool .
2. Select the upper left box by clicking anywhere
in it.
A selected data box is designated by four black
squares at its corners.
3. Click an empty space in the form with the
Selection tool to deselect the box.
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To select multiple boxes:
• Press Shift and click in each box.
NOTE: You can select all the boxes on the form
by choosing Select All from the Edit menu.
The frame and the box work as one object when you
select, move, resize, or delete. To separate them into
two objects:
• From the Edit menu, choose Bring to Front.
To resize a box:
• Select a single box, and resize it by dragging a
side or corner.
To reposition a box:
• Select a box, point within the selection, and
drag the box.
If you select multiple boxes, dragging the center of
a selected boxes moves all of them at once.
To edit with the Clipboard:
1. Select a box.
2. Try each of the following:
• From the Edit menu, choose Cut.
• From the Edit menu, choose Paste.
• From the Edit menu, choose Undo (Paste).
• From the Edit menu, choose Redo (Paste).
NOTE: Undo and Redo work over multiple levels.
You can use Undo and Redo repeatedly to reverse
multi-step operations.
Deleting Data Boxes
To delete a data box:, do one of the following:
• Select a box and press Delete or Backspace.
• From the Edit menu, choose Clear or Cut.
To clear the entire form:
• From the Edit menu, choose Select All, and
press Delete to remove the contents of the form.
Creating and Saving a Form
To create and save a new form:
1. Draw the form shown below.
2. From the File menu, choose Save As.
3. In the Save As dialog box, save the form as
tut3.cfw in the directory you want.
4. From the File menu, chose Close.
Congratulations! You have completed the third
tutorial.
30•Chapter 2: Tutorials CambridgeSoft
Tutorial 3: Using Forms

Tutorial 4: Opening a
Database
After you create a form, you can use it to connect to
a database that actually stores information. In this
tutorial, you use the form you saved as “tut3.cfw” in
the previous tutorial to access and retrieve
information from an existing database.
Connecting a Database to a
Form
To connect a database to your form:
1. From the File menu, choose Open.
The Open dialog box appears.
2. Select tut3.cfw and click Open.
The form you created in the previous tutorial
appears, but all of its fields are blank You can
use this form to display the demonstration
database.
3. Right-click the Structure box and choose Data
Source.
The Box Properties dialog box appears with the
Database tab displayed.
NOTE: The “Data Source” option is only available
in Layout mode. Make sure the Layout mode toggle
button is depressed before performing this
step.
4. Click Open Database.
NOTE: The Open and Create Database
buttons work with ChemFinder databases only.
To access data in other types of databases, use
the Attach Table button. For more information
about data sources, see “Attaching Tables from
Other Applications” on page 70.
The Open dialog box appears.
5. Select CS_demo.mdb and click Open.
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The database opens, and the Box Properties
dialog box appears displaying the Database tab.
6. Select a table.
A list of the tables in the database and the fields
in each table are shown. The field you select
determines what type of data appears in the box.
Assigning Fields to Data Boxes
To display structures from the CS_Demo database in
a Structure box on your form:
• From the list of fields in the Box Properties
dialog box, click Structure, and then click OK.
The Structure field is linked to the Structure
box. In the Structure data box, you can see the
contents of the Structure field for the first
record in the CS_Demo database.
To assign fields to the other data boxes:
1. Right-click in the Name box and choose
Molname.
NOTE: Because you opened a database and
table, the shortcut menu displays the fields in
the database.
The Molname field in the database is linked to
the Name box, and the data item for the first
record appears in the Name box.
2. Right-click in the Formula box and choose
Formula.
3. Right-click in the Mol ID box and choose
MOL_ID.
4. From the File menu, choose Save As.
5. In the Save As dialog box, save the form as
“tut4.cfw” in the directory of your choice.
6. From the File menu, choose Close.
32•Chapter 2: Tutorials CambridgeSoft
Tutorial 4: Opening a Database

Congratulations! You have created your own
customized form for viewing the CS_Demo
database.
Tutorial 5: Creating Your
Own Database
In this tutorial you create a new database using the
techniques you learned in Tutorial 3.
1. Create the following new form. Select the
Layout tool if the Form toolbar is not visible.
2. From the File menu, choose Save As, and save
your form as mydb.cfw.
3. Right-click in the Structure box and choose
Data Source.
The Box Properties dialog box appears with the
Database tab displayed.
4. Click Create Database.
The Save As dialog box appears.
5. Type “mydb.mdb” and click Save.
The name of the database appears in the Name
box in the Box Properties dialog box.
ChemFinder creates one data table (MolTable)
containing four fields: Structure, Formula,
MolWeight, and MOL_ID.
6. Click OK.
The form appears.
Assigning Fields
To assign fields to the Structure, ID, and Formula
boxes:
1. Right-click in the Structure box and choose
Structure.
2. Right-click in the ID box and choose MOL_ID.
NOTE: ChemFinder automatically assigns a
unique identifier to the Mol_ID field for each
record you create. If you delete a record, its
identifier is not reused. This can create
confusion when sorting by Mol_ID because
there will be “gaps” in the sequence. If you
need sequential ordering, you must create an
integer field for it.
3. Right-click in the Formula box and choose
Formula.
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Two data boxes, Name and Boiling Point, do not
have fields assigned to them.
Create a field for the Name data box:
1. Right-click in the Name data box, and choose
Field.
The Box Properties dialog box appears with the
Field tab displayed.
2. Click Create Field.
The Create Field dialog box appears.
3. Type “Compound Name” in the Name box and
click OK.
NOTE: The maximum number of characters
you can enter in any text field is 254 characters.
If you want a text field to contain more than 254
characters, choose Memo/Rich Text from the
Type drop-down list.
The field name appears in the data source tree.
4. Click OK in the Box Properties box.
To create a field for the Boiling Point box:
1. Right-click in the Boiling Point data box, and
choose Field.
The Box Properties dialog box appears with the
Field tab displayed.
2. Click Create Field.
The Create Field dialog box appears.
3. Type “Boiling Point” in the Name box.
4. Select Double from the Type drop-down menu.
NOTE: You use the field type “Double” to
create a field containing real numbers (such as
-123.7 and 43.242) as data.
5. Click OK in the Create Field dialog box, and
OK in the Box Properties box.
You created two fields in the database. Check the
field assignments in the data boxes.
1. Right-click in the Name data box.
There should be a check next to Compound
Name indicating that the Compound Name
field is linked to the Name data box.
2. Right-click in the Boiling Point data box.
There should be a check next to Boiling Point.
Adding Records
Now that you created new fields and assigned them
to data boxes, you can add data to your database.
34•Chapter 2: Tutorials CambridgeSoft
Tutorial 5: Creating Your Own Database

Before you begin to add structures, you might want
to check whether or not ChemFinder is set to use the
ChemDraw ActiveX control.
1. Right-click in the Structure data box, and select
Properties.
2. In the Box Style section of the Box Properties
dialog box, select “ChemDraw style” or
“ChemFinder style”.
When “ChemDraw style” is selected,
ChemFinder defaults to the ChemDraw
ActiveX control. This allows you to edit
structures directly in the Structure data box in
ChemFinder.
Now you are ready to begin adding records to your
database.
1. Deselect the Layout tool to hide the Form
toolbar.
2. Double-click in the Structure box.
ChemDraw opens, or the ChemDraw ActiveX
toolbar appears, depending on your default.
NOTE: Even if your default is ChemDraw
ActiveX control, you can open ChemDraw by
right-clicking in the structure box and selecting
Edit in ChemDraw.
3. Draw benzene.
4. If you are editing in ChemDraw, select Close
and Return to... from the File menu. If you are
using the ChemDraw ActiveX control, click
somewhere outside the Structure data box.
The benzene molecule appears in the Structure
Data box on the form. ChemFinder calculates
the molecular formula, and assigns an ID
number of 1.
5. Click the Name box and type “Benzene”.
6. Click the Boiling Point box and type “80.1”.
To commit your new record, do one of the
following:
• From the Record menu, choose Commit
Changes.
• Click the Commit Changes button .
You entered the first record in your database. The
size of your database is indicated in the Status Bar.
Enter two more records:
1. From the Record menu, choose Add New
Record, or click Add Record .
2. Add a record for n-Pentane (shown below),
with a bp = 36.1.
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3. Repeat step 1 and then add a record for
Cyclohexane (shown below), with a bp = 80.7.
NOTE: After you have two or more records in
your database, you can commit changes by
moving to a different record using the Record
tools.
4. From the File menu, choose Save.
NOTE: Choosing Save saves any changes
made to your form. Clicking Commit Changes
saves the data into your database.
Tutorial 6: Working with
Subforms
Subforms allow you to display relational data. If you
have a database containing two or more data tables,
and these data tables share a common, linking field,
then you can display data from both tables.
Whenever the value of the linking field changes in
the main form, the subform only displays those
records from its table which have the same value in
the linking field. You can also use subforms to
display data from different databases.
In this tutorial, you open the CS_Demo database and
display the MolTable in the main form. Then you
display the Synonyms table of the CS_Demo
database in a subform. By defining the MOL_ID
field as the linking field, you display the two sets of
data relationally. To select a subform, you click the
title bar.
Creating a Subform
1. Open your ChemFinder form tut4.cfw.
Opening this form connects you to the
CS_Demo.mdb database.
2. Maximize the size of the tut4.cfw window by
dragging one of the bottom corners of the
window or by clicking the Maximize button.
3. Click the Subform tool .
4. In the form, click and drag to create a large
subform.
NOTE: If there is not room on the right side of
your form, you can put the subform on the
bottom of the form.
You design a subform exactly like you design a main
form.
• Click the Framed Box button, and create a box
labeled “Synonym” within the subform.
36•Chapter 2: Tutorials CambridgeSoft
Tutorial 6: Working with Subforms

Your form should appear similar to the one
shown below:
NOTE: You may display the subform with or
without a title by right-clicking on the title bar and
selecting Properties, and then selecting the Subform
tab. A check box “Title” toggles the title off and on.
To open a database using the subform:
1. Right-click on the Synonym data box in the
subform and choose Data Source.
The Box Properties dialog box appears.
2. Click the + symbol next to the Synonyms table
to display the fields contained in that table.
3. Select Synonym and click OK.
You are displaying data from the MolTable of the
CS_Demo.mdb in the main form and data from the
Synonyms table of the CS_Demo.mdb in the
subform. However, the two forms are not related.
To demonstrate this:
• Navigate the form using the Record tools, and
note that only one form is changing its records.
NOTE: When the title bar of the subform is
highlighted, the subform is active. The Record tools
and menu commands apply only to the subform. To
deactivate the subform, click any empty space on the
main form.
Linking the Subform
You must define the linking field for each table:
• MOL_ID field for MolTable.
• SYN_ID field for Synonyms.
To define the links:
1. Right-click the title bar of the subform and
choose Properties.
NOTE: Clicking the title bar of a subform box
is equivalent to clicking anywhere inside any
other type of box. You can set the box properties
and manipulate the box. Clicking inside a
subform activates the subform and allows you
to work within it.
The Subform Properties dialog box appears
with the Subform tab displayed.
2. In the Data Source Tree, choose MOL_ID.
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Tutorial 6: Working with Subforms

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The field appears in the Link from… field
section.
SYN_ID appears as the default in the Link to…
field section.
3. Click OK.
The MOL_ID field links the main form and
subform.
4. Click anywhere outside the subform box, and
browse your database using the Record tools.
As each molecule record of the MolTable is
displayed, the subform shows the first matching
ID from the Synonyms table.
5. Click inside the subform box.
Now when you browse, you are browsing only the
entries in the subform.
1. Browse the current Synonyms subset by
clicking a Record tool.
2. With the subform still active, click Switch to
Table , or double-click in the subform.
3. Click outside the subform and browse.
The table window shows you the complete list
of synonyms for each molecule.
To save and close the file:
1. From the File menu, choose Save.
2. From the File menu, choose Close.
Congratulations! You have completed the
ChemFinder Tutorials.
38•Chapter 2: Tutorials CambridgeSoft
Tutorial 6: Working with Subforms

Chapter 3: Creating and Editing Forms
Overview
You use forms to interact with information in a
database. A ChemFinder form is composed of data
boxes for viewing or modifying data items, such as
structures, numbers, text, or pictures. A form can
also contain subforms for relational access to
different data tables and different databases.
You can create a form in the following ways:
• Automatically, using the Form Generator dialog
box.
• Manually, using the Form tools.
The example below shows a form displaying a
single record of information from a database.
Creating a form consists of creating a layout (see
“Creating Forms Manually” on page 44), and setting
box properties (see “Setting Box Properties” on
page 48), tabs (see “Creating and Editing Tabs” on
page 54), and security (see “Securing Forms” on
page 59).
You can edit your form at any time (see “Editing
Forms” on page 55 and “Changing the Layout of an
Existing Form” on page 58).
The first step in designing a form is selecting the
database and deciding which fields to include.
Selecting a Database
A ChemFinder form does not store data directly, but
is simply the window through which you look at
data. When creating a form, you need to specify the
source of the data to display. A form displays data
from a single table in a database. To specify the data
source for a form, you must open or create a
database, and then select a table.
If you want to view data from more than one table,
you must create a form for each table. Typically, you
create a main form for one main table and a subform
for each other table. For more information, see
“Chapter 6: Relational Data and Subforms” on page
103.
You can connect a database to the form before
creating boxes, or any time after. If the form is
already connected to a database, you can change the
database or the data source. If the form has boxes
with fields connected to them, then the boxes
automatically connect to fields of the same name in
the newly-opened database.
Opening an Existing Chemical
Database
To open a database to associate with a form:
1. Right-click on the form and select Data
Source.
The Form Properties dialog box appears.
2. Click Open Database.
The Open dialog box appears.
ChemFinder 8 Chapter 3: Creating and Editing Forms • 39
Selecting a Database

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3. In the Open dialog box, choose a database with
an .mdb file extension, and then click Open.
The Form Properties dialog box reappears. The
CS_Demo database is shown below.
A data source tree appears in the left side of the
Form Properties Database dialog box,
displaying the fields and their tables.
4. Click OK.
The database is associated with the form.
Selecting the Data to Display
You indicated the source of the data to display on the
form, but the form is still blank. To see the data, you
need to indicate what data to show in each box. You
can use the Box Properties dialog box, as described
in “Setting Box Properties” on page 44.
To choose the data box to display:
1. Right-click in a box or frame, then click Field.
The Field properties appears.
2. From the data source tree, select the field to
display.
3. Click OK.
The field data is displayed in the box.
If you use this method with a framed box, the box
label will remain unchanged. If you want to use the
field name as the box label, you can do it in one step
as follows:
1. Right-click in a framed box.
2. Select the field name from the list at the bottom
of the right-click menu.
The frame receives the field name and the data
is displayed in the box.
40•Chapter 3: Creating and Editing Forms CambridgeSoft
Selecting a Database

Opening a Secured MS Access
Database
To open a secured Microsoft Access database in
ChemFinder, you need to set the appropriate
permissions in Access.
NOTE: If your database was created in MS
Access 97 (as, for example, were some of the
ChemFinder sample databases), and you are using
a newer version of Access, you must convert the
database before you can edit it. These instructions
assume a database created in Access 2002.Other
versions may differ slightly as to options and
procedures.
To set the permissions:
1. Open the desired database in MS Access.
2. On the Tools menu, point to Security, and then
choose User and Group Permissions.
3. Select the Users or Groups radio button to
assign permissions to individuals or groups.
4. Select an Object Type from the drop-down
menu.
5. Select the permissions you want to assign for
that object type to each user or group.
6. Click Apply.
7. When you have finished assigning permissions,
click OK.
8. Open the database in ChemFinder.
Creating a Database
You can create a new, empty database and associate
it with a form.
To create a database:
1. Open an existing form, or create a new one.
2. Right-click in the form and select Properties.
The Box Properties dialog box appears.
3. On the Box Properties Database tab, click
Create Database.
The Save As dialog box appears.
4. In the File Name box, type a name for your
database, and then click Save.
A data source tree appears, containing the
database and its tables and fields.
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Selecting a Database

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5. Click OK.
The Box Properties dialog box closes.
Creating Forms
Automatically
ChemFinder provides a Form Generation dialog box
from which you can automatically create a form.
You choose the form style and properties from
pre-defined options.
To begin creating a new form:
1. Open an existing database.
2. Right-click on a blank area of the current form
and choose Data Source.
The Form Properties dialog box appears.
3. In the Form Properties dialog box, click the
Form tab.
4. Click the Generate new form checkbox, then
click Style.
The Form Generation dialog box appears.
5. In the Choose Fields to be included section,
click the field names to include.
6. To have a Structure box created in the upper left
corner of the form, click the Structure in upper
left of form checkbox.
If you do not select this option, the boxes are
generated in the order they appear in the list.
7. Select the form style:
If you want the
boxes to
be surrounded by a
frame
Then, in the Form
style section, click
Framed.
42•Chapter 3: Creating and Editing Forms CambridgeSoft
Creating Forms Automatically

If you want the
boxes to
be labeled above Titled.
be labeled to the left Labeled.
not be labeled Plain.
8. Choose the number of columns, between one
and four.
9. Choose the size and spacing of the boxes and
grid:
If you want the boxes
to be
larger and spaced further
apart
medium, relative to the
Large and Small settings
smaller and spaced closer
together
Then, in the Form
style section, click
Then, for Grid
Size, choose
Large.
Medium.
Small.
10. Click OK.
Your form settings are saved.
11. Click OK.
In the following dialog box, click No to create a
new form.
The generated form appears in the window.
Saving a Form
In most non-database applications—including
ChemDraw and Chem3D—you edit data on the
screen, but your changes are not made permanent
until you choose Save from the File menu.
In database programs such as ChemFinder, your
changes are automatically and permanently saved to
the database when you switch records. This is
“committing” the changes. You then have the
opportunity to revert to the original data by choosing
Undo Changes from the Record menu.
The Save command in the File menu refers only to
changes made on the form itself, such as the position
of boxes. Choosing the Save command from the File
menu has no effect on changes you make to data
stored in the database. Saving a form also saves
subforms and changes that you make to subforms.
After you create a form, you can save it. When you
retrieve the saved form, it automatically opens a
connection to the database defined in the forms.
To save a form:
1. From the File menu, choose Save, or to save the
form under a new File name, choose Save As.
The Save dialog box appears.
2. Choose the directory in which you want to save
the form, type a filename, and click Save.
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Creating Forms Automatically

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ChemFinder saves the form with a .cfw
extension
Creating Forms
Manually
You create a form and define it by using the Form
tools to create objects and the Box Properties dialog
box to set the form properties.
Using the Form Tools
You must use the Form Tools toolbar to design a
form. Box creation commands are not available
from the menu.
To display the Form tools, do one of the following:
• Click Layout on the Main toolbar.
• From the View menu, point to Toolbars, and
then click Form.
The Form toolbar appears providing tools for
you to create and edit a form.
Selection
tool
Data box
Frame
Creating a New Form
To create a new form:
Text
Framed box
Button Subform
Picture
Grid
• From the File menu select New, or click
A blank form, Form1, appears.
.
Using the Grid
In a new form, the snap grid is turned on by default.
This grid helps you align boxes on the form. Turning
on the grid forces objects to snap to the grid as they
are drawn.
To toggle the grid on or off, do one of the following:
• Click the Grid tool on the Form toolbar.
• From the View menu, choose Grid.
NOTE: You can change the grid spacing using the
Preferences dialog box. See “Setting Preferences”
on page 119.
Creating Boxes
A ChemFinder form is composed of a collection of
boxes that display data. Each box displays one data
item of the current record. To create a data box, use
one of the tools on the Form toolbar.
NOTE: The Form toolbar is not visible unless the
Layout button is selected.
The Data Box displays a data item or structure. You
can use it to display any data from a database,
including text, numbers, dates, molecules, reactions,
or pictures. It is the only box that allows you to edit
data in the database. Data boxes do not have labels,
but you can label them by adding a Frame or Plain
Text. You can also use the Data Box to display static
data not from a database.
44•Chapter 3: Creating and Editing Forms CambridgeSoft
Creating Forms Manually

To draw a Data Box:
1. Click the Data Box tool .
2. On the form, press and drag diagonally to create
a box.
To specify what type of data is displayed in the box,
see “Setting Box Properties” on page 48. If the form
already has a database open, you can right-click in
the data box, select Field... and choose from a list of
the available fields.
Creating Frames
The Frame tool allows you to create a label
surrounding a data box or group of boxes. When you
draw a new frame, you are automatically prompted
for a text label to be attached to it.
To create a frame:
1. Click the Frame tool .
2. On the form, press and drag diagonally to create
a frame.
A framed box appears with the label “Data”. To
change the label:
3. Right-click on the label and choose Label from
the drop-down menu.
The “Enter the label” dialog box appears.
4. Type the label you want to attach to the frame.
5. Click OK.
A fixed label appears on the frame.
To change a label:
1. Right-click on the edge of a frame and choose
Label.
2. Enter the new label as above.
Another way to change a frame's label is in the Box
Properties dialog. For more information, see
“Setting Box Properties” on page 48.
You can use a frame to show “live” data from the
database. If a frame is connected to a database field,
it is updated automatically as you browse or search.
For example, you might place a frame around a
structure field, where the label on the frame
represents the name of the current structure. The
label changes every time the structure does. You
must use Box Properties to set up a live data
connection for a frame.
Creating Boxes with Frames
The Framed Box tool allows you to create a data box
and a frame simultaneously. You name the frame in
the Enter the Label dialog box.
When you create a data box and frame with the
Framed Box tool, these two items are connected. To
manipulate them separately:
• Select the Framed box and from the Edit menu,
choose Bring to Front.
ChemFinder 8 Chapter 3: Creating and Editing Forms • 45
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Administrator
To create a framed data box:
1. Click the Framed Box tool .
2. On the form, click and drag to create a box.
3. In the Enter the Label dialog box, type the label
you want to attach to the frame, and click OK.
The framed data box is labeled.
To edit the label of a framed data box:
1. Select the frame by carefully right-clicking near
the edge of the framed box and select Label.
2. In the Enter Box Label dialog box, type the new
label. The label does not have to match the
name of the field displayed in the box.
3. Click OK.
Automatic Labels
You can let ChemFinder automatically label your
framed box with the name of the field from the data
tree. This works slightly differently depending on
whether you created a box and added a frame, or
created a framed box.
To automatically label a framed box:
• Right-click inside the data box and select the
field from the drop down list.
The data appears in the data box and the frame
label changes to match the field name.
To automatically label a frame:
1. Right-click the frame label and select
Properties.
2. On the Box Properties tab, select a field from
the data tree. The field name will appear in the
text box under Data Source.
NOTE: If the text box is grayed out, you have
not clicked on the frame label.
3. Click OK.
The frame label changes to match the field
name selected.
4. Right-click in the data box and select the field
from the drop down list that corresponds with
the new label.
NOTE: When you change a label from the Box
Properties dialog box, the label and the data box are
treated separately. You must update the data box
manually to match the label.
Adding Plain Text
The Plain Text tool allows you to display text
without a box or a frame. You can use it to place a
static label on the form. But, like a frame, you can
use it to display live data if desired.
To use the Plain Text tool:
1. Click the Plain Text tool .
2. On the form, click and drag to create an area to
specify where the text will appear.
The Enter the Text dialog box appears.
46•Chapter 3: Creating and Editing Forms CambridgeSoft
Creating Forms Manually

3. Type the text you want to display.
4. Click OK.
To change the font or color of the text, select it with
the Form toolbar Selection tool . Use the text
formatting toolbar to customize the text.
Adding a Button
To place a button on a form:
1. Write a script using the ChemFinder
Automation Language (CAL).
2. Click the Button tool on the Form toolbar.
3. On the form, click and drag to draw a button.
The Enter the Label dialog box appears.
4. Enter a label. The text can be descriptive
(“Click to browse”) and does not have to
correspond to the name of the script. Click OK.
For more information about using a button to run a
script, see “Executing a Script on a Form” on page
130.
Adding Pictures
The Picture tool allows you to create a Picture Box
to display a Windows metafile. It can display a static
metafile stored in a .WMF file, or a live one stored
in a picture column of a database.
To create a Picture Box:
1. Click the Picture tool .
2. On the form, click and drag to create an area for
the picture to occupy.
The Open dialog appears.
3. In the Open dialog box, select the Windows
metafile (.wmf) you want to display, and then
click Open.
The picture appears in your form.
NOTE: The metafile is not actually embedded in
the form. Only its filename is saved with the form. If
you move or rename the metafile, the form will not
display the corresponding picture. However, if you
make changes to the picture and keep its filename
the same, the picture in the form will be updated.
To read in a picture file or to replace a picture in a
Picture Data Box:
1. Right-click a picture and choose Read File.
The Open dialog box appears.
ChemFinder 8 Chapter 3: Creating and Editing Forms • 47
Creating Forms Manually

Administrator
2. In the Open dialog box, select the metafile you
want to display in the Picture Data Box, and
click the Open button.
The new metafile replaces the picture in the
Picture Data Box.
To save a metafile from a Picture Data Box:
1. Right-click on the Picture Box and choose
Save File.
2. In the Save As dialog box, type a file name and
then click Save.
The picture is saved to a file in Windows
metafile (.wmf) format.
Setting Box Properties
Use the Box Properties dialog box to set
ChemFinder form attributes, including: data source,
display type, font, and box style.
To open the Box Properties dialog box:
• Right-click on a data box and choose
Properties.
The Box Properties dialog box appears.
NOTE: The “Properties” option is only available
in Layout mode.
Setting Data Box Styles
You can use the Box Properties dialog box to change
the style of a data box on a form. For example, you
can change a data box to a frame or picture.
The Box Style menu only shows applicable styles
for each field. For example, you cannot show a real
number in a Picture.
For information about field types, see “Creating
Fields” on page 72.
You can choose from the following styles:
• Data Box—displays alphanumeric data. Can
display multiple lines of data.
• Frame—displays alphanumeric data. Can
display a single line of data.
• Plain Text–displays alphanumeric data. Text
data can be displayed in multiple lines. (Use
Ctrl+Enter to start a new line.) You set the field
size when you create the field, up to a maximum
of 254 characters.
• Picture–displays Windows metafile data.
Pictures are scaled to fit within picture boxes,
with fixed height to width ratios.
• Formula–displays any kind of text but numbers
are subscripted. Formulas are presented in
modified Hill order, as follows: If a substance
contains both carbon and hydrogen, the carbons
are listed first, followed by the hydrogen atoms,
followed by other elements alphabetically by
element symbol. If a substance contains carbon,
the carbons are listed first, followed by other
elements alphabetically by element symbol.
Otherwise, all elements are listed alphabetically
by element symbol.
• Button–used to create buttons to actuate
scripts. Buttons display button labels.
48•Chapter 3: Creating and Editing Forms CambridgeSoft
Setting Box Properties

• Rich Text—displays styled data in multiple
lines. (Use Ctrl+Enter to start a new line.) You
can format text with the Text Format toolbar. If
the data in a field contains rich text, markup
characters are displayed.
• Structure (ChemDraw style)–displays
chemical structures or reactions. Reactions are
laid out for best fit with the box and the layout
may change if the box is reshaped. The box
defaults to using the ChemDraw ActiveX
control to create and edit structures, but you can
reset the preference. For more information, see
“Setting Preferences” on page 119.
• Structure (ChemFinder style)–as above, but
defaults to opening ChemDraw to create and
edit structures.
• Structure (Chem3D style)–as above, but
defaults to display 3D structures.
To set the box style:
1. Right-click in the data box to change and
choose Properties.
The Box Properties dialog box appears.
2. From the Box Style menu, choose the box style.
3. Click OK.
Viewing Structures
You can display structures in a structure box in
ChemFinder, ChemDraw, or Chem3D styles. The
Chem3D style is a display only format that allows
you to rotate and analyze structures within a
ChemFinder structure window. See the Chem3D
User’s Manual for information on using the
Chem3D ActiveX control.
If you choose ChemFinder style, ChemDraw will
open when you want to edit structures or create a
query. If you choose ChemDraw style, editing is
done in the structure box using the ChemDraw
ActiveX control.
The ChemDraw format displays more graphicallyrich
drawings than the ChemFinder format.
However, ChemFinder does not use all of the
Chemdraw drawing features when searching.
For example, textual annotations are ignored,
R-group tables are not recognized. Certain graphics,
such as rectangles and orbitals, are not transferred.
and ChemFinder does not consider their chemical
implications.
To choose how to view structures:
1. Right-click in a structure data box and choose
Properties.
The Box Properties dialog box appears.
2. On the Box tab, in the Box Style section, select
the structure format to view from the menu:
If you want the Then choose
ChemDraw format Structure
(ChemDraw style).
ChemFinder format Structure
(ChemFinder style).
ChemFinder 8 Chapter 3: Creating and Editing Forms • 49
Setting Box Properties

Administrator
If you want the Then choose
Chem3D format Structure (Chem3D
style).
Viewing Structures in Chem3D Format
Unlike the ChemDraw and ChemFinder styles,
Chem3D style is view only. You cannot edit the
structures in Chem3D style. Double clicking in the
Structure Box activates the Chem3D ActiveX
control. When you point inside the Structure Box,
the cursor becomes a hand that lets you “grab” and
rotate the structure.
Dragging within the structure turns the hand into a
fist, and allows you to freely rotate the structure.
Dragging the cursor across or up and down rotates
the structure around the X and Y axes . To rotate
around the Z axis, drag outside the structure.
Right clicking displays a menu that allows you to
modify the display.
For more information on the Chem3D ActiveX
control, see the Chem3D User’s Manual.
Setting Fixed and Live Data
In the Box Properties dialog box, you can designate
whether the data source is fixed or from a field.
Fixed data is attached to the form and does not
change as you browse. Data from a field is stored in
the database and is different for each record. As you
browse, the record display updates according to the
contents of the field.
To specify live data for a data box:
1. In the Box tab, select the field to associate, and
then click Field.
2. Click OK.
The box display updates as you change records.
To specify fixed data for a data box:
1. In the Box tab, select the field to associate, and
then click Fixed.
2. Type a label. If you choose a structure or picture
field, click to browse to the file to display.
3. Click OK.
The box display is fixed.
50•Chapter 3: Creating and Editing Forms CambridgeSoft
Setting Box Properties

Adding a Data Box Menu
You can add a menu containing a list of choices to a
data box so you can choose an item from it to appear
in the data box.
To add a menu:
1. Right-click on a data box and choose
Properties.
The Box Properties dialog box appears.
2. On the Box tab, click the “With drop-down
choices” checkbox.
The Choices tab appears.
3. Take the appropriate action:
If you want to Then click
use a list from a
database table as the
data box menu
create your own list
for the data box menu
From table and
follow the
instructions at the
bottom of the dialog
box.
Fixed list of choices
and follow the
instructions at the
bottom of the dialog
box.
If you want to Then click
use a list from a
database table and
add your own items to
the data box menu
4. Click OK to close the dialog box, then click in
the data box.
A button appears in the lower right corner of the
box when you click in the box.
5. Click the button to display the menu.
6. Select any item on the menu—the text appears
in the top left corner of the box and the button
disappears.
Click within the data box to make the button
reappear.
Adding Scroll Bars
You can add scroll bars to a data box so you can
scroll through any additional data that is not visible
within a data box.
To add a scroll bar:
1. Right-click a data box and choose Properties.
The box properties dialog box appears.
2. In the Box style section, select With scroll
bars.
3. Click OK.
a. From table. A
list appears.
b. Click Fixed list
of choices, and
edit the list.
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Setting Box Properties

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The scroll bar appears on the bottom right in the
data box.
need a graphic here of a data box with scroll bar.
Hiding Data Boxes
You can show or hide boxes when switching
between query and browse mode. For example, hide
data boxes when you want hide non-searchable
boxes during query entry. Show data boxes to
display information useful for query entry.
When you are in form layout mode, all boxes are
visible, regardless of the setting.
To set when boxes are hidden:
1. Right-click on the box and choose Properties.
2. In the Box Style area, select Hidden in Browse
Mode or Hidden in Query Mode.
3. Click OK.
4. Deselect the Layout Mode button to view the
results.
Customizing Text
You can customize text fonts, sizes, styles, colors,
and alignment in form boxes using the Text Format
toolbar. All of the standard text formatting options
are available.
To display the Text Format toolbar:
• From the View menu, point to Toolbars, then
select Text Format.
The Text Format toolbar appears.
NOTE: Text copied from a word processor such as
Microsoft Word retains its styles when pasted into a
Rich Text box.
The text format toolbar is active:
• When you are editing a memo field in a rich text
box. In this case, font changes apply only to the
current selection within the text.
• When you are editing in a regular data (or
structure) box. Font changes apply to the entire
contents of the box.
• When you are in form edit mode, with the
selector tool active, and one or more boxes are
selected. Font changes apply to all selected
boxes (except frames around data boxes).
Customizing Fonts
All the labels on ChemFinder objects can be edited
to your specifications. You can edit any label’s font,
font style, size, and color.
To set the font for a label:
1. Click Font.
The Font dialog box appears.
2. Set the text font, style, size, and color.
The sample area previews the font.
52•Chapter 3: Creating and Editing Forms CambridgeSoft
Setting Box Properties

3. Click OK to commit the changes.
NOTE: To change the color of the atom labels in
the structure box, you must use the Periodic Table.
See “Using the Periodic Table” on page 127
Customizing Numbers
Using the Box Properties dialog box, you can
specify how numeric data is displayed in forms you
can customize the following properties:
• Currency symbol
• Decimal position
• Scientific notation
To specify the numeric format:
1. Right-click on a data box containing numeric
data and choose Properties.
The Box properties dialog box appears.
2. Click Format.
The Numeric Format dialog box appears.
3. Select the appropriate option:
If you want to
display
a varying number of
decimal places
Then click
Unformatted.
a currency symbol Currency and select
the symbol from the
drop-down menu.
the currency symbol
to the right of the
number
a standard
floating-point value
with a selected
number of decimal
places
the numbers
displayed in scientific
notation
Symbol on right
when a currency
symbol is selected.
Fixed point and
select the number of
decimal places.
Scientific and select
the number of
decimal places.
An example of the format you select is shown in
the Sample area of the dialog box.
4. Click OK.
The format is applied to the current data box.
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Setting Color
You can set the following color options:
• The form background color
• The color of the form in query mode
• The default background for all forms
To set the form background and form query colors:
1. Right-click on a data box and choose
Properties.
The Box Properties dialog box appears.
2. Click the Form tab.
The Form properties appear.
3. Take the appropriate action:
To set the
background color
of the
Click
form Form Background.
form in query mode Query Background.
The Color dialog box appears.
4. Select a color.
5. Click OK.
The Form or Query Background button changes
to reflect the color you choose.
To set the default background color:
1. From the File menu, choose Preferences.
2. In the Preferences dialog box, click Color.
3. On the Color tab, click Form Background.
4. In the Color dialog box, select a color and click
OK.
The color you chose becomes the default form
background color.
Creating and Editing
Tabs
If you have a large number of fields in a database,
you can access information more easily, and make
the form less cluttered, by using tabs to divide a long
form into smaller parts contained on separate tabs.
54•Chapter 3: Creating and Editing Forms CambridgeSoft
Creating and Editing Tabs

To create tabs on a form:
1. Right-click an empty part of a form and choose
Add Tab.
Two tabs appear in the lower left corner of the
form. Clicking on the second tab will present
you with a new empty form.
To rename a tab:
1. Right-click the tab and choose Rename Tab.
The Tab Name dialog box appears.
2. Type a name for the tab and click OK.
The new name appears on the tab.
To remove a tab:
• Right-click the tab and choose Delete Tab.
The tab is removed.
Editing Forms
Tabs
You can move or resize boxes and other objects on
your form with the Selection tool and the items in
the Edit menu.
Selecting Objects on a Form
You can use the Selection tool to choose data boxes
and other objects on a form so you can move, resize,
or delete them.
When the selection tool is active, the Edit menu
commands apply to the boxes themselves. When the
selection tool is not active, the Edit Menu
commands apply to the contents of the active data
box.
To select an object on a form:
• On the Form toolbar, click the Selection
tool , and then click an object on the form
to select it.
A highlight appears around the object
indicating that it is selected.
Selection Marks
To select multiple objects on a form:
1. On the Form toolbar, click the Selection
tool .
2. Do one of the following:
• Press Shift and click on the multiple objects.
• Drag the Selection tool around the boxes
you want to select.
To select all the objects in the form:
• From the Edit menu, choose Select All.
Moving Objects
You can move data boxes or any other object to a
different place on a form with the Selection tool.
To move objects on a form:
1. On the Form toolbar, click the Selection
tool .
2. Select the objects to move.
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Editing Forms

Administrator
3. Drag the objects to a different place.
NOTE: To move a subform, you must click- drag
the title bar of the subform, not its contents.
To move objects one pixel at a time:
1. Select the objects you want to move.
2. Press an arrow key in the direction you want to
move the objects.
The objects move one pixel in the direction of
the arrow key.
Resizing Objects
You can resize a data box or any other object by
stretching it with the Selection tool.
NOTE: You cannot resize more than one object at a
time or simultaneously resize a box and its frame,
unless you create a framed box using the Framed
Box tool. For more information, see “Creating
Boxes with Frames” on page 45.
To resize objects on a form:
1. On the Form toolbar, click the Selection
tool .
2. Position the pointer over an edge or corner of
the object until the pointer is a double-headed
arrow.
3. Drag in the direction you want to resize.
To resize objects one pixel at a time:
1. Select the object you want to resize.
2. Place the mouse pointer over an edge or corner
of the object until it is a double-headed arrow.
3. Press an arrow key in the direction you want to
resize the object.
The edge of the object moves one pixel in the
direction of the arrow key.
Deleting Objects
You can remove data boxes and other objects from a
form with the Selection tool or items on the Edit
menu.
To remove objects from a form completely:
1. On the Form toolbar, click the Selection
tool .
2. Select the objects you want to delete.
3. From the Edit menu, choose Clear.
The object is removed from the form.
Reversing and Restoring
Changes
You can use the items on the Edit menu to reverse or
restore changes you made to a form.
56•Chapter 3: Creating and Editing Forms CambridgeSoft
Editing Forms

To reverse or restore changes:
• From the Edit menu, take the appropriate
action:
If you want to Then choose
reverse the effect of
the last change you
made to the form or
object
reverse the effect of
Undo
Undo.
Redo.
NOTE: Undo and Redo work over multiple
changes. Either command can be used repeatedly to
reverse multi-step operations.
Ordering Objects
You can use the Bring to Front and Send to Back
commands to place data boxes in a specific
sequence as follows:
• Select which overlapping data box is on top.
• Set the order in which the cursor moves when
you press the Tab key.
To put a box on top or bottom:
1. Select the box.
2. From the Edit menu, choose Bring to Front to
put it on top, or choose Send to Back to put it
on the bottom.
The order in which data boxes are created is the
order in which the cursor moves as you press Tab.
You can set to which data box the cursor moves first
or last.
To set the cursor to move to a data box first:
1. Select a data box.
2. From the Edit menu, click Send to Back.
3. Press the Tab key.
The cursor moves to the box you set.
To set the cursor to move to a data box last:
1. Select a data box.
2. From the Edit menu, click Bring to Front.
The box you set is the last box the cursor moves
to when you press Tab repeatedly.
Aligning and Distributing
Objects
You can line up objects relative to each other by
aligning them and space objects at an equal distance
apart by distributing them.
NOTE: In framed dialog boxes, the inner data box
is aligned, not the frame.
To line up objects on a form:
1. Press Shift and click the objects to align.
2. From the Edit menu, point to Align, and then
take the appropriate action:
If you want to line
up along the
top edge of the first
object you place on
the form
middle of an object in
a vertical line
Then choose
ChemFinder 8 Chapter 3: Creating and Editing Forms • 57
Editing Forms
Top.
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Administrator
If you want to line
up along the
bottom edge of an
object
Bottom.
left edge of an object Left.
middle of an object in
a horizontal line
right edge of an object Right.
The form objects line up according to your
choice.
To evenly space objects on a form:
1. Press Shift and click the objects to distribute.
2. From the Edit menu, point to Distribute, and
then take the appropriate action:
If you want to
space objects
evenly between the
Horizontal Center.
Then choose
outer boxes of the form Vertically.
left and right of the
form
Then choose
Horizontally.
The form objects are spaced according to your
choice.
Changing the Layout of
an Existing Form
You can use the Form Generation dialog box to
automatically change the overall layout of an
existing form.
To change the layout of an existing form:
1. In a form, right-click the background, and then
choose Data Source.
2. In the Form Properties dialog box, click the
Form tab.
3. Click Generate new form, and then click Style.
The Form Generation dialog box appears.
4. In Choose Fields to be included section, click
the field names to include.
5. To have a Structure box in the upper left corner
of the form, click Structure in upper left of
form.
58•Chapter 3: Creating and Editing Forms CambridgeSoft
Changing the Layout of an Existing Form

6. In the Form style section, select the form style:
If you want the
boxes to
be surrounded by a
frame
7. In the Columns list, choose the number of
columns, between one and four.
8. In the Grid size list, choose the size and spacing
of the boxes and grid:
9. Click OK.
A message box appears.
Then, in the Form
style section, click
Framed.
be labeled above Titled.
be labeled to the left Labeled.
not be labeled Plain.
If you want the boxes to
be
larger and spaced further
apart
medium, relative to the Large
and Small settings
smaller and spaced closer
together
Then choose
Large.
Medium.
Small.
10. Take the appropriate action:
If you want to Then click
change the overall layout for
the current form
create a new form based on the
existing form
Securing Forms
You can control the options available to users of
your forms by setting the security options.
You can also provide the database connection
information used to log on to an MS Access
database. MS Access provides a security system that
allows the creation and management of usernames
and passwords, and the assignment of permissions
to those usernames. MS username password account
information is stored in the Workgroup Information
file (.mdw, .mda). For more information about
securing an MS Access database, see “Opening a
Secured MS Access Database” on page 41.
Setting Security Options
To set what ChemFinder form options are available
to users:
1. Right-click in the form you want to secure, and
choose Properties.
The Form tab of the Box Properties Dialog box
appears.
ChemFinder 8 Chapter 3: Creating and Editing Forms • 59
Securing Forms
Yes.
No.

Administrator
2. Click Security.
NOTE: The Security button does not appear if
the security on your form has been set to not
allow access to the Security options.
The Form Security dialog box appears.
The lower left corner of the dialog box indicates
whether security is defined.
3. Type the user name to use for logon in the
Username box.
The Enable button becomes available.
4. Type the password to use for logon in the
Password box.
Use of a password is optional.
To enforce Workgroup Security in an MS Access
Workgroup Administrator database:
• Take the appropriate action:
If you want to Then
enter a workgroup
file name
browse for the
workgroup file
NOTE: Enforcing workgroup security is optional.
To select the Database Security options you want
enabled:
• Take the appropriate action:
Type the name of the MS
Access Workgroup
database in the
Workgroup Information
file box.
Click File and select the
file.
If you want users to Then click
be prompted to log on
with a username
password to open a
form
use a username
password to log on to
the MS Access
database (.mdb files)
be prompted to log on
to a database with a
username password
when the form is open
Password to open
Form
Logon to MS
Access database
Prompt for
database logon
60•Chapter 3: Creating and Editing Forms CambridgeSoft
Securing Forms

If you want users to Then click
use a username
password to open the
molecule database
(.mst files)
be able to access the
Form Security dialog
box
encounter all of the
above options
To select the Forms options you want enabled:
• Take the appropriate action:
Protect molecule
database
Security dialog
available.
Database security.
If you want users to Then click
open or create
databases
Open/create
database
create forms Create new forms
open forms Open other forms
edit forms Save changed
forms
change the layout of a
form
use all of the above
options
Change form
layout
Forms
NOTE: The behavior of Forms permissions has
changed from earlier versions of ChemFinder. If you
disable Forms permissions you cannot open the
Properties dialog box by right clicking on the form.
You must go to the File menu and select Database to
open the Properties dialog box.
To select the Automation options you want enabled:
• Take the appropriate action:
If you want users to Then click
access OLE
automation writing and
programming
To select the Edit options you want enabled:
• Take the appropriate action:
Allow CAL/OLE
Automation access
NOTE: Must be
checked to enable
export to Excel
use scripts Can use scripts
menu
edit scripts Edit scripts
use all of the above
options
Automation
If you want users to Then click
clear forms Clear
delete relational and
structural data
copy relational and
structural data and
multiple table rows to
the clipboard
ChemFinder 8 Chapter 3: Creating and Editing Forms • 61
Securing Forms
Cut
Copy

Administrator
If you want users to Then click
paste relational and
structural data from
the clipboard
Perform all of the
above functions
To select the Browse options you want enabled:
• Take the appropriate action
If you want users
to
Paste
Cut/copy/paste
Then click
browse databases Browse database
records
view data in forms in a
table
view data in
continuous view
edit and view
structures in
ChemDraw
view structures in
Chem3D
perform all of the
above options
View form as table
View in continuous
forms view
Edit/view
structures in
ChemDraw
View structures in
Chem3D
Browse
To select the Search options you want enabled:
• Take the appropriate action:
If you want users to Then click
submit queries Query database
records
use current hit list for
searching
search the entire
database
save and manipulate hit
lists
search exact structure
only
search substructures
only
search similar
structures only
use all of the above
options
To select the Update records options you want
enabled:
• Take the appropriate action:
If you want users to be
able to
Search over current
list
Search over full
database
Enable hit list tools
Full structure
Substructure
Similarity
Searching
Then click
update database records Update records
add database records Add new records
62•Chapter 3: Creating and Editing Forms CambridgeSoft
Securing Forms

If you want users to be
able to
delete database records Delete records
To allow users to import data SDFiles or RDFiles:
• Click Import data.
To allow users to export data, including delimited
text files:
• Click Export data.
To select the Print options:
• Take the appropriate action:
If you want users to Then click
print a single record only Single record
Print several records Several records
Use print preview mode Print preview
perform all of the above
functions
To finish selecting options:
1. Click Enable.
2. Click OK.
The options you choose are applied to the form.
Disabling Security
Then click
Print
You can disable security and reset the defaults.
To disable security and reset defaults:
1. In the Form Security dialog box, click Disable.
The Validate Security dialog box appears.
NOTE: This form only appears if you entered a
password when you enabled security. See“Setting
Security Options” on page 59
2. Enter your password, then click OK.
Security is disabled and the defaults are reset.
“Security Disabled” appears in the lower left
corner of the Form Security dialog box.
Overriding Security
You can temporarily remove security in order to edit
the security options.
To temporarily disable security:
1. In the Form Security dialog box, click Override
Security.
The Validate Security dialog box appears.
NOTE: This form only appears if you entered a
password when you enabled security. See“Setting
Security Options” on page 59
ChemFinder 8 Chapter 3: Creating and Editing Forms • 63
Securing Forms

Administrator
2. Enter your password, then click OK.
You are allowed to edit the security options.
“Security Overridden” appears in the lower left
corner of the Form Security dialog box.
To turn the security back on:
• In the Form Security dialog box, click Override
Security to toggle security back on. “Security
Enabled” appears in the lower left corner of the
Form Security dialog box.
64•Chapter 3: Creating and Editing Forms CambridgeSoft
Securing Forms

Chapter 4: Working with Data
Overview
Working with data includes:
• “Opening Databases”
• “Browsing Databases”
• “Creating a Database”
• “Creating a Portal Database”
• “Entering Data into a Database”
• “Editing Data”
• “Changing the Database Scheme”
You work with data within ChemFinder by entering
it into a database, editing it, and interfacing with
ChemDraw and Chem3D.
You can perform all of these functions on data using
the commands in the menus, or you can use the
buttons in the Record toolbar for most of these
functions.
Add Commit
Record Changes
Undo
Changes
Opening Databases
Omit
Record
Delete
Record
When you open a database in ChemFinder, you can
access the data in any of three ways:
• Normal access—you can read and write data.
• Read-Only access—you can read but not write
data. The database is write-protected.
• Secured access—you must open the database
with a user name and password. You are subject
to the security restrictions applied to the
database.
NOTE: Earlier versions of ChemFinder cannot
read ChemFinder 7.0 .cfw files.
Read-Only Access
Any of the following conditions determine whether
a database opens in read-only mode:
• If the component files (extensions .cfw, .mdb,
.ldb, .mst, .msi) have read-only attributes.
• If the files are on read-only media, such as
CD-ROM.
• If you select Read-only in the File Open dialog
box when you open a form or database.
When you open a read-only database, the following
conditions apply:
• READ appears in the status line.
• You can not modify data in text or structure
boxes.
NOTE: If only the form (.cfw) file is set to read-only
READ does not appear on the status line and the
database can be modified.
ChemFinder 8 Chapter 4: Working with Data • 65
Opening Databases

Administrator
Multi-user Access
If a database resides on a network, more than one
ChemFinder user may access it at the same time.
Each user can view, print, or modify records
independently of the others.
The following table shows how the type of user
affects the other users in the group.
User type Affect on other users
Multiple readers in
read-only access
Multiple writers in
normal access
One writer,
multiple readers
If two people are viewing the same record within a
database, and one person changes the data in that
record, the second person will not see the changes
immediately. The changes will be visible when the
second user switches to another record, and then
back to it.
Secured Access
User actions do not affect each
other.
All users can read and write. A
user may see another user’s edits.
If two users try to edit the same
area at the same time, one is
alerted that the database is
temporarily locked.
The writer, in normal access, is
not affected by the readers. The
readers, in read-only access, may
see the writer’s edits.
ChemFinder supports the following types of
security:
• Form access—ChemFinder enforces form
access security by requiring a user name and
password, which are stored in the form (.cfw)
file.
• Molecule file access—ChemFinder enforces
molecule file access security by requiring a user
name and password, which are stored in the
database’s .mst file.
• Microsoft Jet Relational Database Engine—
the database engine that underlies Microsoft
Access enforces security. The user names and
passwords are stored in an MS Access
Workgroup Administrator database.
For more information on Form access, see
“Securing Forms” on page 59. For more information
on MS Access security, see “Opening a Secured MS
Access Database” on page 41.
When you open a form or database that has security
options applied to it, you are prompted to enter a
username and password to log on.
When you open a secured MS Access database from
within ChemFinder, a username, password, and
workgroup information file is required. Contact
your Access Database Administrator for this
information.
To open a secured form:
1. In the Validate Form Security dialog box, type
your username and password, and then click
OK.
If the form you access includes a secured
molecule database, the Database Logon dialog
box appears:
66•Chapter 4: Working with Data CambridgeSoft
Opening Databases

2. Type your username, password, and
Workgroup Information File name, and then
click OK.
The form opens.
Browsing Databases
You can browse a database using the buttons on the
Record toolbar.
First Record Go to Record
Previous Record Next Record
To Browse:
Last Record
• Click First Record to display the first record in
the database.
• Click Previous Record to display the record
before the currently shown record.
• Click Next Record to display the record after
the currently shown record.
• Click Last Record to display the last record in
the database.
You can go directly to a specific record as follows:
1. From the Record menu, choose Go To Record,
or click the Go To Record tool .
The Record Number dialog box appears.
NOTE: The current record number is
displayed in the Status Bar.
2. Type the number of the record (within the
current list) to display, and click OK.
The specified record is displayed.
NOTE: Record numbers are temporary, referring
only to positions within the current list in its current
sort order. For example, if you have done a search
that found ten hits, then the only valid record
numbers are 1–10. If you want to move to a specific
absolute location in a database, you must run a
search for a value in a field that identifies that
location.
The Data Table
Sometimes browsing through a data record set is
more convenient if the data is presented in tabular
format.
NOTE: You cannot add or modify records while
viewing data in a table.
To display data in a table:
• On the View menu, point Data Table, and then
choose In Separate Window.
A list window containing the fields and records
in the form appears.
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Browsing Databases

Administrator
To display a particular record in the form:
• Click that record’s entry in the list window.
By default, the fields in the Data Table are displayed
in the order in which they were created.
To reorder the columns in the Data Table:
NOTE: The column order is not stored in the form.
3. Click one of the column headers to select the
column.
4. Drag that header to a new position.
The cursor changes to the icon shown below.
The new position is indicated with a dashed
vertical line.
To resize the column widths in the Data Table:
1. Place the cursor on the dividers in the top
header.
The cursor changes to the icon shown below.
2. Click-drag to adjust the column width.
NOTE: To hide the column, continue dragging
until the border overlaps with the border of the
adjoining column.
To resize the row heights in the Data Table:
1. Place the cursor on the dividers in the left
header.
The cursor changes to the icon shown below.
2. Click-drag to adjust the row height.
Creating a Database
Instead of opening an existing database, you may
want to create a new, empty one. This procedure
results in a simple database with one table for
storing structures.
To create a database:
1. Right-click and choose Properties.
2. Click Create Database.
68•Chapter 4: Working with Data CambridgeSoft
Creating a Database

The Save As dialog box appears.
3. Choose the directory to which you want to save
the database.
4. Specify a name for the database, and click
Save.
ChemFinder creates the database containing one
table (called MolTable) with four fields:
• Structure
• Formula
• Molecular weight
• Mol_ID
The Mol_ID field corresponds to a column in the
table where a numeric ID is automatically entered as
each structure is registered. The other fields
represent information stored in the structural portion
of the database, linked to the assigned ID.
Molecular formulas and molecular weights are
automatically calculated from a structure. These
internal fields cannot be edited or deleted.
After creating a database, you can create fields for
storing other types of data. It is not necessary to
create the entire set of fields before working with the
database. You may add more fields later.
Creating Tables
There is no limit to the number of tables a database
can contain. You may want multiple tables in a
database in order to manage relational data, or
simply to organize different collections of
information in the same place.
A table must contain at least one column. When you
create a new table, ChemFinder creates a numeric
column called ID. You can use this column to store
integer data, or delete it and replace it with your own
columns.
Table names must:
• Begin with a letter
• Not contain punctuation characters
• Not be the same as a table already on display
To create a new, empty table:
1. Right-click and choose Properties.
The Box Properties dialog box appears.
2. Click the Table tab.
The Table tab appears:
3. Click Create Table.
The Create Table dialog box appears.
4. Type a name for the new table, and then click
OK.
The table appears in the Data Source tree.
ChemFinder 8 Chapter 4: Working with Data • 69
Creating a Database

Administrator
Deleting Tables
To delete a table from the database:
5. In the data source tree, select the table to delete.
6. Click the Delete Table button.
7. Click Yes.
The table and all data it contains are
immediately deleted from the database.
CAUTION
You cannot undo a deleted table. Before you delete a
table, create a backup copy of the database to prevent
accidental loss of data. For more information, see
“Backing up Databases” on page 75.
Attaching Tables from Other
Applications
You can use ChemFinder to add chemical structures
to a database you have already developed. If your
database was developed in Microsoft Access, you
can open it directly in ChemFinder.
If you are using another database system such as
FoxPro, dBASE, Btrieve, Paradox, or Oracle, you
cannot open the database directly. You must open or
create a ChemFinder database, and use Attach Table
to link to tables in the data source. After you attach
a table, it appears and functions as if it were part of
your local ChemFinder database.
The procedure you use depends on whether the
tables you want to attach are from a file-based
(Access, FoxPro, dBASE) or non file-based
(Oracle) database system.
Attaching Files from a File-Based
Database
To attach a file-based database table:
8. Right-click and choose Properties.
9. Click the Table tab, and then click Attach
Table.
The Attach Table dialog box appears.
10.Click Open MS Access Database.
11.From the Files of Type drop-down menu,
choose the type of database you want to access.
NOTE: The list of file types available in the
Attach Table Open dialog varies from one
computer to another. The files for which you
have drivers installed shown. For example, if
70•Chapter 4: Working with Data CambridgeSoft
Creating a Database

the Paradox is not installed, you may not have
Paradox drivers on your system or in the
drop-down list.
NOTE: If the database type you wish to access
is not on the list, it may not be a file-based
system, and you need to connect using ODBC.
For detailed instructions, see “Attaching Files
from a Non File-Based Database” on page 71.
12.Choose the database to access, and then click
OK.
13.In the tree diagram, click the name of the table
you want to attach, then click OK.
The Database dialog box appears, showing the
newly-attached table along with the original
MolTable. The database is ready to use.
Attaching Files from a Non File-Based
Database
If the database you want to attach is not file-based,
such as Oracle, you can attach it using Microsoft's
Open Database Connectivity (ODBC).
To attach a non-file-based database table:
1. Right-click and choose Properties.
2. Click the Table tab, and then click Attach
Table.
The Attach Table dialog box appears.
3. In the Attach Table dialog box, click Open
Oracle/ODBC Data Source.
The Select Data Source dialog box appears.
4. From the Machine Data Source tab, select the
ODBC data source to access, and then click OK.
NOTE: The ODBC data source dialog box
shows all data sources known to ODBC,
including ChemFinder, Access, and other
file-based data sources. If you attempt to open
one of these through the ODBC dialog, you get
an error message. File-based data sources must
be opened using Open Database, as described
above.
NOTE: If the ODBC data source dialog does
not show the database you seek, you may need
to create a new data source. You can do this
using the New button. For details, click the
Help button in the ODBC dialog box.
5. If you are prompted for a user name and
password, enter it. If you don't know what name
and password to use, see your System
Administrator.
6. Click on the name of the table you want to
attach, then click OK.
The source of the data to display on the form is
indicated, but the form is still blank. To access the
data, you need to draw some data boxes, and
indicate what data to show in each of those boxes.
ChemFinder 8 Chapter 4: Working with Data • 71
Creating a Database

Administrator
Creating Fields
Whether you created a new database or are working
in an existing one, you can add or remove fields in
the selected table.
You can choose from the following types of fields:
Text field—Allows you to enter text such as
names, comments, and references. A text field is
fixed in length, and requires that you choose a
maximum length (“width”) for any data item to be
stored in the field. If you enter a width of 50, then
you can’t store any item with more than 50
characters in that field.
You can specify widths of text fields as large as 254
characters. If this is insufficient, you need to create
a Memo/Rich Text field instead.
Because the text field width cannot be modified
after a field is created, it is often wise to err on the
side of caution and make it longer than you need
initially. On the other hand, larger field widths also
create larger files and slower search times.
NOTE: Non-ASCII characters will not display
correctly in a data table text field.
Integer field—Used for whole numbers such as
ID's. All integers in ChemFinder are long, so can
accommodate billions of values (2 32 of them).
Real field—Used for real numbers such as
physical constants and unit prices. Real numbers in
ChemFinder are double-precision.
Picture field—Allows you to store a Windows
metafile, such as a spectrum or experimental setup,
as a data item in a database.
NOTE: A Picture box on a form may be used to
display a static, decorative picture attached to the
form, or it may be used to show pictures stored in the
database which change as you move from record to
record.
Memo/Rich Text field—Used to display text.
Memo fields can be of any length. Because memo
fields are less structured, searching them can be
slower than searching a text field. Additionally,
memo fields cannot be sorted.
To search for text:
1. Right-click in a memo or plain text field.
2. Select Find Text.
The “Find Text” dialog box appears.
3. Enter the text and the match conditions.
4. Click Forward or Backward to search.
5. Click Find Next on the right click menu, or use
F3 to search for the next occurrence.
Memo fields can store Styled Text. For more
information, see “Styled Text” on page 81.
Date field—Allows you to store dates. The dates
are displayed according to the settings in the
Windows Regional Settings control panel.
72•Chapter 4: Working with Data CambridgeSoft
Creating a Database

Structure field—Consists of four fields: a
numeric ID stored in the relational database, plus
three fields (Structure, Formula, MolWeight) that
take data from the ChemFinder structure database
files.
You can create more than one set of structure fields
in a table. Each is assigned a unique set of names,
and each refers to its own ID column in the table,
although all structural data is taken from the same
structure database files.
To create a field:
6. Right-click on a data box and choose
Properties.
The Box Properties dialog box appears.
7. Click the Field tab.
The Field properties appear.
8. Click Create Field.
The Create Field dialog box appears.
9. In the Name box, type a name.
10.In the Type box, choose a data type.
11.For text fields only, in the Width box, choose a
width.
12.Click OK.
The name of the new field appears in the data
source tree.
Deleting Fields
Just as you can create any field and assign it to a data
box at any time, you can modify the database by
deleting fields from the selected table.
To delete a field:
13.In the field list, select the field to be deleted.
14.Click Delete Field.
15.When prompted whether you want to delete the
selected field, click OK to delete it or click
Cancel to leave it unmodified.
CAUTION
When you delete a field, all data contained in the field
is also deleted. You are not warned explicitly about
this.
Adding Multiple Structures
You can include more than one structure on the same
form by creating multiple structure columns in a
table. Each structure column you create represents
four types of data:
• The structure displayed as a diagram.
• The Molecule ID, which connects the structure
to a record in a relational table.
• The formula derived from the structure.
• The molecular weight derived from the
structure.
ChemFinder 8 Chapter 4: Working with Data • 73
Creating a Database

Administrator
To create multiple structure columns in a table:
16.From the File menu, choose Database.
The Form Properties dialog box appears.
17.Create or open a database.
18.Click the Field tab.
19.Select the Table in which you want to create
new structure columns.
20.Click Create Field.
The Create Field dialog box appears.
21.Select Structure from the Type drop-down list.
An uneditable name is assigned to the field.
22.Click OK.
Four new fields appear in the list and are named
to belong to the same set of structure columns.
23.Connect the new fields to boxes by
right-clicking on the appropriate data box and
choosing the field.
Adding Structures to
Non-Chemical Databases
If you opened a database that you created using a
program other than ChemFinder and you want to
add structures to it, you can create structure fields in
any modifiable (non-attached) table.
To create a structure field:
24.Open a database.
25.Right click, choose Properties.
26.Click the table to which you want to add
structures.
27.Click the Field tab.
28.Click Create Field.
The Create Field dialog box appears.
74•Chapter 4: Working with Data CambridgeSoft
Creating a Database

29.From the Type drop-down list, choose
Structure, and then click OK.
You do not provide a name or other details when you
create Structure columns. ChemFinder
automatically creates four columns and names them.
These columns contain no data until you enter
structures into the database.
Backing up Databases
ChemFinder does not back up databases. To back up
a ChemFinder database, use Windows Explorer to
make backup copies.
To back up the current database:
30.If necessary, obtain the database name and
location by viewing the Box Properties:
Database dialog box.
The Name box shows the full pathname of the
main database (.mdb) file.
31.In Windows Explorer, navigate to the folder
containing the database files.
Accompanying the .mdb file are several
associated files with the same name but
different extensions.
32.Make backup copies of files with extensions:
.mdb, .mst, and .msi. Select the files and drag
them to another directory or use the Edit menu
to Copy and Paste.
NOTE: Your database may not contain files with
all the indicated extensions. Not all of these files are
present in all databases.
You do not need to back up the ChemFinder form
file (.cfw extension) or the Jet lock file (.ldb).
To use the saved data, you may directly open the
backed-up .mdb file as you would open any
database. Alternatively, you may replace a database
with its backup copy by restoring the backup file
copies to their former locations.
Moving Databases
ChemFinder saves only the definition of the form
and information for connecting to the database. The
actual data are stored in files with .msi and .mst
extensions for structure data and in files with an
.mdb extension for non-structural data. If you want
to move a database to another computer, you must
move (for a default ChemFinder database) at least
four separate files. This number might be greater if
you have several forms that access the same
database.
NOTE: The .msi, .mst, and .mdb files all have the
same file name, but the name of the .cfw files might
be different depending on how you saved them.
After you move the database to its new location,
open your forms to make sure the data source links
have been retained. If ChemFinder cannot locate the
data source and displays an empty form, you need to
use the Database command on the File menu to
reconnect to the data source.
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Administrator
If the form is connected to a remote data source on a
network, you have fewer files to move. The data
source can remain on the remote machine, and you
only move the .cfw file that contains your form for
accessing the data. You may need to reconnect it to
the data source if it is not done automatically. This
situation is common in large organizations where
several people access the same central data source.
Creating a Portal
Database
To carry out certain operations, such as sorting
structural data, ChemFinder needs to create
temporary tables in a database.
Instead of accessing the read-only source directly,
you can create a portal database–a local, writable
database with attachments to the external tables of
interest. The portal looks and behaves just like the
target database, but without the limitations.
ChemFinder creates a portal database when needed.
For example, if you use a database CD, search, and
attempt to sort by formula, a message appears that
offers to create a local database, attach the current
table, save the form, and proceed with the sort. If
you create the local database, you can use the new
form to get the data with full functionality and
performance.
When you are using a read-only database,
ChemFinder offers to create a portal database.
ChemFinder does not automatically create a portal
database during searching because it would destroy
the hit list. When this happens, ChemFinder displays
a message. You can manually create a portal
database or sort to automatically create one, and
then repeat the search.
Entering Data into a
Database
You enter data into a database by adding a new
record. Adding a new record consists of three steps:
• Clearing the form
• Adding new data
• Committing the new entries
Clearing the Form
To begin adding a new record:
1. Create a form and link it to a database. For more
information, see “Creating Forms Manually” on
page 44.
The form should contain all the data boxes you
want to view and edit. The boxes should be
assigned to their appropriate fields.
2. From the Record menu, choose Add New
Record, or click the Add Record tool .
All of the boxes in the form are cleared to
prepare for entering new data. The Status Bar is
updated to show that you are in record addition
mode:
Adding New Data
To add alphanumeric data:
• Click in a box with an alphanumeric field and
type the data.
76•Chapter 4: Working with Data CambridgeSoft
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To add a structure:
1. Right-click in a box with a structure field.
2. Do one of the following:
If you want to Then right-click and
choose
draw a structure
import a
structure
a. Edit Structure.
ChemDraw opens.
b. Draw the new structure
in the From
ChemFinder window.
c. From the File menu,
select Close and Return
to... to insert the
structure into the form.
a. Read Structure.
b. Select the file to insert
and click Open.
The file is inserted into
ChemFinder.
NOTE: See the ChemDraw User’s Guide for
information about using ChemDraw.
Committing the New Data
When you finish entering all of the data items, do
one of the following:
• Perform another action such as moving to
another record or printing.
The record is automatically committed.
• From the Record menu, choose Commit
Changes or click the Commit Changes tool
.
The new record is added to the database.
NOTE: Selecting Commit Changes (or moving to
another record if you have two or more records)
saves the data to the database. You do not need to
select Save from the File menu; choosing Save saves
any changes to the form layout, not changes to data
in a database.
Duplicating Records
You can create a new record by modifying an
existing one. To duplicate a record:
• From the Record menu, choose Duplicate
Record.
You are in Add Mode and the form fills with
data from the previously displayed record.
When you select Commit Changes, you create a
new record whose fields contain the data on
displayed. Before committing the duplicate,
you can modify fields or structure and commit
changes just as you would with any other new
record.
NOTE: When duplicating records, only those fields
that are visible on the form are duplicated. Data in
fields present in the database but not visible on the
form are not copied into the new record. The new
record has a new Molecule ID.
Undoing Data Entry
Before committing a new data entry, you can revert
the contents of the form to its previous unmodified
state.
To undo your changes:
• From the Record menu, choose Undo
Changes, or click the Undo Changes button
.
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Administrator
After you commit the changes, they cannot be
undone.
Editing Data
Modifying the data in a database is performed by
directly changing the data items on the form and
committing those changes.
NOTE: The Formula and MolWeight fields are
automatically calculated by ChemFinder from the
Structure field and cannot be edited by the user. The
MOL_ID field is also set automatically by
ChemFinder and cannot be edited.
Editing Data
To edit data:
• Click the data box whose data item you want to
edit.
If you click on a Structure data or a picture box it is
highlighted. If you click on a data box containing
alphanumeric data, a cursor appears in the data box.
To edit alphanumeric data:
1. Replace it with the text or number you want.
2. From the Record menu, choose Commit
Changes, or move to a different record.
NOTE: Moving to a different record always
commits changes first.
Sorting Data
You can sort most types of data in a form. Sorting the
Mol_ID field, the molecular weight field, or any
other numeric field arranges the current list in
increasing or decreasing order. Sorting the structure
field arranges that field by increasing number of
atoms contained in the structure. Implicit hydrogens
are not counted. Sorting the formula field orders the
records by increasing C-H-N count (for compounds
containing carbon) followed alphabetically by any
other elements. Formulas for compounds without
carbon are sorted in alphabetical order. Sorting text
fields such as molecular name sorts the records
alphabetically.
After sorting, the database must be reset to its
original state before you can update it.
NOTE: You cannot edit records sorted by formula
or molecular weight. However, if you attempt to sort
one of these fields, ChemFinder offers to set up a
database (a portal database) which allows the
operation. For details, see “Attaching Tables from
Other Applications” on page 70.
Sorting Fields
To sort a field:
• Right-click in the field you want to sort, point to
Sort, and then choose Ascending or
Descending.
Sorting from the Data Table
To sort directly from the Data Table:
3. From the View menu, choose Data Table.
4. In the Data Table, double-click on the table
header of the field you want to sort.
Sorting in Reverse Order
To sort a column in reverse order:
• Double-click on the table header again.
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Editing Data

Sorting Languages Other Than English
Text that you sort must be in the same language as
default language of the system on which the
database was created, or an incorrect sort order can
occur.
The ChemFinder sample databases, created in
English, can be sorted correctly using the following
languages:
• English
• German
• French
• Portuguese
• Italian
• Modern Spanish
If you want to sort text in a different language than
the one in which the database was created, perform
the following procedure:
1. On a computer using the same language as the
text you want to sort, open MS Access.
2. Open the .mdb file you want to sort.
3. Compact the database: on the Tools menu,
point to Database Utilities, and then click
Compact Database.
4. After the database is compacted, close MS
Access.
The correct sort information is written into the
database. When you perform a sort in
ChemFinder, the sort order will be correct.
Resetting the Database
To reset the database to its original state:
• From the Search menu, choose Retrieve All.
Editing Structures
You can edit structures by using the ChemDraw
drawing tools. You can also neaten the appearance
of a structure by cleaning it up.The Clean Structure
command is used to neaten the appearance of
molecules by regularizing bond lengths and angles.
Since the degree of change required cannot be
determined a priori, the Clean Structure command
begins gently. You may need to repeat the command
to get the changes you wish. For more details about
how the command works, see “Using Structure
CleanUp” in Chapter 7: Advanced Drawing
Techniques of the ChemDraw User’s Guide.
Before committing a data entry, you can revert to the
previous unmodified record by choosing Undo
Changes from the Record menu or clicking the
Undo tool.
To edit structural data:
1. Do one of the following:
• Right-click in the structure box and choose
Edit Structure.
• Double-click the structure box.
ChemDraw opens and the structure appears in
the From ChemFinder window.
2. Edit the structure using ChemDraw.
3. Click in the ChemFinder window or close the
ChemDraw window when you are finished.
4. From the Record menu, choose Commit
Changes, or move to a different record.
The changes are stored.
To clean up a structure:
1. Right-click in the box containing the structure
to neaten.
2. Choose Clean Structure.
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3. To save the cleaned up structure, choose
Commit Changes from the Record menu.
Working with Structures Using
ChemDraw
You can enter or edit ChemDraw structures within
Data Boxes that are of the Structure field type.
To edit a structure:
• In the structure data box, do one of the
following:
• Right-click and choose Edit Structure.
• Double-click in the structure data box.
ChemDraw opens.
If you already have a structure in a data box, that
structure appears in the From ChemFinder window
in ChemDraw. You can modify and manipulate the
structure just like any other ChemDraw structure.
If there is no structure in the ChemFinder data box,
the From ChemFinder window is blank. You can
draw a structure to store in the ChemFinder
database.
1. In the From ChemFinder window, edit the
existing structure or draw a new structure.
2. Click in the ChemFinder window or close
ChemDraw to insert the ChemDraw structure.
3. From the Record menu, choose Commit
Changes, or move to a different record.
The changes are stored.
With a few exceptions, ChemFinder can store any
chemically meaningful structure or reaction that can
be drawn in ChemDraw. Within ChemDraw, you
can confirm that a structure is chemically
meaningful by selecting it and choosing Check
Structure from the Structure menu. For more
information, see the ChemDraw User’s Guide.
Two exceptions are:
• ChemFinder does not support importing
molecules with multiple or variable points of
attachment such as ferrocene.
• ChemFinder does not recognize “bare”
heteroatoms. For example, if you draw the
following structure:
ChemDraw reports an illegal valence when you
choose the Check Structure command. ChemFinder
automatically infers hydrogen atoms to main-group
elements as necessary to fill their lowest acceptable
valence. The structure above is registered in
ChemFinder as methylamine, CH 3NH 2.
Structures and reactions drawn with query
properties are generally meaningful only in the
context of a query. Query structures can be stored in
a ChemFinder database, but they are not treated as
Markush structures and are not guaranteed to be hit
by all valid search queries. For more information,
see “Appendix A: Structural Query Features” on
page 1.
ChemDraw allows you to draw many objects that
have no chemical meaning. These include boxes,
circles, arrows, orbitals, and others. It also allows
you to assign non-chemical styles (color) to objects
80•Chapter 4: Working with Data CambridgeSoft
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that have chemical meaning. ChemFinder ignores
these properties, and stores only objects with
chemical meaning in structure fields.
To store a ChemDraw drawing exactly as drawn,
store it as a picture. You can copy and paste a
ChemDraw drawing into a Picture field.
NOTE: Objects stored in a Picture field have no
chemical significance and cannot be searched.
Viewing Models using Chem3D
ChemFinder also provides access to Chem3D. From
a Structure data box, you can view the
three-dimensional model of the structure.
To view the molecular model for a structure:
4. In a Structure data box containing a structure,
right-click, and then choose View Model.
Chem3D opens an untitled window and converts the
two-dimensional structure into a three-dimensional
model. You can manipulate the model like any other
Chem3D model.
NOTE: See the Chem3D User’s Guide for more
information about using Chem3D.
5. Click on the ChemFinder window to return to
the form.
NOTE: Unlike interaction with ChemDraw,
changes you make to a model within Chem3D are
not transmitted back to ChemFinder. You can put a
picture of the Chem3D model into a database by
saving the Chem3D model as a metafile and
inserting it into a Picture field. The picture does not
retain a connection table and cannot be edited.
Styled Text
You make changes to text fonts, sizes, styles, colors,
and alignment with the tools on the Text menu or the
Text Format toolbar shown below.
To display the Text Format toolbar if it is not visible:
6. On the View menu, point to Toolbars, and then
choose Text Format.
The Text Format Tool appears.
ChemFinder 8 Chapter 4: Working with Data • 81
Editing Data
.
Font
Bold
Subscript
Align
Left
Bullets
Font Size Superscript Center
Right
You can format text in plain text or Memo/Rich Text
data fields.

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Undoing Changes
Before committing your changes, you can revert to
the previous unmodified state.
To undo your changes:
• From the Edit menu, choose Undo or click
.
After you commit the changes, they cannot be
undone.
Redoing Changes
When you undo an action, the Redo command
becomes active. You can reverse the effect of the
Undo command by choosing the Redo command.
To redo the last action performed:
• From the Edit menu, choose Redo or click
.
The last action undone is reinstated.
Deleting Data
You can delete the contents of individual fields by
using the Delete or Backspace keys. You cannot
delete a structure, formula, molecular weight or
Mol_ID.
To delete an entire record:
7. Move to the record that you want to delete using
the Record commands or tools.
8. From the Record menu, choose Delete Record,
or click the Delete Record tool .
The record is permanently removed.
NOTE: You can delete multiple records if you use
the Table view.
Changing the Database
Scheme
You can create or remove tables or fields in an
existing or new database as long as the database is
not read-only and you have permission to modify it.
You may also attach, or link, tables from external
data sources.
You use the Box Properties dialog box to perform
the following procedures.
To access the Box Properties dialog box:
1. Create or open a form and link it to a database.
For detailed instructions, see “Creating a
Database” on page 68.
2. Do one of the following:
• From the File menu, choose Database.
• Right-click any empty space in the form
window and choose Data Source.
The Box Properties:Database dialog box
appears.
If the database contains more than one table, only
one is selected at any given time. The contents of the
Field tab of the dialog box, and of the form, reflect
the selected table.
To select a table:
• Click the table name.
82•Chapter 4: Working with Data CambridgeSoft
Changing the Database Scheme

Chapter 5: Searching
Overview
ChemFinder performs chemical structure searches
and text searches. When searching text, you can
search in fields such as molecular weight, formula
and references. When structure searching, you can
search by substructure, full structure, or structural
similarity. You can also combine structure searching
with text searching.
To search, use the Search menu or the corresponding
tools in the Search toolbar.
Enter Retrieve
Query All
Find Find Current
Molecule
Beginning a Search
Searching includes the following steps:
• Clearing the form.
• Entering the query in the form.
• Submitting the query to the search engine.
Clearing the Form
To clear the form:
Previous
Query
Save
List
Restore
List
Restore
Previous
List
Over
Current
List
Find
List
• From the Search menu, choose Enter Query, or
click Enter Query .
You are in Query mode.
In Query mode:
• The form background color changes.
• QRY appears in the status bar.
• Form boxes are displayed according to their
visibility properties. For more information, see
“Hiding Data Boxes” on page 52.
Entering and Submitting a
Query
To enter the query:
1. Position the cursor over the field you want to
search and click to select it.
2. Enter the query in the data boxes.
To submit the search, do one of the following:
• From the Search menu, choose Find.
• Click Find .
• Press Enter.
ChemFinder searches. The number of hits is
shown in the Status Bar at the lower right corner
of the window.
NOTE: If a search gets no hits or an error occurs,
an alert appears and you are returned to Query
mode to enter a different query.
Because the hit list is a subset of the complete
database, you can browse it as you would any
database using the Record commands in the Record
menu.
For example, to view the hits in tabular form:
• From the View menu, choose Data Table.
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Stopping a Query
To stop a structure query in progress, press Esc. The
query stops and you return to browse mode.
NOTE: Only queries that involve structural data
(structure, molecular formula, and molecular
weight searches) can be stopped in this manner. SQL
searches and searches that involved non-structural
data cannot be aborted.
Viewing Results
You can view search results in:
• A single form
• In a table containing multiple forms
• Continuous forms
You can also view chemical markers on structures
and search for a particular atom or bond number.
Viewing Forms in Table View
To view forms in table view:
• From the View menu, point to Data Table, and
take the appropriate action:
If you want a table to Then choose
replace the current form In Current Window.
appear in a different
window
In Separate Window.
A table appears with all the information from
the form.
Viewing Continuous Forms
You can view multiple records at one time with the
Continuous Form View. Multiple records appear in
a miniform.
To see records in the continuous forms:
• From the View menu, point to Continuous
Forms, and then choose the appropriate option:
If you want to Then choose
replace the current
form
create a new window
to display the forms
Switching Views
When you switch views they follow the order: Form
to Table to Continuous Form.
To switch views:
In Current Window.
Continuous forms are
shown in the current
window.
In Separate Window.
An additional window
opens and displays the
continuous forms.
1. From the View menu, choose Switch Views or
press Ctrl+W.
The view changes sequentially.
Viewing Chemical Markers
ChemFinder enables you to display the following
chemical markers in structure boxes:
• Atom numbers
• Bond numbers
• Stereochemistry
• Reaction info
• Atom-to-Atom map
For detailed information about the markers, see the
ChemDraw User’s Guide.
84•Chapter 5: Searching CambridgeSoft
Viewing Results

You can also find specific atom or bond numbers.
To view chemical markers:
• On the View menu, point to Structure, and then
choose the marker to view.
The Atom number markers are shown on the
following structure:
NOTE: For a complex molecule, where there are
too many atoms or they are too close together, the
atom and bond numbers will not display. In some
cases, enlarging the structure box will allow them to
display.
To locate a particular atom or bond:
1. On the View menu, point to Structure, and then
choose Locate atom/bond.
The Locate atom or bond dialog box appears.
2. Type A and the atom number or B and the bond
number to find.
A circle appears on the structure temporarily to
show where the number is located.
Refining a Search
You can refine a hit list of one or more records by
entering a query that searches only the hit list, not
the entire database.
To refine a search:
1. On the Search menu, verify that Over Current
List is selected.
2. From the Search menu, choose Enter Query,
or click Enter Query .
ChemFinder searches over the previously
retrieved hit list. If no hits are found, a message
appears asking whether to search over the entire
database.
Restoring a Previous
List
After you refine a hit list, you have a smaller list. To
return to the previous, less-refined list:
• From the Search menu, choose Restore
Previous List, or click on the Search
toolbar.
The previous hit list is restored.
Resetting the Database
After you perform a search, you can return to the
complete database. If you want to refine your search
by searching the hit list from your first search, do not
reset the database. When you reset the database, the
hit list from your first search is discarded.
To reset the database:
• From the Search menu, choose Retrieve All or
click the Retrieve All tool on the Search
toolbar.
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The hit list is discarded, and the complete
database is reset, with the current record on
display.
Text Searching
Text searching allows you to search for strings of
text. You could use text searching to find chemical
names, comments, etc.
For text searches, ChemFinder interprets the query,
then passes it as Structured Query Language (SQL)
to the relational database. The following rules apply
to these queries:
• A text string is taken as an “anchored
substring,” which hits any string starting with
the indicated substring.
• Text strings may contain wild cards or Boolean
operators. Wild cards are “%” and “*”; these
characters are equivalent and hit any string.
• Boolean operators are ”NOT”, “OR”, and
“AND.” They may be used to combine search
terms within one field.
NOTE: Use NOT * to search for empty fields.
• If the text query has a “=” in front (=toluene),
then the search requires an exact text match.
Examples of queries:
Entry Possible hits
benz benzene, benzoic acid, not
bromobenzene
benz or
*bromo*
strings starting with benz or
containing bromo
=benzene Benzene, not benzoic acid, not
benzene-d 6 , not bromobenzene
Numerical Searching
Searching numerical data allows you to find
information such as boiling points and molecular
weights.
Ranges are specified using a hyphen between the
values at either end of the range.
For numerical searching, the query is a decimal
value or range. If a single value is given, the number
of significant digits determines the precision of the
search. A hit is any value that rounds off to the
query.
Examples of queries:
Entry Possible hits
90 values from 89.5 to 90.5
90.1 values from 90.05 to 90.15
90–100 values from 90 through 100,
inclusive
>=90 and 90 and

Dates are always displayed according to the
preferences set in the operating system’s
International control panel.
The following table shows query examples.
Entry Possible hits
Apr 11, 1971 the exact date April 11, 1971
March 31, 1971–
July 1, 1971
any date in the second quarter
of the year 1971
>April 11, 1971 any date after April 11, 1971
Molecular Formula
Searching
Formula searching allows you to search molecular
compositions, exact or in the range that you specify.
The following table shows query examples.
Entry Possible hits
C6H6 compounds with 6 carbons and
6 hydrogen atoms, plus any
number of other elements.
=C6H6 compounds with 6 carbons and
6 hydrogen atoms and no other
elements.
C6N0 compounds with 6 carbons, no
nitrogens, plus any number of
other elements.
C6 N1-3 compounds with 6 carbons and
one to three nitrogen atoms, plus
any number of other elements.
Formula queries consist of element symbols and
element counts or ranges. The following rules apply:
• Symbols may be one or two letters. Symbols
may be in upper or lower case; if there are
ambiguities, the program resolves them
according to rules described in Appendix B.
• Capitalize the symbols properly.
• Insert spaces between symbols.
• Use the Periodic Table to enter formulas. For
more information, see “Using the Periodic
Table” on page 127 and “Appendix B: Formula
Input Rules.”
• Element counts are single integers or ranges
(two integers separated by a hyphen). If a count
is omitted, it is assumed to be 1.
• If the formula query is precede by “=” (=C6H6
for example), then the search requires an exact
formula match, containing no elements other
than those indicated. If there is no “=”, then the
search is a partial match: other elements may be
present in the hits.
• Symbols may be repeated. For example,
“CH3CH3” is interpreted as “C2H6.”
NOTE: Formula searches are completely nonstructural:
CH3CH2OH matches both dimethyl
ether and ethyl alcohol because both
compounds have the same condensed formula:
C2H6O.
• Parentheses may be used to group elements and
apply a count to the entire group. For example,
“(CH2)3” is interpreted as “C3H6.”
• Spaces or non-alphanumeric characters other
than parentheses are ignored.
ChemFinder 8 Chapter 5: Searching • 87
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Find List
You can search for records using any text or number
field. Use the Find List command to search for lists
of values on any non-structure field. Type
parameters into the Find List box as follows:
• If the column you search is an integer type, you
can use hyphens to indicate ranges.
• If the column you search is a number or text
type, you cannot use hyphens to indicate
ranges; you must search for an exact match.
NOTE: To search for a list of records using
partial text (a “wildcard” search) or range of
numbers, do a search (Query) on the relevant
field.
• If the column you search is a text type, you must
use quotes around any item that contains
commas. For example, you must type 1,2-Pyran
as ‘1,2-Pyran’.
To find a list:
1. From the Search menu, choose Find List.
The Find List dialog box appears.
2. From the Column menu, choose an ID.
3. Paste or type a list of ID parameters into the
Find List box.
4. Click OK.
The list of matching records is retrieved.
Structure Searching
ChemFinder allows you to search structures in four
ways: by full structure or substructure, with an exact
match or by similarity. In addition, ChemFinder also
supports most of the query functions in ChemDraw
so you can define the search more precisely.
Entering a Structural Query
To begin a structural query:
• From the Search menu, choose Enter Query, or
click Enter Query, to clear the form.
To place a structure into a data box use any of the
following methods:
• Double-click in the structure box and open
ChemDraw.
• Right-click and use Edit Structure to open
ChemDraw.
• Right-click and use Read Structure File to
open an existing molecule file.
• Use Paste from the Edit menu to insert a
structure from the clipboard.
Enter the query:
1. From the File menu, choose Preferences and
click the Search Type tab.
2. On the Search Type tab, select the appropriate
options.
3. From the Search menu, choose Find.
The status bar counters indicate search progress.
When the search is complete, the form displays the
first hit. The list you can browse is limited to the
hits. In a complete structure or substructure search,
88•Chapter 5: Searching CambridgeSoft
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the hit portion of each molecule is highlighted in
red. If a search doesn’t find any hits, you are
returned to query mode.
Types of Structural Searches
There are five structural search types that can be
selected in the Preferences dialog box:
• Exact Substructure.
• Exact Full Structure.
• Identity.
• Similar Full Structure.
• Similar Substructure.
Substructure searches can be performed on single or
multiple fragments.
Substructure Searching
Substructure searching, the default searching type,
finds structures that contain the query and any
additional attachments at the open positions. Results
have the substructure highlighted in red. Using
ChemDraw Pro, you can attach different features,
such as atom lists and variable bond types, to a query
to perform a narrower or broader search.
For more information about what query features you
may use and how these features affect a search, see
“Appendix A: Structural Query Features” on page 1.
An example of substructure searching of
Cyclopentane:
This substructure query
NOTE: In searching substructures, ChemFinder
finds the substructure query regardless of its
orientation or drawing presentation in the targeted
molecules. Bonds shown in bold above are actually
highlighted in red in ChemFinder.
For more examples of substructure searching, see
“More Search Examples” on page 97.
Fragment Searching
You can draw more than one structure or structure
fragment in your substructure search query. You can
choose whether to permit fragments to overlap in the
target structure Search Preferences dialog box. For
more information, see “Chapter 8: Customizing
ChemFinder.”.
For example, if you perform the following
substructure query with “Query fragments can
overlap in target” selected:
ChemFinder 8 Chapter 5: Searching • 89
Structure Searching
HO
O
will hit
O
and other molecules
O

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The hit list will include the following:
The dot indicates an atom shared between the two
fragments. The hit list will not include this molecule
if “Query fragments can overlap in target” is
deselected.
When you perform a full structure search in a
database that contains mixtures or reaction data, you
may get hits containing more than one structure. You
can choose whether to include hits with extraneous
fragments in the Search Preferences dialog box. For
more information, see “Chapter 8: Customizing
ChemFinder” on page 119.
For example, if you perform the following full
structure query with “Permit extraneous fragments
in full structure searches” selected:
The hit list will include the reaction that produces
these products:
Cl
Cl
+
OH
OH
Cl
Match Extraneous Fragment
The hit list will not include this reaction if “Permit
extraneous fragments in full structure searches” is
deselected.
Exact Full Structure Searching
Selecting the Full Structure radio button in the
Search Type Preferences finds structures that
completely match the query. You may get more than
one hit if there are duplicates in the database or if
there are stereoisomers in the database and you did
not specify a particular one to be matched. For more
information, see “Stereochemistry” on page 91.
Identity Searching
The Identity search type is intended for use in
compound registration, when you must know if a
perfectly identical copy of your query compound is
already present in the database. It is similar to an
exact full-structure search, except that generic atom
and bond types such as “R”, “A”, and “Double-or-
Aromatic” in the query match corresponding atom
and bond types in the target only if they are also of
the special generic type. Thus, an “R” hits only
another “R” atom. Moreover, stereochemistry must
match precisely between query and target. If the
stereochemistry of the query is unspecified, then the
target's stereochemistry will also be unspecified.
Similarity Searching
A Similarity search finds structures that have
structural features that generally correspond to those
in the query. Similarity searches are by their nature
“fuzzy”. In a full structure similarity search, the
results are guaranteed to include all those you would
obtain from a substructure search with the same
query. Usually, they include additional hits. For this
reason, similarity searches are useful if you have a
general idea of the types of compounds you are
looking for, but don’t have a precise conception of
the target compound.
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Structure Searching

Unlike exact searches, similarity searches do not
highlight matched portions of the target compounds.
Similarity searching matches general structural
features and not specific atoms and bonds, so
highlighting specific areas would not be appropriate.
You can adjust the degree of similarity using the
Search Preferences dialog box.
For a detailed description of the similarity searching
algorithms, see “Appendix C: Similarity Rules” on
page 11.
Stereochemistry
You can specify whether or not you want a structure
search to consider stereochemistry. Given a
structure with one or more stereocenters, you can
store four different possibilities:
• A given absolute configuration. To specify this,
centers must be drawn with stereo bonds, and
the entire structure marked Abs (CHIRAL).
• A racemic mixture of the drawn configuration
and its mirror image. This is drawn as above,
but without the Abs / CHIRAL mark.
• An unmarked structure, representing unknown
stereochemistry, or a mixture of all possible
stereoisomers.
• A given relationship between centers. That is, a
known orientation of the substituents with
respect to each other, rather than a known
absolute configuration. To specify this, centers
are drawn, not with the standard hashed and
wedged bonds, but with thick stereo bonds.
If these options are checked in the Search tab of the
Preferences dialog, then any stereochemistry
indicated on the query must be matched by the
target. For more information on changing searching
preferences, see “Search Details Preferences” on
page 122.
3D Properties
3D queries are particularly useful in pharmacophore
searching where the user is looking for a particular
3D relationship among atoms and bonds, for
example in a series of potential receptor ligands.
You can create a 3D query in ChemDraw Pro by
adding geometries (lines, planes, etc.) and
constraints (specified as ranges) to a query structure.
For example, you might specify that two atoms must
be between 4Å and 5Å apart, or that two planes must
be separated by 80-100°. ChemFinder can then use
these properties to refine a search. See the
ChemDraw User’s Manual for information on how
to add 3D properties to structures.
Using the Current Molecule as
a Query
As you browse through a database, you may submit
any structure on the screen as the structural query.
Often, you use similarity or substructure searches
(see above) with this type of query to find related
compounds.
To use the current molecule for a query:
1. Using the Record commands, go to the record
containing the structure that you want to use as
a query.
2. From the Search menu, choose Current Mol As
Query.
All boxes of the form are cleared except the
structure so that the molecule on display can be
used as part of the query. You can then continue
with the query as if you had drawn the structure
from scratch.
Finding the Current Molecule
The Find Current Molecule command, located in the
Search menu and on the Search toolbar, is similar to
the Current Mol as Query command discussed
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above. As you browse through the database you may
find a molecule that interests you, and want to find
other related records.
The Find Current Molecule feature lets you perform
a quick structural search of the structure currently
being displayed on the form. However, this feature
does not allow you to enter other search terms. The
type of structure search (complete structure,
substructure, and/or similarity) is determined by
what you have selected in the Search menu.
To find the current molecule:
1. Browse to the record containing the structure of
interest.
2. From the Search menu, choose the type of
structure search you want to perform.
3. From the Search menu, choose Find Current
Mol, or click Find Current Mol tool .
ChemFinder begins the search and displays the
search status on the lower right corner of the status
bar. When the search is complete, the form displays
the first hit, and the list you can browse is restricted
to the records hit by the query.
Reaction Searching
You can search and store reactions. In a reaction, one
or several compounds (reactants) are transformed
into other compounds (products). Individual
reactants (or products) are separated from each other
with plus signs. The reactants are separated from the
products with an arrow.
Reactions may have multiple steps, for example
(A)—>(B)—>(C)—>(D). Here, (A) is the reactant
and (D) is the product. (B) and (C) are intermediates
for the complete reaction.
A multi-step reaction is actually a shorthand
notation for many related reactions. In the example
above, (B) is an intermediate for the complete
reaction, but it is also a reactant relative to (C) or
(D). It is also a product relative to (A). The complete
reaction implies many subreactions, such as:
(B)—>(D) and (A)—>(B).
Entering a Reaction Query
The general procedure for creating a reaction query
is very similar to creating a structural query.
Clear the form:
• From the Search menu, choose Enter Query, or
click the Enter Query tool .
The form clears.
Enter the query:
1. Right-click in the Structure box and choose Edit
Structure.
2. Draw the structure or substructure or reaction in
the From ChemFinder window.
3. From the File menu, select Close and Return
to... to bring the structure back from
ChemDraw.
Now you can enter more query terms in the other
data boxes for a combined search.
1. From the Search menu, select or deselect the
Substructure option.
NOTE: The Similarity option is not available
for reaction queries.
2. From the Search menu, choose Find.
The search proceeds as with simple structure
searching.
Reaction Centers
The most important part of a reaction is the part that
actually changes from the reactants to the products.
This part, which probably includes a number of
atoms and bonds, is called the reaction center. For
92•Chapter 5: Searching CambridgeSoft
Reaction Searching

example, only the bold bond below (and the two
atoms on either side) is part of the reaction center.
The rest of the structure is unchanged from the
reactant to the product:
By default, ChemFinder considers reaction centers
whenever you search for reactions. For information
on changing searching preferences, see“Setting
Preferences” on page 119. ChemFinder assumes that
any atoms and bonds that change in the query must
be part of the reaction center of the target.
For example:
does not hit
O
F Cl
when the “Reaction query must hit reaction center”
preference is selected. Even though there is a C-F
bond in the target reactant and a C-Cl bond in the
target product, these bonds do not participate in the
reaction, which really affects another part of the
compound. If you deselect the “Reaction query must
hit reaction center” preference, this query hits the
target above.
When creating reaction queries, it is important to
consider what sort of information you are really
looking for. Suppose you want to convert n-decanal
to n-decanol:
OH
F Cl
F Cl
O
F Cl
OH
F Cl
Are you really interested only in these two
compounds? You might be interested in any reaction
that converts a straight-chain aldehyde to the
alcohol:
Since the corresponding n-octanal—>n-octanol
reaction would probably occur under very similar
conditions, it is a reasonable thing to look at.
Generally, you want to use substructure queries that
include little beyond the reaction center in question
when you are searching for reactions.
NOTE: ChemFinder supports several query
properties to allow you to specify exactly how a
bond participates in a reaction center. For more
information about these properties, see “Search
Details Preferences” on page 122.
Atom-to-Atom Mapping
The second most important part of reaction
searching is the atom-to-atom map. You can specify
maps in ChemDraw, where they are stored as part of
the data about a reaction. Maps are used during
searching to resolve certain types of structure search
hits.
Consider a simple esterification reaction:
ChemFinder 8 Chapter 5: Searching • 93
Reaction Searching
O
H H
H H
OH
+
H
O
OH
O
O
O
H H
OH
+ H 2O
OH

Administrator
Does the ester oxygen come from the acid or the
alcohol? You specify the fate of individual atoms
through an atom-to-atom map. In reality, the ester
oxygen in this reaction originates in the alcohol, so
the atom-to-atom map looks like this:
O 3
6
O 3
+ OH
1 1
2 OH 5
2 O
4 6
By matching numbers across the arrow, you can see
where atoms move during the course of the reaction.
The other reaction (not observed experimentally),
where the ester oxygen comes from the acid, would
be mapped like this:
O 3
6
O 3
+ OH
1 1
2 OH 5
2 O
4 4
ChemFinder uses atom-to-atom map information to
determine reacting centers for reactions. If only
some atoms are mapped, ChemFinder uses that
information and does not worry about the specific
fates of the other atoms. For example, if you don’t
know (or don’t care) about the mapping of some
atoms, you can leave them unspecified in the atomto-atom
map.
By default, atom-to-atom mapping is not displayed
within ChemFinder. To turn on this display, select
Atom-to-Atom Map on the Structure sub-menu of
the View menu. For more information, see “Setting
Preferences” on page 119.
NOTE: For information about specifying
atom-to-atom maps with ChemDraw, see the
ChemDraw User’s Guide.
Searching for Reactants
4
+ H2O If you know what starting materials you are
interested in but don’t know their products, you
might perform a reactants query. A reactants query
5
5
6
+ H2O is very similar to a reaction search, except that there
is nothing to the right of the arrow. For example,
consider the query:
If you are doing a substructure search, this finds any
reactions in which maleic anhydride or a compound
containing a maleic anhydride substructure is
consumed or transformed.
Searching for Products
If you know the desired end product but not how to
get there, you can do a products query. A products
query is similar to a reaction search, except that
there is nothing to the left of the arrow. For example,
consider the query:
If you are doing a substructure search, this finds any
reactions in which bicyclo[2.2.1]heptane or a
compound containing this substructure is produced.
Searching for Intermediates
Rarely, you may be looking for reactions for which
you only know something about an intermediate. An
Intermediate Search is very similar to a normal
reaction search, except that there are arrows on both
sides of the target structure. For example, consider
the query:
94•Chapter 5: Searching CambridgeSoft
Reaction Searching
R
O
O
O
C C O

This finds any reactions containing the Ketene
structure shown as an intermediate.
NOTE: ChemFinder cannot predict products or
intermediates of reactions. It finds this information
only if it is already present in the database.
SQL Searching
SQL (Structured Query Language) can be used to
create powerful searches. The details of the
language are not discussed here.
Queries beginning with a backslash (\) are taken as
straight SQL, and passed directly to the database as
the WHERE clause of the SQL query. These must
contain column names and punctuation as dictated
by SQL. For example, a valid query might be
“\[molname] like 'benz*' and [bpoint] > 200”.
A straight SQL query may be entered in any box of
the form which contains non-structural data. The
SQL query is not associated with the box in which it
is entered.
Combined Searching
You can combine structure searching with text
searching to find a specific class of compounds. For
example, you may want to find all compounds in the
database whose names end in “mycin” and whose
structures contain a phenyl ring. Because you are
entering multiple queries in different data boxes,
there is an “AND” condition between data items in
different fields.
To perform a combined search:
1. From the Search menu, choose Enter Query, or
click Enter Query to clear the form.
2. Enter the structural query, if any.
3. Enter the text and/or numeric queries.
4. From the Search menu, choose Find, or press
Enter.
An example of combined searching:
Suppose you want to find all molecules in the
CS_Demo database that contain a benzene ring and
which have names related to “penicillin.”
1. From the Search menu, choose Enter Query, or
click Enter Query, to clear the form.
2. Draw a benzene ring in ChemDraw and import
the structure into ChemFinder.
3. Enter *penicillin in the Molname field.
4. From the Search menu, choose Find, with the
Substructure option selected.
You get 2 hits of molecules whose names contain
“penicillin” and whose structures have an aromatic
ring of six carbon atoms.
NOTE: In a combined search, progress reports are
given only during the structure search part. When
the counters at the bottom of the screen are
advancing, structures are being searched. You can
press Esc to end a search during the structure
searching. You cannot end a search during the SQL
searching by pressing Esc.
Managing Search
Results
After you have created a query, performed the
search and retrieved the results, you can save the hit
list. This hit list can serve as a record of your search
results. You can also combine hit lists in various
ways.
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SQL Searching

Administrator
Saving a Hit List
Create a query and perform the search.
1. When you have received the hit list, from the
Search menu, choose Save List or click Save
List .
The Save As dialog appears for you to save the
hit list as a text file.
2. In the Save As dialog, type a filename for the
hit list, and click Save.
The file consists of a list of values of the primary key
of each record in the hit list. If there is no primary
key, the molecule ID is used.
To edit a saved hit list, open the text file with a text
editor such as Notepad and edit the values you want
changed.
Restoring a Hit List
Once you have saved a hit list, you can perform
another search and then integrate the results from
the second search with the results from the first.
Thus, you can perform Boolean operations on
different searches.
To integrate the results of two searches:
1. Perform a search and save the hit list.
2. Perform another search.
3. From the Search menu, choose Restore List or
click the Restore List button .
The Open dialog appears for you to choose the
file that you want to integrate with the current
hit list.
4. From the Open dialog box, open the text file
that you want to integrate with the current hit
list.
The Restore List dialog box appears.
5. Select the integration option and click OK.
• Replace current list—discards the current
hit list and display the records from the hit
list you chose to open.
• Intersect with current list—displays only
those records that appear in both the current
hit list and in the saved hit list. This is a
Boolean AND operation.
• Subtract from current list—displays only
those records that are in the current hit list
but that are not in the saved hit list. For
example, if the current list contains records,
1, 2, 3, 4, and 5, and the restored list contains
records 4, 5, 6, and 7, then only records 1, 2,
and 3 will be displayed. This is a Boolean
NOT operation; it shows the records in the
current list that are not also in the restored
list.
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Managing Search Results

• Union with current list—displays all
records in either the current list or the saved
hit list. This is a Boolean OR operation.
The hit lists are integrated. You can browse and
save this new hit list just as any other hit list.
NOTE: If you merge two lists and get an empty
result, an alert appears and the list is reset to
the full database.
Search Examples
The following are examples of searching options.
By specifying atom and bond properties, you see
how to use the query functions in ChemDraw to
search the database more effectively. All
substructure search query properties recognized by
ChemFinder are listed and described in
“Appendix A: Structural Query Features” on page 1.
Working with Multiple Hit Lists
A detailed example of how you can use hitlist
management to perform specific, sophisticated
searches follows.
Suppose you want to search for all compounds in the
CS_Demo database that contain a benzene
substructure and have molecular weights between
50 and 200. After you perform this combined
search, you want to find which of these compounds
do not contain a carbon-nitrogen bond. By
integrating hitlists, you can perform this search.
To create the hitlist for the first part of this search:
1. Open the CS_Demo database.
2. Create the first query by drawing benzene in the
Structure data box and entering 50-200 in the
Molecular Weight Data Box.
3. Search the query.
You get 75 hits.
4. From the Search menu, choose Save List.
5. Save the hitlist as benz.txt.
To create another hitlist for the second part of the
search:
1. Draw the query shown below in the Structure
Data Box.
C N
2. Search the query.
You get 103 hits.
3. From the Search menu, choose Save List.
4. Save the hit list as c-n.txt.
Integrate the two hitlists:
1. From the Search menu, choose Restore List.
2. In the Open dialog box, open the benz.txt file.
3. In the Restore List dialog box, click Replace
current list, and then click OK.
You return to your first list of 75 hits
4. From the Search menu, choose Restore List.
5. In the Open dialog box, open the c-n.txt file.
6. In the Restore List dialog, click Subtract from
current list, and then click OK.
The hit list is reduced to the 60 records with
compounds containing a benzene substructure,
not containing a C-N substructure, and having
molecular weights between 50 and 200.
If you had chosen the “Replace current list” option
in the last step, then only the “C-N” records would
be displayed. Choosing “Intersect with current list”
would display those records in either list. Finally,
choosing “Union with current list” would display all
records from both lists.
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Managing Search Results

Administrator
Using Atom Lists
Using the text tool in ChemDraw, you can enter in a
structural query a list of possible atom types, one of
which must match in the target compound.
If you want to search for molecules containing a
benzene ring with an ether, amine or phosphane
group, a query might look like the following:
Atom Types and Bond Types
To broaden or narrow a search query, you can define
the properties of the atoms and bonds in a structural
query. These properties are definable in ChemDraw
Pro using the Atom Properties and Bond Properties
dialogs accessible from the Structure menu.
Suppose you want to find all molecules that contain
a non-oxygen chalcogenide bonded to another atom,
not necessarily carbon. You also want the bond type
between the chalcogen and the other atom to be a
single or double bond. The query, drawn in
ChemDraw Pro, may look like this:
S/D
A
[S,Se,Te]
[O,N,P]
This atom can be any non-hydrogen atom
This may be a single or double bond
This atom must be S, Se, or Te
The “A” label denotes that the atom may match any
atom except hydrogen. The indicator near the bond
indicates that the bond has been defined; in this case,
in the Bond Properties dialog of ChemDraw, you
specified that the bond type may be single or double,
S/D. Finally, by entering “S,Se,Te” enclosed in
brackets, you specified that one of these elements
must match in the target molecules.
Searching Fullerenes
A search of fullerenes can illustrate the restrictions
you can place on a formula search. Suppose you
want to find all fullerenes containing 20 to 80 carbon
atoms, but you also do not want to include large
organic molecules.
The formula query could be:
C20-80 H0
By designating zero hydrogen atoms, you exclude
hydrocarbons from the hit list. By clearly
capitalizing the elements and spacing the query, you
avoid searching ambiguities, although there were no
ambiguities in this example.
Searching Link Nodes and Multivalent
Rs (MVRs)
ChemFinder 8 contains a new atom type, the link
node. A link node is a placeholder for zero or more
unspecified atoms. It is especially useful when
searching for targets with any of several ring sizes,
or chains substituted in particular ways at either end.
While link nodes are traditionally divalent,
ChemFinder does not limit the upper limit of the
98•Chapter 5: Searching CambridgeSoft
Managing Search Results

ange. Multi-valent R (and A) atoms are
functionally similar to link nodes. They may be
thought of as “higher valent” link nodes.
O
(CH 2) 1-2
Hits cyclopropanones,
cyclobutanones, and
ß-lactams
Cl
The traditional representation of a link node is
“CH 2 ”, but this is misleading because any atom type
can substitute for the link node. For this reason,
ChemFinder represents link nodes as “LN”.
NOTE: Because ChemDraw does not support a
“LN” atom type, “(R) x-y ”, where x has a lower limit
of zero, is the preferred representation in
ChemDraw.
Although any atom type of a target atom matches a
link node, you can impose two restrictions the on the
link node:
• Unsaturation
• Ring topology.
A
Ph Cl
Br
(CH 2) 0-200
Br
Hits alpha, omegadibromides
and
bromine
Ph
(LN) 1-999
A multivalent “A” query
Using ChemDraw's Atom Properties menu to apply
either of these properties to the link node restricts
the range of target atoms to the specified topology.
For example, specifying the link node to be aromatic
would give the following results:
Query Results
(CH 2) =
aromatic
Will hit
Will not hit
Searching More Than One
Substructure
A substructure search may contain more than one
substructure unit. Suppose you want to find all
compounds in the CS_Demo database which
contain a benzene substructure and another
substructure unit containing chlorine bonded to any
atom. A structure query, as drawn in ChemDraw
would look like this:
You should get five hits. Browse the hits. By
specifying the query as above, you obtain hits such
as benzyl chloride, shown below, where the
substructure units are not connected.
ChemFinder 8 Chapter 5: Searching • 99
Managing Search Results
Br
(CH 2) 0-200
Br
Br
Br
Br
A Cl
Br
Br
Br Br
Br

Administrator
The substructure units can overlap; they can share a
common atom. Examples of this overlap are shown
below
.
Cl
Printing
ChemFinder can print high-quality hard copies of
your forms and tables. You can customize the format
of the printout by specifying the number of forms
per page and the layout of the forms.ChemFinder
uses the standard system commands to print
ChemFinder forms. The available options depend on
the printer you are using. Refer to your printer’s
documentation for more detailed information.
Printing a ChemFinder document consists of four
steps:
1. Specify the page layout.
2. Specify the printer options.
3. Optionally, from the File menu, choose Print
Preview and confirm the layout of the pages.
4. Print.
Page Layout
Cl
H H
O Cl
OH
The Page Setup dialog box allows you to format and
layout the printed document. You can customize the
number of forms printed per page, the size of the
O
O
O
Cl
OH
margins, and the layout of the forms. There are
separate Page Setup dialogs for printing forms and
for printing tables.
Forms
To display the Page Setup for forms:
1. Make sure a form is the active window.
2. From the File menu, choose Page Setup.
The Page Setup dialog box appears.
3. In the top drop-down menu, choose the unit of
measurement (inches or centimeters) for the
margins.
4. In the margin boxes, enter the size of the
margins.
5. In the Layout section, choose the tile or the
stacked format by clicking the appropriate radio
button.
6. Select the number of forms (up to eight) you
want printed per page.
7. To size the forms proportionately to fit flush
within the chosen margins, select Scale to Fit.
8. Click OK when you are finished.
100•Chapter 5: Searching CambridgeSoft
Printing

Tables
To display the Page Setup for tables:
1. Make sure a table is the active window.
2. From the File menu, choose Page Setup.
3. In the Margin section, enter the size of the
margins.
4. In the Titles and Grid Lines section, set the
preferences for which parts of the table get
printed.
NOTE: When you print a table, the columns are
printed in the width and order they appear in the
Data Table window. If columns are too wide, adjust
their widths in the Data Table window. To prevent a
particular column from printing, adjust it to zero
width in the Data Table window.
For tables that are still too tall or too wide to fit on
one printed page, you can choose the order in which
the pieces are printed.
• In the Page Order section, indicate the order
you want the pages printed.
For tables smaller than one page, you can choose
how to position the printout on the paper:
1. In the Center on Page section, select either (or
both) of horizontal and vertical centering.
2. Click OK when you are finished.
Print Preview
The Print Preview dialog box displays the document
on screen as it looks when printed. This preview
allows you to see the output so you can make any
changes before printing. You can print the document
from the Print Preview dialog box.
NOTE: Print Preview is especially useful when
printing tables.
To access the Print Preview dialog box:
1. From the File menu, choose Print Preview.
2. Select view options as required:
• Next Page or Previous Page to scroll to the
next or previous page.
• One Page or Two Page to toggle the
preview to one or two pages at a time.
• Zoom In or Zoom Out tool to magnify or
reduce the preview on screen.
3. Edit the layout or print:
• Click Close to exit Print Preview and make
changes.
• Click Print to print the document.
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Printing

Administrator
Print
To print forms or tables, do the following:
• From Print Preview or the File menu, choose
Print
The Print dialog box appears:
If you are printing forms, the default Print Range is
“Selection”. When printing from Table View, the
default is “All”.
Selection means: print one page starting from the
current record, taking into account the number of
records per page as established in Page Setup. All
prints the entire database. You may also enter a page
range. The page range must take into account the
number of records per page as established in Page
Setup.
NOTE: If a subform is active when you choose
Print, the entire form is printed. You can no longer
print just the contents of the subform, as in previous
versions of ChemFinder.
102•Chapter 5: Searching CambridgeSoft
Printing

Chapter 6: Relational Data and
Subforms
Overview
Subforms allow you to work with multiple data
tables in a relational database. You should be
familiar with working with ChemFinder forms and
databases before proceeding to subforms.
Accessing Relational
Data Using Subforms
A subform is a special box within a form that
behaves like a separate form file. A subform is used
to display information stored within a database, but
it usually displays data from a different database (or
different table within the same database) than the
main form. A subform is usually linked to the main
form, so that retrieval of data in the main form also
retrieves related records in the subform.
Like other types of boxes, you can move select and
resize a subform on the main form. However, you
cannot select it by clicking inside it. You must click
the title bar. When you click inside a subform, you
you activate the miniature form inside the box and
can work within it.
Below are examples of subform use:
• You have data that is associated in a
“one-to-many” relationship. For example, you
want to view a chemical structure together with
its physical properties, stored in a separate
table.
• You are running a stockroom and you want to
store package sizes and prices in the same place
because they are related. Each chemical may be
available in lots of package sizes, and you
wouldn’t want to re-draw the structure every
time you added a new package. You can use a
subform so the physical property information is
entered once in the main form and the package
sizes and prices are entered many times in the
subform.
By linking these two data tables with a linking
field you can make these tables relational; one
table can interact with the other. The contents of
a linking field are not important, as long as they
are different for each record in the main form.
Various forms of ID numbers are often used as
linking fields. As you browse through the main
form, corresponding records in the subform
appear.
Creating a Subform
You create a subform, place form objects on it, and
connect the subform to a database just as you do a
regular form. For detailed information, see
“Chapter 3: Creating and Editing Forms.”
.To create a subform:
1. Click the Subform button .
2. Draw a large box on a form.
A subform appears with a border and scroll
bars.
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Accessing Relational Data Using Subforms

Administrator
Within the subform, you can use the form tools to
create data boxes just as you would with a regular
form. You can also add tabs to your subforms. For
more information, see “Chapter 3: Creating and
Editing Forms.”
By default, newly created subforms are associated
with the same database as the main form.
To use a different database from the form as the data
source for the subform:
1. Right-click on the title bar of the subform data
box and choose Data Source.
The Subform Properties dialog box appears.
2. Click the Database tab, and then click Open
Database.
The Open dialog box appears.
3. Choose a database and then click Open.
The Database properties appear. The following
illustration shows the CS_Demo database.
4. Click OK to link the database.
To use the subform relationally to the main form, the
two forms must have one field in common. This
Linking Field must share the same data type (text,
integer, real) as a field in the main form. The fields
do not need the same name.
104•Chapter 6: Relational Data and Subforms CambridgeSoft
Creating a Subform

To link the field to the subform:
1. On the Subform Properties dialog box, click the
Subform tab.
NOTE: The subform tab is only available if
you right-click the subform’s title bar.
2. Select the Main Form field to link to the
subform from the “Link from …(main form)”
drop down menu. For example, the illustration
above shows the MOL_ID field selected.
Alternately, click the field in the Data Source
tree.
3. Select the matching field from the “Link to
…(subform)” drop down menu. For example,
the illustration above shows SYN_ID selected.
4. Choose the display options (scroll bars, table
view, show title, hide in query or browse mode)
Click OK.
The Subform is connected to the database you
chose.
In this example, when a record is retrieved in the
main form, its “Molname” is used to search the
“Synonym” field of the Synonyms table. The
subform displays the hits from this search.
Changing the Layout of
an Existing Subform
You can use the Form Generator to automatically
change the overall layout of an existing subform.
To change the layout of an existing subform:
1. Right-click on the title bar of the subform data
box and choose Properties.
2. Click the Form tab.
3. Click the Generate New Form checkbox, and
then click Style.
4. In the Form Generation dialog box, click the
checkboxes of fields you do not want to
include. (The default is all fields selected.)
5. In the Form style section, select the form
options you want. For a detailed description of
the options, see “Changing the Layout of an
Existing Form” on page 58.
6. Click OK.
7. In the Properties dialog box, click OK.
An alert box appears.
8. Take the appropriate action:
If you want to Then click
change the overall
layout for the current
subform
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Changing the Layout of an Existing Subform
Yes.
create a new subform No.

Administrator
The subform is automatically changed.
By default, the table name of the subform is
displayed in bold, 8 point Arial font.
Working with Subforms
You must select a subform to work with it. The
subform title bar is highlighted when the subform is
selected. After a subform is selected, the toolbars
affect the subform. You can use the Record tools to
browse the subform and add records.
To select a subform:
• Click anywhere in the subform.
To return to the main form:
• Click the main form.
To select a subform box:
• With the selection tool, click in the title bar.
Searching a Subform
You search a subform the same way you search the
main form. You can search a subform and the main
form simultaneously.
To search:
1. From the Search menu, choose Enter Query to
clear the subform and main form.
2. Enter a query in the data boxes you want.
3. From the Search menu, choose Find.
If the subform is linked to the main form, a
cleared form appears. The search is executed,
and ChemFinder returns you to the main form
where it displays a hit list containing records
related to those that match in the subform
search. You can browse and save this hit list just
as you would a hit list from a main form search.
If the subform is not linked to the main form, it
behaves independently of the main form and is
searched separately.
Viewing Subform Data in a
Table
If you have more than one record in the subform
associated with a single record in the main form, it
may be more convenient to view the subform as a
table while you browse through the main form. The
table view shows you the complete list of related
records for each entry in the main form.
To display a subform in Table view:
• Select the subform and do one of the following:
• Double-click on a record in the table.
• From the View menu, point to Data Table,
and then choose In Current Window.
A table view of the records in the subform
appears.
To return to the Form view, repeat the above action.
Using Scripts in Subforms
You can specify a CAL script to be executed when
you click an item in a subform in table view. The
subform can then be used as a list selection box. The
script can use CAL commands to retrieve the
clicked item, and perform an action on it. For more
information about CAL, see “Appendix D: CAL
Commands.”
To specify a CAL script:
1. Right-click on the subform header and choose
Properties.
The Subform Properties dialog box appears.
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2. In the Table script box, type the name of a CAL
script or click and select a script.
3. Click OK.
In Table view, the entries are blue and
underlined indicating that they are hot linked to
a script.
4. Click any of the hot links to run the script.
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Chapter 7: Importing and Exporting
Data
Overview
You can move data into and out of a database if the
data is in ChemFinder supported file formats. You
can import single files, import or export databases,
or add data to an existing database.
Supported File Formats
ChemFinder allows you work with individual
chemical structures and reactions in various file
formats. The supported formats are:
• ChemDraw (cdx)
• ChemDraw XML (cdxml)
• Chem3D (c3d)
• Connection Table (ct)
• MDL Molfile (mol)
• MDL RXNfile (rxn)
• MDL RDFile (rdf)
• MDL SDFile (sdf)
• MDL Sketch (skc)
• MDL Graphic (tgf)
• Questel F1D (f1d)
• Questel F1Q (f1q)
• SMD 4.2 (smd)
Supported formats for output files only:
• Bitmap (bmp)
• Encapsulated Postscript (eps)
• GIF (gif)
• TIFF (tif)
• Windows metafile (wmf)
For information on the .cdx, .ct, and .cdxml file
formats, see the ChemDraw Users Guide. For
information on the .c3d file format, see the Chem3D
User’s Guide. For information on MDL file formats,
see http://www.mdli.com/ (A document describing
the file formats is available in PDF format.)
Saving Structures
To save the structure on display:
1. In its structure data box, right-click and choose
Save Structure.
The Save As dialog box appears.
2. Choose the destination directory.
3. Type the file name and choose a file format.
4. Click Save.
The structure is saved to the indicated file. You can
read these files with any application that supports
the specified file format.
NOTE: To save most of the file types listed above,
you must have ChemDraw Pro installed.
Reading a Structure
ChemFinder can read files of any of the supported
structural formats. For example, if you have
structures stored in ChemDraw format, you can
open them directly from ChemFinder without
having to redraw them.
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To read a structure from a file into a structure box:
1. In the structure box, right-click and choose
Read Structure.
The Open dialog box appears.
2. Choose the file to read.
3. Click Open.
The structure is read into the structure box. The
database is not affected by this operation until
you choose Commit Changes or move off of the
record.
Drag and Drop
You can drag certain types of files from the
Windows Explorer or Desktop onto ChemFinder.
The following table summarizes the ChemFinder
Drag and Drop options.
type of file supported
file types
Structure • CDX
• SKC
• MOL
• MST
Graphic • WMF
• EMF
comments
Must be dropped into a
structure box.
Must be dropped into a
picture box.
Form • CFW Does not need to be
dropped onto an
existing form.
Multiple files can be dropped at once, but you
cannot mix types (as defined in column 1 of the
table). If several structure or graphic files are
dropped at once, they are loaded into successive
ChemFinder records. If only one is dropped, you are
asked if you wish to append the structure/graphic in
a new record or overwrite the existing record. If
more than five structures/graphics are dropped, an
alert will ask you if you wish to proceed.
Dropping one or more form files opens the forms,
without affecting the current form and database.
Importing Structures
ChemFinder enables you to import a collection of
structures into a new database, or append or merge
them with an existing database. You can import
single files or individual structure-data files.
Importing Individual Structure
Files
To import structures:
1. From the File menu, choose Import Structures.
The Open Chemical Structures dialog box
appears.
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2. From the Files of type menu, choose one of the
following:
To import files
from
Choose
a single directory the file type to import
and click Open.
multiple directories
a. Files in folders.
b. In the Choose
Structure Files
dialog box, select
the directories to
import.
c. Select or type the
file types to import.
d. Click OK.
The Data Import dialog box appears.
3. Set the options as described in “Importing
Structure Data and Reaction Data Files” on
page 111.
4. Click Import.
The structures are imported to the specified
database.
Importing Structure Data and
Reaction Data Files
ChemFinder allows you to import and export
Structure Data files (SDFiles) and Reaction Data
files (RDFiles) directly into and out of a database.
Because these files contain both structures and data,
ChemFinder creates fields in the database to
accommodate the incoming data.
In RDFiles, incoming data may be hierarchical and
complex. When loading RDFiles, ChemFinder
converts the data to a relational form, creating new
tables as necessary and generating linking data.
NOTE: When importing RDFiles, boxes are
automatically created on the form only for fields in
the root table of the RDFile. Subforms must be
created and positioned manually.
If you have a blank form when you import,
ChemFinder creates boxes. If you have a form with
boxes when you import, no new boxes are created.
However, new fields are always created in the
database as necessary. You can add more data boxes
later if you want to display these fields. For
example, if the database has a MOLNAME field but
no MOLREGNO field, and you import an SDFile
that contains both, ChemFinder uses the existing
MOLNAME field, but creates a new MOLREGNO
field.
You can import with a form linked to a database, a
blank form, or no form. If you import with no form,
ChemFinder creates a new form.
To import structure and reaction data files:
1. From the File menu, point to Import, and then
take the appropriate action:
If you want to import a
file with
an .sdf extension SDFile.
The Open dialog box appears.
Then choose
an .rdf extension RDFile.
2. Choose the file to import and click Open.
The Data Import dialog box appears.
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The Import dialog box scans the file to determine
what data fields are present and how much space to
allow for them in the database. The number of
records scanned is shown in the status bar. If the
input file is large, the scan may take a while.
To interrupt the scan:
• Press Esc.
A message box appears to confirm that you
really want to stop. The scan continues until
you click Yes.
To abort the scan:
• Click Stop scanning.
NOTE: You should let the scan go to completion so
that all needed fields are created in the database
before loading.
When the scan is finished, the progress bar is
replaced by the output database name. The dialog
box for the Sample.sdf file is shown below.
The default output database name and location is the
same as the input file.
To import to a different database:
• Type a pathname or click , browse to
another location, and then click OK.
Adding Data to an Existing
Database
When you import new data into an existing
database, incoming records may coincide with those
already in the database. You may choose one of
three options for adding data to an existing database:
Overwrite—Deletes the existing database, creates a
new database in the same location, and imports the
data into the new database.
Append—Adds new data to the end of the existing
database. Data existing before the import is
unchanged. Appending may lead to duplicate entries
in the database, but it is fast and no data is lost.
Merge—Combines the new data with the existing
data. As each record is read from the SDFile or
RDFile, ChemFinder looks up its structure and/or
other data in the (growing) target database and
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processes it according to one of the following
options on the Merge tab of the Data Import dialog
box:
Replace existing data—If there is new, incoming
data of type A, and the existing structure already has
data of type A, then the old data is erased and
replaced with the new. Existing data of type B is
untouched if there is no type B in the incoming file.
Append to existing data—If there is new, incoming
text data of type A, and the existing structure
already has data of type A, then the resulting data on
file becomes a multi-line concatenation of the old
and the new. Append is not available for numeric
data; incoming numeric data always replaces
existing.
Skip entry—If there is new, incoming data of type
A, and the existing structure already has data of type
A, then the incoming data is ignored and the existing
data is left untouched.
Merge Options
The Merge tab of the Data Import dialog box allows
you to choose how your data is merged.
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The following table describes the Match by options
on the Merge tab:
Option Description
Structure Search for exact match on
molecule or reaction in input file.
Other field Search for match on text or
numeric data.
Both structure
and other
Requires match in structure and
specified text or numeric data.
Custom SQL General mechanism for more
complex matching.
If no hits are found in the search, a new record is
added to the database. If hits are found, the first
record hit is modified as specified in the If match is
already on file options.
To choose how data is added to an existing database:
1. Click Overwrite, Append, or Merge.
2. If you chose Merge, click the Merge tab and
specify how to match the files and what to do
with matches that are already on file.
3. Click OK when you have entered all of the
options you want.
The file is imported into the database.
Changing the Data Field
Definitions
ChemFinder can determine what sort of fields to
create in the database, based on the characteristics of
incoming data. For example, if all items of type
“Melting Point” in an SDFile are numeric, then a
numeric field is created for them. The field scan
shows the results of this determination.
You can override this automatic determination. For
example, if you are loading another SDFile into the
same database later, and it contains Melting Point
entries with non-numeric text, then you may want to
establish this as a text field instead of numeric.
If you select a Text field type, you can specify the
width of the text field by entering a new value in the
Width box. Text fields are limited to 254 characters.
Longer strings of text must be stored in Memo
fields. Because the width of a text field cannot be
changed after it is created, make fields that are long
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enough to hold any text you might add later. For
more information on text field widths, see “Creating
Fields” on page 72.
To change the definition of a field before it is created
in the database:
1. In the Import tab dialog box, click the field to
change.
The Data Field Import dialog box appears.
2. Take the appropriate action:
If you want to Then
change the name of
the column being
loaded
in the Output
Column Name box,
type a new name.
If you want to Then
change the data type
of the column
change the width of
the output column
import this field into
the database
3. Click OK.
The Input Field information changes.
Using Log Files
from the Output
Column Type menu,
choose a different
data type.
type the width.
click Import this
field. If deselected,
data in this field is
disregarded.
During the import, ChemFinder creates a log file of
the actions taken. The log file (.log) is a text file that
is created alongside the input file and overwrites any
previous log file. The log records data of your choice
form the following options during the import.
• Errors—errors and warnings
• General data—information about the input file
and import process
• Records processed—logs an entry for each
record of the input file
• Structures registered—logs an entry for each
structure stored in the database
• Data registered—shows each data item stored
in the database
• Database schema—shows input fields found
and columns generated
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The log file for an RDFile import additionally
presents an overview of the data table hierarchy
within the RDFile.
You can choose whether to create the log file or not.
If you choose to create the log file, you can save it
with a different name or append to an existing log
file.
To set logging options:
1. From the Data Import dialog box, click the
Logging tab.
The Logging tab appears.
2. In the Log File section, click the appropriate
options:
If you Click
do not want a
log file
Do not generate log file.
If you Click
want a log file
a. Log to file.
b. If desired, type or
browse to a new name
and path.
c. If desired, click
Append to existing
file.
3. In the Log Data section, click the data types to
include in the log.
4. If you want the import to pause when errors are
encountered, click Show alerts and warnings
during import.
5. If you want to view the log automatically when
the import finishes, click Display log file after
import.
6. If you selected to merge the incoming data,
click the Merge tab and in the Log section,
select whether to log hits, misses or both.
Importing from a Specified
Location
You can start an import from an arbitrary location in
an SDFile or RDFile, such as a byte or line number.
To set the location from which to import:
7. Click the Advanced tab.
The Start Position dialog box appears.
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8. Select the position and click OK.
The Advanced tab appears.
9. Select the appropriate options.
To start from Click
the beginning of the
SDFile or RDFile
a specified line
number
a specified byte
number
• beginning.
• line and type the
line number.
• byte and type the
byte number.
To start from Click
a specified record • record and type
the record
number.
Exporting Data Files
You can create a new SDFile, RDFile, or delimited
text file by exporting records from an existing
database. When you export a file, all records in the
current hit list are saved. For each record, all fields
present on the form are written to the file. You can
prevent fields from being output by hiding their
columns in Table view.
To export a file:
1. From the File menu, point to Export, and then
take the appropriate action:
To export a file Then choose
with the .sdf extension SDFile.
with the .rdf extension RDFile.
with the .txt extension Delimited Text.
in the ChemFinder 5 format ChemFinder 5.
in the ChemFinder 7 format ChemFinder 7.
The Save As dialog box appears.
2. Type a name for the file you export, and click
Save.
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The file is exported.
NOTE: In ChemFinder 7.0 you can save data in
SDFiles, RDFiles. Use Export Subform Data in the
Preferences dialog box.
Exporting an ASCII File
Delimited text files may be the most universal file
format used by non-chemical applications. In a
delimited text file, each line represents a record, and
all fields in the record are listed in order from left to
right, separated by some character such as a tab or a
comma. Individual records are separated by carriage
returns. ChemFinder allows you to include a header
line at the start of the file that lists the names of all
of the fields.
When exporting a delimited text file, all records in
the current hit list are saved. For each record, all
fields present on the form are written to the file.
You can import a delimited text file saved by
ChemFinder into many other applications, including
spreadsheets and external database systems.
To choose options for exporting an ASCII file:
1. From the Preferences dialog box, click the
General tab.
The General Preferences tab appears.
2. Take the appropriate action:
To export an ASCII
file with
a delimited list of
field names as the first
line
tabs as the type of
delimiter
commas as the type of
delimiter
a different, specific
type of delimiter
structures in the
database as SMILES
strings
3. Click OK.
Click
Include header.
Tab delimited.
Comma delimited.
Other, and type the
symbol you want to
use as a delimiter.
Export SMILES.
subform data included Export subform
data.
NOTE: Subform data
is saved as one string
of text, rather than as
multiple records.
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Chapter 8: Customizing ChemFinder
Overview
You may customize ChemFinder in the following
ways:
• Customize display of your molecules, fonts,
pictures and forms.
• Design the toolbars to your specifications.
• Perform automated tasks, such as interfacing
with Microsoft Excel, or by using CAL, the
ChemFinder Automated Scripting Language.
Setting Preferences
The Preferences dialog box allows you to customize
the display of molecules, pictures, and forms, and
set options for searching and exporting.
1. Click the tab containing the preferences to set.
2. Select the preferences, and click OK.
Display Preferences
To set the Display preferences:
• From the File menu, choose Preferences.
The Preferences dialog box appears with the
Display tab on top.
Structure Display
To display carbon atoms on methyl groups or on
interior aliphatic or aromatic chains, check the
relevant check boxes in the Carbon labels section.
To display hydrogen atoms on heteroatoms or on
terminal carbons:
• Select the Fill valence radio button in the
Hydrogen Labels section.
Selecting None means these types are displayed
without implicit hydrogens.
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To display reaction centers:
• On the View menu point to Structure, then
select Reaction Info.
With reaction centers shown, any bond that
changes in the course of a reaction is colored.
Additionally, any atoms that participate in
reaction centers are circled if none of their
adjacent bonds participate in the reaction
center.
To display atom-to-atom maps:
• On the View menu point to Structure, then
select Atom-to-Atom Map.
With atom-to-atom maps shown, equivalent
atoms in reactants and products are colored the
same.
These two preferences affect only the display of
reactions. Not checking the boxes means these
types are displayed as all other atoms and
bonds.
Using Keyboard Shortcuts
When using a form, you can use keyboard shortcuts
to show or hide atom-to-atom maps, reaction
centers, atom numbers, and bond numbers.
To use keyboard shortcuts select Enable keyboard
shortcuts on the Display tab of the Preferences
dialog box.
When keyboard shortcuts are enabled, the following
keys toggle these properties:
• A: show/hide atom numbers
• B: show/hide bond numbers
• M: show/hide atom-to-atom maps
• R: show/hide reaction centers
• S: show/hide stereochemistry
Scaling Structures
To scale each structure so that it is as large as
possible within its structure box:
• Click Fit to box.
To display all structures with a constant bond length:
1. Select Uniform bond length.
2. Select the bond length percentage.
With “Uniform bond length” selected,
structures may be reduced in size if they are too
large to fit within the structure box, but they
will never be enlarged.
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Setting Preferences

Framing Pictures
To select whether the pictures in a form are
surrounded by a border:
• Select Framed.
Grid Spacing
To set the grid spacing (in pixels) on a form:
• Type in a number, or press the up and down
arrows to change the current value by one unit.
Choosing a small grid spacing allows you to place
objects more precisely by snapping to a tighter
matrix.
Color Preferences
To set the color preferences:
• In the Preferences dialog box, click the Color
tab.
The color tab allows you to specify the color of
various interface elements.
To set a color:
3. Click the button corresponding to the interface
element you want to change.
The color dialog box appears.
4. Select the new color.
5. Click OK.
Search Type Preferences
You can set preferences for the type of structure for
which you want to search.
To set Search Type preferences:
1. From the File menu, choose Preferences.
The Preferences dialog box appears.
2. Click the Search Type tab.
The Search Type tab appears.
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3. Take the appropriate action:
If you want to Then click
search for a substructure of
the molecule
search for the whole
molecule
search for an exact match of
the molecule
search for compounds with
characteristics similar to the
query
Substructure.
Full Structure.
Identity.
Similar and set
the degree of
similarity.
NOTE: The
higher the
value, the fewer
hits found.
If you want to Then click
search for compounds with
characteristics similar to the
query
limit the next search to the
current hit list.
When Search over current
list is deselected, queries
run over the entire database.
4. Click OK.
Search Details Preferences
You can set preferences for the details of each
search.
To set Search Details preferences:
Similar
Substructure
and set the
degree of
similarity.
NOTE: The
higher the
value, the fewer
hits found.
Search over
current list.
1. From the File menu, choose Preferences.
The Preferences dialog box appears.
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2. Click the Search Details tab.
The Search Details tab appears.
3. Take the appropriate action:
If you want to Then click
Allow uncharged atoms
in the query to match
charged atoms in the
target.
NOTE: Charged atoms
in the query must always
match charged atoms in
the target, regardless of
this setting.
Allow uncharged carbon
atoms in the query to
match charged carbon
atoms in the target.
NOTE: Charged atoms
in the query must always
match charged atoms in
the target, regardless of
this setting.
Allow hits to contain
molecular fragments in
addition to that which
was hit by the query.
Allow fragments in the
query to overlap (share
one or more atoms) in
the target.
Hit any charge on
heteroatom.
Hit any charge on
carbon.
Permit extraneous
fragments in full
structure searches.
Query fragments
can overlap in
target.
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If you want to Then click
Require that any
reaction center present
in the query overlap with
reaction centers in the
target. This preference
applies only to reaction
searching.
Prohibit generic
structures from hitting
any other structures in a
query.
Require full-word text
matching. If you do not
check this box, the query
will hit any matching
text fragment.
Require that the
stereochemistry of the
target structure match
that of the query
structure.
Reaction query
must hit reaction
center.
Generics hit only
generics.
Text: match full
word only
Match
stereochemistry
and click How to set
how the
stereochemistry is
matched.
The Stereochemical Search Preferences dialog
box appears.
4. Set the Tetrahedral stereo center hits:
If you want a
tetrahedral
stereocenter in the
query to
Then
match the target exactly. in Tetrahedral stereo
center hits, click
Same.
match same or opposite
configuration at the
center of the target.
in Tetrahedral stereo
center hits, click
Either.
match any target. in Tetrahedral stereo
center hits, click
Any.
match a relative
relationship between
centers
click Thick bonds
represent relative
stereochemistry.
When “Thick bonds represent relative
stereochemistry” box is unchecked (default), thick
bonds are interchangeable with hash/wedge bonds.
When the box is checked, and “Tetrahedral stereo
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center hits” is set to Same, a query marked with
thick bonds will only hit a target that has the same
relative relationship between centers.
5. Set the Double bond hits:
If you want the
stereocenters of a
database in the
query to
match the target
structure exactly.
match any
configuration in the
target.
6. Click OK.
Then in
General Preferences
The general preferences are as follows:
• ASCII file export (see “Exporting an ASCII
File” on page 118)
• Alerts
• ChemFinder opening window
• List of the last files used
To set the general preferences:
Double bond hits,
click Same.
Double bond hits,
click Any.
1. From the File menu, click Preferences.
The Preferences dialog box appears.
2. Click the General tab.
The General tab appears.
Structure Registration Options
To have ChemFinder present an alert when
attempting to enter a structure with an atom in a
non-standard valence state:
• In the Registration section, click Check
valences.
To have ChemFinder confirm when you are about to
modify data in the database:
• In the Registration section, select Ask to
commit changes.
ChemFinder Opening Options
You can set ChemFinder to open with the
ChemFinder Opening dialog box or to open the last
form you were using.
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To set the options for what ChemFinder displays
when it starts up:
1. On the General preferences tab, select one of
the following:
If you want to set
ChemFinder to
start with the opening
dialog box
open the last form you
used
2. Click OK.
Setting the Recent File List Size
You can set the number of files you opened recently
that ChemFinder shows.
To set the list size for the most recent files opened:
1. From the General preferences tab, choose the
number of file names to display.
2. Click OK.
Then click
Show opening
dialog.
Open last form on
startup.
Customizing Toolbars
ChemFinder lets you format your toolbars. You can
Customize the toolbars by dragging buttons on or
off.
To open the Customize dialog box:
• From the View menu, point to Toolbars, and
then choose Customize.
The Customize dialog box appears.
To add an option to a toolbar that is already in the
ChemFinder window:
1. In the Customize dialog box, click the
Commands tab.
2. Locate the command and click+drag an option
from the Commands window to a toolbar in the
ChemFinder window.
The option appears where you drop it on a
toolbar.
You can delete a button by dragging it off the
toolbar.
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To return a toolbar to the default settings:
1. In the Customize dialog box, click the
Toolbars tab.
The Toolbars tab appears and shows all of the
toolbars that currently appear in the
ChemFinder window.
2. Click the toolbar you want to return to default
settings, and then click Reset.
The toolbar in the ChemFinder window
changes to the default settings.
To return all the toolbars to the default settings:
1. In the Customize dialog box, click the
Toolbars tab.
The Toolbars tab appears and shows all of the
toolbars that currently appear in the
ChemFinder window.
2. Click Reset All.
Using the Periodic Table
ChemFinder features a periodic table for data
display and formula entry. Selecting an element
displays physical and historical data.
To display the Periodic Table window:
1. From the View menu, choose Periodic Table.
2. Click on an element to display its name, mass,
and other properties in the top box, and to
display its symbol in the bottom edit box.
By clicking on different elements and numbers
sequentially, you can create a molecular formula in
the bottom editable text box. You can then paste this
formula into the form for a formula query.
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To copy a formula from the Periodic Table to the
form:
1. Click+drag the text to copy, and then press
Ctrl+C.
2. Click OK in the Periodic Table window to close
it.
3. In the form, click the formula box into which
you want to paste the text and press Ctrl+V.
To display data about the selected element in the
Element Editor, do one of the following:
• Display the desired element and click the
display box at the top of the Periodic Table
window.
• Double-click the desired element button.
The Element Editor displays properties of the
selected element. The color of the element is shown
in the periodic table for that element and in any
structure data boxes in which that element is present.
To change the color of an element:
• Click Color.
To reset an element’s color to the default:
• In the Element Editor, click Revert to Default.
NOTE: The data of the Periodic Table is stored in
a tab-delimited ASCII file called CS ChemFinder
Custom Elements.txt located in your ChemFinder
system directory. It can be easily edited with a text
editor or spreadsheet program if you want to change
default data values.
ChemFinder
Automation Language
(CAL)
ChemFinder is equipped with its own scripting
language, the ChemFinder Automation Language
(CAL). CAL is used to operate the program from the
keyboard, or to create custom scripts for automating
simple operations such as switching between forms
or sending data to Microsoft Excel.
For more information, see The CambridgeSoft SDK
site on the World Wide Web at:
http://sdk.cambridgesoft.com/
To perform a CAL command:
• From the Scripts menu, choose Command
Line.
The Enter CAL Command dialog box appears. You
can type CAL commands and execute them one at a
time.
The Command drop-down list contains previously
entered commands.
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ChemFinder Automation Language (CAL)

To rerun a previously entered command:
1. Select the command from the list.
2. Click Execute.
For detailed information about the command
language, see “Appendix D: CAL Commands.”
Getting CAL Help
To display information about the CAL scripting
language:
• In the Enter CAL Command dialog box, click
Help.
The CAL Scripting Help window appears
containing commands, variables, and syntax
notes.
Writing a Script
To create a script:
1. Open Notepad or another text editor.
2. Type CAL commands, and save the file with
extension .cfs in the System subdirectory.
The name of the script appears on the Scripts
menu.
Alternatively:
1. Create a button on a form.
2. Label the button.
3. Right-click and choose Edit Script.
The following dialog box appears.
4. Click Yes to create a new file.
To execute a script:
• Choose the script from the Scripts menu.
NOTE: To execute a script that does not appear on
the menu, use the Command line and enter “Call
”.
Debugging a Script
You can step through a script line-by-line when
debugging it.
To view a script line-by-line:
1. From the Scripts menu, choose Command
Line.
The Enter CAL Command dialog box appears.
2. Type step on and click Execute. this turns on
the step mode, where each step is displayed.
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3. Run a CAL script by doing one of the
following:
If your script Then
appears in the Scripts
menu.
does not appear in the
Scripts menu.
choose the appropriate
script.
in the Enter Script
Command dialog box,
type call and the name
of your script, and
then click Execute.
4. Press any key except Escape to execute the
command and go to the next command.
As each step is encountered, it is displayed in
the status line.
5. Press Esc to stop debugging the script.
6. In the Enter Script Command dialog box, type
step off to exit the debugging mode.
Executing a Script on a
Form
You can execute a script from a button placed on a
form. When you click the button, ChemFinder looks
for the script specified in the button’s Properties
dialog box in one of three places:
• The same directory that contains the form.
• The ChemFinder System directory.
• The directory containing the ChemFinder
application.
For more information, see “Adding a Button” on
page 47.
Communicating with
Other Applications
There are two general methods of communicating
with other Windows applications such as Microsoft
Excel: by using a script within ChemFinder, or by
using a Visual Basic procedure within the other
application. The following is an overview of each
method.
Using Scripts
A ChemFinder (CAL) script can communicate with
other Windows applications using either of two
commands:
EXEC—to start an application and possibly pass
information on the command line.
DDE—to communicate using Dynamic Data
Exchange with a DDE-ready application.
Using EXEC is straightforward, but limited. You
can start all Windows applications by this command.
Most can be passed a filename on the command line,
such that the specified file is opened (or printed) on
startup. A few applications can accept more detailed
instructions. Consult the application’s manual for
information about how it can be operated using the
command line.
If you have Visual Basic or similar programming
language, you can extend the power of EXEC. You
can write an application using the advanced features
of Visual Basic, and then call the application from
within ChemFinder using the EXEC command.
Using DDE is more complicated. You can operate
most Microsoft Office components and many other
programs to varying extents with DDE. For
example, practically every command on the Excel
menu can be executed by DDE. The syntax is rather
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Executing a Script on a Form

difficult, but can usually be worked out by
experimenting and consulting ChemFinder help. An
example is given below.
DDE is the most direct way of using Excel to view
data from ChemFinder.
To use MS Excel to view ChemFinder data:
1. Start MS Excel. You can start it manually using
a CAL script or by starting the application in
Windows.
2. In ChemFinder, obtain the hit list you want to
transmit to Excel. If you want to work with the
entire database, from the Search menu, choose
Retrieve All.
3. Execute a short CAL script (below) which
exports the hit list as comma-delimited text to a
temporary file, then instructs Excel with DDE
to load that file into a spreadsheet.
4. Activate Excel to work with the data in the
spreadsheet.
This procedure takes data one way, from
ChemFinder to Excel. Returning modified data from
Excel to ChemFinder can be done using other
techniques described in this chapter.
Here is a script to start up Excel:
*RUNEXCEL.CFS – script to start Excel
*
EXEC “c:\msoffice\excel\excel.exe”
If the Excel program is on your search path, you can
eliminate the complete pathname and just give the
executable name (“exec excel.exe”); if not, you may
need to modify this script to indicate where
EXCEL.EXE is located on your system.
Here is a script to transfer the current hit list from
ChemFinder to Excel:
*TOEXCEL.CFS – script to send data
*to Excel
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Communicating with Other Applications
*
WRITETEXT C:\DATA.TMP
DDE Excel System [OPEN(“C:\DATA.TMP”)]
DDE Excel
System [COLUMN.WIDTH(1,”C1:C4”,,3,1)]
The first line writes out the current ChemFinder hit
list as a temporary delimited ASCII file. By default,
all fields that appear in boxes on the current form—
except structure, but including formula and
molecular weight—are written. The second line
instructs Excel to open the file. Excel can
automatically recognize the file format as tabdelimited.
The third line instructs Excel to auto-size
column widths 1–4 to fit their contents.
NOTE: This example requires that the text export
delimiter be set to TAB in the General tab of the
Preferences dialog, otherwise Excel may not read
the file correctly.
You can include either or both of these scripts on the
Scripts menu, and you can activate them with
buttons on the form. To include a script on the
Scripts menu, give it a filename with extension
“.cfs”, and place it in the ChemFinder System
directory, or in the directory containing the
ChemFinder application. To activate a script from a
button, label the button with a script filename or
string which can be converted into a filename. For
example, if TOEXCEL.CFS exists in the
ChemFinder System directory, label a button
“ToExcel” to start the script. For more information,
see “Adding a Button” on page 47.

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Using Visual Basic
The second method of communicating between
ChemFinder and other applications such as Excel is
using OLE Automation. ChemFinder is an OLE
Automation server, meaning that it offers a
collection of data management capabilities to
outside programs capable of communicating with
OLE objects. While this collection is currently fairly
small, it is adequate for a variety of data retrieval
and search tasks. This feature allows you to write a
custom Visual Basic procedure that directly
retrieves and manipulates data from ChemFinder.
The general procedure for accessing ChemFinder
data from within a Visual Basic script is as follows.
1. Create a ChemFinder Document object,
typically passing a filename so that you open a
form complete with its database connection.
2. Use methods of the Document object to move
through the database, search, and access data.
Document methods include some that access
Field objects, used to query the data in the
database, and Molecule objects, for accessing
details of molecular structures.
For more information, see the CambridgeSoft SDK
web site:
http://sdk.cambridgesoft.com/
Using Microsoft Access with
ChemFinder
The methods described above for communicating
between ChemFinder and Excel apply also to
Access. You can start Access using the EXEC
command. You can send it DDE commands
contained in a CAL script, although Access provides
fewer capabilities with DDE than does Excel. Or
you can write programs using Access Basic that rely
on the OLE Automation methods found in
ChemFinder. In addition, you can use Access
directly to operate on a ChemFinder database.
A ChemFinder molecule database consists of three
components: the structure storage files (with file
extensions .mst and .msi), the data storage files,
which include a Microsoft Access database (file
extensions .mdb and .ldb), and the forms (with file
extension .cfw) used to view the structures and the
data.
If you have Access on your system, double-clicking
an .mdb file in Explorer starts up Access and opens
the specified database.
When you open a ChemFinder database in Access,
you will see the same tables as displayed in the
ChemFinder Database dialog box, including the
main structure table (usually named “MolTable”),
but you will not see columns for structure, formula,
or molecular weight. These fields cannot be
manipulated directly using Access.
The following are some of the operations you can
perform on a ChemFinder database using Access.
Most of these capabilities are not available through
the current version of ChemFinder:
• Compress or repair the database
• Change column (field) or names or formats
• Change table names
• Add or delete columns or tables
• Import or export tables
• Load non-structural data from various file
types, including delimited ASCII, Excel, Word
• Move quantities of data from one column or
row to another
• Carry out complex queries on non-structural
data
• Permanently change the sort order of a table
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For more information about these actions, please
consult the Microsoft Access User’s Guide.
Do not add or delete records to the MolTable within
Access, because the data component of the database
will become out of synchrony with the structure
component.
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134•Chapter 8: Customizing ChemFinder CambridgeSoft
Communicating with Other Applications

Chapter 9: Accessing the
CambridgeSoft Web Site
Online Menu Overview
You can access different areas of the CambridgeSoft
web site from within ChemFinder with the Online
menu. To use the Online menu, you must have
internet access.
Finding Chemical
Suppliers on
ChemStore.com
Find Suppliers on ChemStore.Com opens the
ChemACX.Com page (ACX—Available Chemical
Exchange) of the CambridgeSoft web site.
To access Lookup Suppliers on ChemStore.Com:
• From the Online menu, choose Find Suppliers
on ChemStore.com.
The ChemACX.Com page opens in your
browser.
You can search ChemACX.Com for chemicals by
supplier or by chemical name.
Finding Information on
ChemFinder.com
Find Information on ChemFinder.com opens
ChemFinder.com, where you can search the
ChemFinder database for chemical information.
To access ChemFinder.Com:
• From the Online menu, choose Find
Information on ChemFinder.com.
ChemFinder.com opens in your browser.
You can search for chemical information by, name,
CAS number, molecular formula, or molecular
weight. Follow the links to do substructure queries.
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Finding ACX Structures
and Numbers
ChemFinder searches ACX and returns information
about related structures and numbers. You can place
the returned information in your document.
ACX Structures
To find an structure that corresponds to an ACX
number:
1. From the Online menu, choose Find ACX
Structure from Number.
The Find Structure from ACX number dialog
box appears.
2. Type the ACX registry number.
3. Click OK.
The Structure appears in your document.
ACX Numbers
To Find an ACX number for a structure:
1. In a ChemFinder document, select the structure
for which you want to find an ACX number.
2. From the Online menu, choose Find ACX
Number from Structure.
The ACX number appears in the Find ACX
Number from Structure dialog box.
Browsing
ChemStore.com
Browse ChemStore.com opens the ChemStore page
of the CambridgeSoft web site.
To access Browse ChemStore.com:
• From the Online menu, choose Browse
ChemStore.com.
The ChemStore.Com page opens in your
browser.
136•Chapter 9: Accessing the CambridgeSoft Web Site CambridgeSoft
Finding ACX Structures and Numbers

You can search ChemStore.Com for chemicals, lab
supplies, chemistry-related software, and other
items you want to buy. You can access
ChemACX.Com, LabEqwip.Com, and other pages
from ChemStore.Com.
Browsing
CambridgeSoft.com
Browse CambridgeSoft.com opens the Home page
of the CambridgeSoft web site.
To access the CambridgeSoft Home Page:
• From the Online menu, choose Browse
CambridgeSoft.com.
The CambridgeSoft web site in your browser.
Check the CambridgeSoft web site for new product
information. You can also get to ChemStore.Com,
ChemNews.Com, and other pages through
CambridgeSoft.Com.
Accessing the Online
ChemFinder User’s
Guide
Browse CS ChemFinder Documentation opens the
Technical Support Manuals page where you can
access current and previous versions of the
ChemFinder User’s Guide.
To access the CambridgeSoft Manuals page:
1. From the Online menu, choose Browse
CS ChemFinder Documentation.
2. Click version of the manual to view.
A PDF version of the ChemFinder User’s Guide
appears.
Accessing
CambridgeSoft
Technical Support
Browse CS ChemFinder Technical Support opens
the Tech Support page of the CambridgeSoft web
site.
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To access CS ChemFinder Technical Support:
• From the Online menu, choose Browse
CS ChemFinder Technical Support.
The Technical Support page opens in your
browser.
Use the Tech Support page to find answers to
Frequently Asked Questions (FAQs), the technical
support newsletter, documentation, downloads, and
contact a Technical Support Representative.
Registering Online
Register Online opens the ChemClub page of the
CambridgeSoft web site, where you can register
your copy of ChemOffice.
To register online:
1. From the Online menu, choose Register
Online.
The CambridgeSoft home page opens in your
browser.
2. Click the Register tab.
3. Click Register Your Software.
4. Register ChemFinder.
Using the ChemOffice
SDK
The ChemOffice Software Developer’s Kit (SDK)
enables you to customize your applications.
To browse the ChemOffice SDK:
• From the Online menu, choose Browse
ChemOffice SDK.
138•Chapter 9: Accessing the CambridgeSoft Web Site CambridgeSoft
Registering Online

The CS ChemOffice SDK page opens in your
browser.
The ChemOffice SDK page contains
documentation, sample code, and other resources
for the Application Programming Interfaces (APIs).
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140•Chapter 9: Accessing the CambridgeSoft Web Site CambridgeSoft
Using the ChemOffice SDK

Appendix A: Structural Query Features
Overview
To perform a substructure search in ChemFinder,
you must first draw the query structure itself. Query
structures can be drawn in many different programs,
but we recommend using ChemDraw, and this
Appendix is focused on using ChemDraw to draw
query structures. For more information about the
structure drawing and query capabilities of
ChemDraw, please consult the ChemDraw User’s
Guide.
ChemFinder does its best to follow your instructions
even if those instructions are contradictory. For
example, you can create a query such as the
following:
That bond is already in a ring, so ChemFinder
returns no hits for this query.
General Properties
Chn
ChemFinder allows the following general properties
to be assigned to a query:
• Atom
• Bond
• Substituents
• Charges and radicals
• Isotopes
• Stereochemistry
• Normalization
this bond is marked so
that it must not be in a ring.
Atoms
Atom types specified in the query must match atoms
at corresponding positions in the target. Hydrogen is
an exception—see “Substituents” on page 2.
Bonds
All bonds explicitly drawn in the query must match
in the target. For certain caveats, see
“Stereochemistry” on page 3 and “Normalization”
on page 4. ChemFinder recognizes the following
standard bond types:
Bond Type Description
Single target must have single bond
here
Dashed same as Single
Hashed same as Single
Thick same as Single
Wedged Hashed specifies stereochemistry down
from the point end to the wide
end
Wedged specifies stereochemistry up
from the point end to the wide
end
Wavy specifies stereochemistry
“either” at both ends
ChemFinder 8 • A-1
General Properties

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Bond Type Description
Hollow Wedged same as Wedged
Dative same as Single
Double target must have double bond;
stereo dictated by geometry
Double Either target must have double bond;
any stereochemistry ok
Double Bold same as Double
Triple target must have triple bond
here
Substituents
In ChemFinder, a substituent is defined as a nonhydrogen
atom connected by a bond of any order.
For example, a carbonyl oxygen is a substituent of
the carbonyl carbon.
All unfilled valences in the query may be filled by
hydrogen atoms or by non-hydrogen substituents.
The normal valence of an atom is determined from
data in the Periodic Table window. For example,
carbon has a valence of 4, while sulfur has valences
of 2, 4, and 6. Any explicit charges, radicals, or
query properties modify the normal valence. For
example, a carbocation has a valence of 3.
Hydrogen atoms in the query may match nonhydrogen
substituents in the target if the hydrogen in
the query is implicit on an unlabeled carbon atom or
heteroatom.
Hydrogen atoms in the query must match hydrogens
in the target when the query hydrogen is at the end
of an explicit bond. The matched hydrogen in the
target may be implicit in an unlabeled carbon atom.
finds any of: does NOT find any of:
Charges and Radicals
Charges or radicals specified on atoms in the query
must match those in the target. Uncharged atoms in
the query may or may not match charged atoms in
the target, depending on the state of the appropriate
check box in the Search tab of the Preferences
dialog.
The valence of a charged atom is taken to be the
valence of the isoelectronic neutral atom.
With a substructure search, the query:
finds any of: does NOT find any of:
A-2 • CambridgeSoft
General Properties
H
H
HN O
Br
Br
OH
N
Cl
NH 2
H
H
O
O
H
H
O
N
N+
OH
NH 2
OH
NH 2
OH

Isotopes
Isotopic labels specified in the query must match the
target. Unlabeled atoms in the query match
unlabeled or isotopically labeled atoms in the target.
Additionally, D is treated interchangeably with 2 H,
and T is treated the same as 3 H.
With a Substructure Search, the query:
finds any of: does NOT find any of:
2 H
O
D
O
13 C
NH 3+
N+
H 2+
N
HO-
13 CH3
D D
Stereochemistry
O
13 CH3
D
Stereochemistry specified on the query must match
the target if the relevant Match Stereo item is
selected in the Search tab of the Preferences.
Stereochemistry is specified at a tetrahedral site by
using stereo bonds (up, down, either).
Stereochemistry about a double bond is specified by
T
O
HO
NH 2
N
13 CH3
HO
13 CH3
N-
the geometry of the drawing. ChemFinder cannot
currently interpret other stereochemistry types
(allenic, square planar, octahedral, etc.) and ignores
them during a search.
When evaluating a possible match, the following
rules are applied:
• Unspecified stereochemistry (a plain bond)
may match any stereochemistry (either a
wedged, hashed, bold, or a plain bond).
• Specific bond types need not match as long as
the overall stereochemistry at a given atom does
match.
• Implicit hydrogens are taken into consideration
in both the query and the target if doing so helps
to determine the chirality of a stereocenter.
With a full structure search and the Match
Tetrahedral stereo option selected, the query:
finds any of: does NOT find any of:
Relative Tetrahedral Stereochemistry
Relative Tetrahedral Stereochemistry, or RTS,
specifies a given relationship between the centers.
That is, a known orientation of the substituents with
respect to each other, rather than a known absolute
ChemFinder 8 • A-3
HO
HO
HO
N
H
H
N
N
H
H
HO
O
O
OH
OH
O
OH
N
H
O
OH
HO
HO
HO
N
H
H
N
N
H
General Properties
O
OH
OH
O
O
OH

Administrator
configuration. To specify this, centers are drawn, not
with the standard hashed and wedged bonds, but
with thick (bold) stereo bonds.
Relative and absolute configurations may be
registered separately in ChemFinder, and can be
distinguished by various search options. The basic
ChemFinder search philosophy can be summarized
as follows: a more specific query is a more precise
request, and should get fewer hits than a more
general query. If the query represents a particular
absolute configuration, it should hit only that; if it
represents a mixture, it should hit any of the
components.
If you choose Same in the stereo search choices, you
are requesting that whatever stereochemistry is
specified in the query must match that of the target.
If the query has relative bonds and RTS is activated,
a hit must have the same relationship between
centers.
MDL File Formats
All bond styles available in ChemDraw are retained
in CDX files. The same is not true of major MDL
structure files: MolFiles, SDFiles, and RDFiles. In
these formats, only three stereo bond types are
available: hash, wedge, or either (squiggly bond);
thick bonds are not recognized. This presents a
problem for the ChemFinder user wishing to import
or export structures having relative stereocenters.
ChemFinder addresses this problem by using a
proprietary tag in the file, recognized only by
ChemFinder. The tag is BOND_RELS, and is
applied to every stereo bond of thick type. For
example, here is an excerpt from the bond table of a
molfile with relative bonds.
...
4 5 1 0 0 0 0
2 6 1 1 0 0 0

finds any of: does NOT find any of:
Atom Properties
ChemFinder allows special atom properties to be
assigned to an atom in a query. These properties are
usually only meaningful during a search. They
generally serve to broaden or narrow the scope of
the search.
Special Atom Types
H
OH
OH
O
ChemFinder recognizes six special atom types that
can match any one of a predefined set of elements:
• Amatches any non-hydrogen atom.
• Qmatches any heteroatom (non-hydrogen, noncarbon).
• Rmatches any atom, including hydrogen.
• Xmatches any halogen (F, Cl, Br, I, At).
• LNmatches a link node (placeholder for
unspecified atoms). See “Searching Link Nodes
and Multivalent Rs (MVRs)” on page 98 for
details.
• Mmatches any metal atom, shaded gray in the
periodic table below:
H
OH
OH
O
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac
Atom Lists
As with the predefined special atom types, an atom
list is a list of atoms, one of which must match the
target atom.
For example:
[Cl,Ag,N] atom must be Cl or Ag or N
Atom lists may contain only elements. Special atom
types, nicknames (Ph), and structural fragments
(NH 2 , OCH 2 CH 3 ) may not be included in an atom
list. ChemFinder recognizes a maximum of five
atoms in an atom list.
Atom Not-Lists
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
The opposite of an atom list is a list of atoms, none
of which must match the target atom. For example:
[NOT O,S,Se] atom must not be O or S or Se (but
may be any of the 100 other elements)
Atom not-lists have the same restrictions as atom
lists.
Substituents: Exactly
This property specifies a precise value for the
number of substituents on an atom, including those
explicitly drawn. This property is only meaningful
in a substructure search.
With a substructure search, the query:
ChemFinder 8 • A-5
Atom Properties

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finds any of: does NOT find any of:
HO
O
Substituents: Up To
Cl
This property specifies a maximum value for the
number of substituents on an atom, including those
explicitly drawn. This property is only meaningful
in a substructure search.
With a substructure search, the query:
X3
This atom is marked
with the atom property
Substituents:Exactly 3
U2
finds any of: does NOT find any of:
O
O
This atom is marked
with the atom property
Substituents:Up to 2
Substituents: Free Sites
The Substituents: Free Sites property specifies the
maximum number of additional substituents that
may be present on an atom. This property is only
meaningful in a substructure search.
NOTE: Specifying Free Sites: 0 is a quick way to
indicate that you want no further substitution at a
site. Target structures will match the query structure
as drawn, with no additional ligands.
With a substructure search, the query:
finds any of: does NOT find any of:
A-6 • CambridgeSoft
Atom Properties
H
O
CH 3
*2
HO
O
This atom is marked
with the atom property
Substituents:Free Sites 2

HO
O
Implicit Hydrogens
Cl
This atom property may have either of two values:
Allowed (default) or Not Allowed. If implicit
hydrogens are Not Allowed, the atom must be fully
substituted in the target.
This property is only meaningful in a substructure
search.
NOTE: This atom property does not affect the
display of implicit hydrogens, only their presence in
a search. For more information about displaying
implicit hydrogens, see “Setting Preferences” on
page 119.
Unsaturation
Sometimes it is useful to specify that an atom must
or must not be attached to unsaturated (aromatic,
double, or triple) bonds. ChemFinder allows
searches for atoms whose unsaturation Must Be
Absent (all bonds to the atom are single). It also
allows searches for atoms with at least one multiple
(double, triple, or aromatic) bond. The default value,
Undefined, finds targets without regard to the
hybridization of the atom.
This property is only meaningful in a substructure
search.
O
O
With a substructure search, the query:
finds any of: does NOT find any of:
Bond Properties
ChemFinder allows special properties to be assigned
to bonds in a query. These properties usually will
only be meaningful during a search. They generally
serve to broaden or narrow the scope of the query.
Special Bond Types
The table below describes the special bond types
that ChemFinder allows.
ChemFinder 8 • A-7
HO
O
This atom is marked
with the atom property
Unsaturation: Must Be Present
O
OH
Bond Type Description
O
OH
Aromatic target bond must be aromatic as
defined by the Hückel 4n+2 rule
Any target can have any bond type here
S/D target must have a single bond or a
double bond here
S
O
O
HO
OH
OH
OH
O
O
Bond Properties
OH

Administrator
Bond Type Description
Tautomeric same as S/D
D/A target must have a double bond or
an aromatic bond here
S/A target must have a single bond or
an aromatic bond here
Topology
If Ring or Chain is chosen, the target bond must or
must not be in a ring, respectively.
Reaction Center
The reaction center refers to those bonds that are
directly affected by a reaction. This property allows
you to specify just how a given bond is affected.
Property Description
Unspecified target must have a bond here,
but the bond can participate
in the reaction in any fashion,
or not at all
Center
Make/Break
target must have a bond here
that directly participates in
the reaction in some way
target must have a bond here
that is either made (if in a
product) or broken (if in a
reactant)
Property Description
Change target must have a bond here
whose bond order changes
over the course of the
reaction, but is not made or
broken
Make&Change target must have a bond here
that is either made (if in a
product) or broken (if in a
reactant) or whose bond
order changes over the course
of the reaction
Not Center target must have a bond here,
and that bond must not
participate in the reaction
Not Modified target must have a bond here,
and regardless of whether it is
part of the reaction center or
not, its order must not change
over the course of the
reaction
This property is only meaningful when searching a
reaction database.
A-8 • CambridgeSoft
Bond Properties

Appendix B: Formula Input Rules
Overview
When you type a formula in ChemFinder, you are
not required to enter symbols in any particular case.
This can give rise to ambiguities. This appendix
describes how ChemFinder interprets formulas and
resolves these ambiguities.
Consider an example. In entering a formula query,
you type:
cooh
Most chemists recognize this as a carboxyl group:
carbon, two oxygens, hydrogen. However, it might
be interpreted as cobalt (Co), oxygen, hydrogen.
Similarly, “CLI” might be carbon-lithium or it might
be chlorine-iodine. “PHE” might be phosphorushelium
or, since ChemFinder allows 3-character
amino-acid symbols as special atom types, it might
be phenylalanine (Phe).
One way to avoid ambiguity is to separate letters
with spaces. For example, the string “c o” cannot
possibly be interpreted as cobalt. Another way to
avoid ambiguity is to enter formulas using the
Periodic Table instead of typing them. ChemFinder
allows free-format input, and attempts to make the
most reasonable interpretations of them by using the
rules described below.
Rules
If a symbol is properly capitalized (first letter upper
case, followed by zero, one, or two lower-case
letters), then the longest valid symbol which
matches is preferred. Thus “Phe” matches
phenylalanine rather than phosphorus; “Co”
matches cobalt.
Because of this rule, if you properly capitalize all
symbols, no ambiguities will arise.
If symbols are not properly capitalized (such as all
lower-case), then, with the exception noted below,
the shortest symbol which matches is preferred.
Thus “co” is taken as carbon-oxygen instead of
cobalt.
The exception is: if two characters represent a valid
two-letter symbol and also a valid one-letter symbol
followed by an invalid one, then the two-letter
symbol is favored. Thus “cl” is not taken as carbon
followed by the (invalid symbol) L, but instead is
taken as chlorine.
Examples
There is an easy way to experiment with formula
interpretation: use the Periodic Table. Type a
formula into the text box at the bottom, then click
anywhere outside that box. ChemFinder interprets
the formula and redisplays it with correct
capitalization.
ChemFinder interprets some ambiguous formulas as
follows:
Formula Chemfinder Interpretation
cooh COOH
Cooh CoOH
cnosi CNOSI
cNoSi CNoSi
ChemFinder 8 • A-9
Rules

Administrator
Formula Chemfinder Interpretation
bru BrU
b ru BRu
A-10 • CambridgeSoft
Examples

Appendix C: Similarity Rules
Overview
Often you might not be looking for a specific
compound, but any compound that is “close
enough” will do. ChemFinder uses the Tanimoto
equation to determine if compounds are similar. You
can specify “how similar” in the Searching tab of the
Preferences dialog.
Exact searching relies on the notion of an atom-andbond
table: a specific set of atoms joined to each
other in a certain order by a given set of bonds. If
some atoms or bonds are missing, added, or
different, the query structure and the target structure
do not match.
Most similarity searching, on the other hand, relies
instead on the notion of molecular descriptors. Each
compound can be represented by a collection of
qualitative terms that describe general aspects of the
structure.
For example, benzoic acid might be described as:
• organic acid
• contains 6-membered ring
• contains delocalized ring
• contains C-double-bond-O
As you can see, the descriptors can be very broad,
and they can overlap. The set of descriptors used by
ChemFinder is very large.
When you draw a compound, ChemFinder
compares it against all of the descriptors it knows
about. Some descriptors will be present in your
compound and some will not. Since each descriptor
for a given compound is either Present or Not
Present, they are often stored as bits, and another
name for a compound’s set of descriptors is its
bitscreen.
Consider the query and target compounds shown
graphically below. Both have similar numbers of
descriptors present - the query has 23, while the
target has 24. But are they “close enough”?
Bitscreen Desc. # Name
Query 2
3
Target 2
4
Q and
T
Complete Structure
Similarity
One of the hallmarks of a good similarity algorithm
is whether it is commutative. That is, two
compounds should have the same similarity value
no matter which you compare to which. The full
structure Tanimoto similarity test is commutative. It
compares the number of descriptors they have in
common (in the intersection of the query and the
target) to the number of descriptors they have in
total (in the union of the query or the target). The
ChemFinder 8 • A-11
1
7
Q or T 3
0
Complete Structure Similarity
Q
T
Q ∩ T
Q∪T

Administrator
ratio of these two values is known as a Tanimoto
coefficient, and is always a value between 0% and
100%.
Q∩T
Q∪T
Tanimoto Coefficient
For the two compounds above, the Tanimoto
coefficient is 17/30, or about 57%. This is not very
similar. Although ChemFinder will allow you to
specify any Tanimoto value down to 0%, for most
cases you will likely be looking for compounds that
have Tanimoto coefficients of 90% or higher.
Substructure Similarity
Unlike full structure similarity, substructure
similarity is not commutative: you are comparing a
portion of one structure against the entire other
structure, and so it does matter which you compare
to which. In considering substructure similarity,
ChemFinder finds what percentage of descriptors in
the query are also present in the target.
This value will always be at least as large as the
complete-structure Tanimoto coefficient for the
same two compounds, and usually it will be larger.
The two compounds above are 17/23, or about 74%
similar by substructure similarity. For a given
coefficient value, a substructure similarity search
will always return all of the hits in a full structure
similarity search, and will often return additional
ones as well.
A-12 • CambridgeSoft
Substructure Similarity

Appendix D:
CAL Commands
Overview
ChemFinder Automation Language (CAL) is a set
of commands that control many ChemFinder
operations.
You invoke CAL commands in either of two ways:
• Interactively—You type commands and
execute them one at a time on a command line.
• Scripts—You use ASCII files containing a
series of CAL commands to be executed
automatically in sequence.
Arguments to commands consist of numbers and
text strings. You can enter a text string without
punctuation unless the argument is not the last one
on the command line and contains multiple words or
spaces. In this case, you must enclose the argument
in quotation marks.
CAL Help
Information about the CAL command and variables
is available in the CAL Scripting Help window.
To access CAL Help:
1. From the Scripts menu select Command Line.
The Enter Cal Command dialog box appears.
2. In the Enter Cal Command dialog box, click
the Help button.
The CAL Scripting Help window appears:
Menu Commands
Menu commands consist of a two-word command
from the main menu and in some cases an optional
argument.
Following are examples of commands:
file new
edit paste
search find
record next
You do not need to spell out menu commands. You
can enter just enough letters to uniquely identify the
menu option. For example, to execute the Record
Next command, type:
rec n
Some menu commands open a dialog box and wait
for user feedback. To avoid this, a limited number of
menu commands can take explicit arguments:
FILE OPEN [filename]
FILE SAVE [filename]
RECORD GO TO RECORD [recno]
ChemFinder 8 • A-13
CAL Help

Administrator
Box Creation
Commands
DBOX coords [fieldname]
FRAME coords [text]
TEXT coords [text]
PICT coords [filename]
BUTTON coords [scriptname]
SUBFM coords
ARROWBOX coords
FRAMEDBOX coords [fieldname] [text]
To create a new box on the form:
1. Specify the box type with the appropriate
keyword.
2. Type four integers giving the rectangular
coordinates of the box after the keyword.
3. If desired, type a text string giving further
information appropriate to the box type, as
shown below:
Box Type String
Data box
Frame
Text
Picture
Button
Subform
name of database field to be
displayed in the box
static label for upper left
static text
pathname of a Windows
metafile
pathname of a script file, or
name as it appears on Scripts
menu
Box Type String
Arrowbox
Framedbox
name of database field to be
displayed in the box, and static
label for upper left
If the text string is omitted, you can supply it later
using SETFIELD or SETTEXT. For a button, you
must use SETTEXT if you want its visible label to
be different from the name of its script.
Box coordinates are specified in this order: left, top,
right, bottom. Units are in pixels; the origin is at the
upper left, with coordinates increasing from left to
right and top to bottom, so that coordinates will
range from left = 0 to right = 640 or 1024 or
whatever fits your screen, and from top = 0 to
bottom = 480 or 768 or similar.
When a new box is created, it adopts the current
font. To specify a particular font for a box, use the
FONT command prior to creating the box.
When specifying a script name, give one of the
following:
• The complete pathname of the script file.
• A simple name without extension, if the script
is stored in the standard scripts subdirectory
with the standard file extension. If the script
name appears on the Scripts menu, you can use
the name from the menu.
The table below shows examples of Box Creation
Commands:
Command Action
FRAME 10 10 300
60 Molecular
Formula
create frame with label
at upper left
A-14 • CambridgeSoft
Box Creation Commands

DBOX 20 20 290
50 formula
TEXT 100 100 300
150 “A Label”
PICT 500 300 600
400 C:\LOGO.WMF
BUTTON 500 10
550 40 DEMO
Box Manipulation
Commands
create data box for
formula in above frame
create a static text
string
put specified picture at
lower right
create button at upper
right to run script
DEMO.CFS
FORMEDIT ON|OFF
SELECT box
UNSELECT box
DELBOX box
SETFIELD box fieldname
SETTEXT box text
ACTIVATE subform
DEACTIVATE
SCALE
SCALE_TO_FIT
To work with a box or subform on the form, you
specify a keyword followed by a box identifier. A
box is identified in one of two ways:
• By point—Give the coordinates of a point
anywhere within the box. When coordinates fall
in more than one box, the most recently created
box is used.
• By text—The text you enter to identify a box
may be:
• The field name, if the box contains data from
a database.
• The text label, if the box contains static text,
such as frames or text labels.
• The box name assigned in Box Properties.
• For subform boxes, the table name.
In all cases, you need not spell out the entire
name, just enough to be unique.
Often, more than one box matches the text you
enter, for example a box displaying field
“molweight” within a frame labelled
“MolWeight.” In this case, preference is given
to the box connected to the database.
FORMEDIT controls the behavior of the SELECT
command. With FORMEDIT ON, SELECT affects
boxes. With FORMEDIT OFF, SELECT affects the
contents of those boxes.
SELECT and UNSELECT choose boxes to be
modified by editing operations. DELBOX is a
shortcut for FORMEDIT ON, followed by
SELECT, followed by Edit Clear. SETFIELD
connects a database field to an existing box; for a
button, it attaches a script name (see above
regarding script names). SETTEXT attaches a text
string to a box or replaces the one currently attached;
see box creation commands (above) for a list of what
the text strings mean for various box types.
ACTIVATE and DEACTIVATE are the same as
SELECT and UNSELECT, but work on subforms.
Following an ACTIVATE command, all subsequent
commands apply to the active subform and any
boxes it contains. The DEACTIVATE command is
required to once again refer to the main form and its
contents.
SCALE scales all items in the current form by the
percentage factor you specify. Use this to fit your
forms to different size screens. See
SCALE_TO_FIT below.
ChemFinder 8 • A-15
Box Manipulation Commands

Administrator
SCALE_TO_FIT scales all elements in the form
such that the string you specify will fit in the form at
the currently selected font size. See FONT below.
The table below shows examples of Box
Manipulation Commands:
Command Action
SELECT 11 11 select formula frame created
above
SELECT formu select formula data box created
above
SETFIELD 21
21 molweight
change field for formula data
box to molweight
Program Execution
Commands
CALL scriptname
DOS doscommand
EXEC wincommand
DDE ddecommand
LAUNCH filename
Program execution commands call up external
processes and pass data to them. All require an
argument, which may need multiple components.
CALL executes a specified CAL script. If the call is
made from within another script, when the called
script finishes executing it returns control to the
caller. CALL must be followed by a scriptname, as
described above.
DOS executes a DOS command line. Follow the
DOS keyword with any string you might type at a
DOS command prompt. If you do not type any
arguments after the DOS command, you get an
interactive command prompt window. You can use
this feature to manipulate files, execute programs or
batch files, get directory listings, format disks, etc.
During execution of the command, a command
prompt window appears on the screen; when
finished, the window goes away and control returns
to the calling script.
EXEC starts a Windows program and optionally
passes it command-line arguments. Follow the
EXEC keyword with any string you might use in the
Program Manager’s File Run command. This
command starts a program, but does not return from
it. To return to ChemFinder, you need to use Task
Manager or click in the ChemFinder frame window.
DDE sends a Dynamic Data Exchange message to a
specified application. Follow the DDE keyword
with three arguments:
• The service name—usually the name of the
recipient application.
• The topic name—a string recognized by the
recipient, identifying the nature of the message.
It is typically SYSTEM.
• The command—an instruction to the service
indicating what you want it to do.
Details of these components depend on the service
you’re addressing.
The table below shows examples of Program
Execution Commands:
Command Action
CALL
myscript
execute script file located in
scripts directory
A-16 • CambridgeSoft
Program Execution Commands

DOS erase
junkfile.dat
EXEC notepad
myfile.txt
DDE CHEM3D
CFWIN "open
benz.mol"
execute DOS command to
delete a file
execute Windows program
send DDE message to
qualified service
General Commands
MSG message
TIMEDMSG [n] W
FONT fontname [size [style r g b]]
SEEPTAB [decisecs]
QUIETCLOSE
HIDETABLE
SET
CLEAN [cleanup, tidy, redraw, denovo]
HELP
GET [v] section number, itemnumber
SOUND filename.wav
SYSMETRIC [v] index
MSG displays a message box with the specified text,
and waits for the user to click OK.
TIMEDMSG displays a message box similar to the
MSG command, but the message disappears
automatically after a specified number of seconds.
For example: TIMEDMSG 10 ″This message will
disappear automatically after 10 seconds.″
FONT changes the current font. Any boxes created
subsequently adopt this font. Follow the keyword
with a name from your Windows font list, followed
optionally by:
1. Font size in points (default is 8).
2. Style from the list below (default is 0, or plain
text).
3. Color; three values for red, green, and blue,
each ranging from 0 to 255 (default is 0,0,0, or
black).
Font styles are sums of bold (1), italic (2), and
underline (4). Thus a style value of 1 means bold, 3
means bold+italic, 6 means italic+underline, and so
on.
SEEPTAB briefly displays the periodic table
window, then closes it. The window will be
displayed for the amount of time specified (1
decisecond = 0.1 second). If the duration is omitted,
it will be displayed for four seconds.
QUITECLOSE closes the active form. This
command is similar to FILE CLOSE, but
automatically discards any changes instead of
prompting the user what to do.
HIDETABLE closes the Table View window for the
current form. If a subform is active, it returns the
subform to form view.
SET allows you to modify basic ChemFinder
settings, including most of those found in the
Preferences dialog and several that cannot be
accessed in any other way. See the online help for a
complete listing of parameters that can be SET.
CLEAN will attempt to standardize the bond lengths
and angles of the current molecule. It is the same as
opening the molecule in ChemDraw, and selecting
the Clean Up Structure command. The arguments
are optional.
HELP displays a list of all valid CAL commands.
The valid parameter types are listed for each
command, as is a brief description.
GET retrieves a value from the ChemFinder.ini file.
Follow the keyword with a variable name and the
section and item number of the value you want to
retrieve.
SOUND plays a .wav file you specify.
ChemFinder 8 • A-17
General Commands

Administrator
SYSMETRIC retrieves the specified system metric
into a variable.
The table below shows examples of General
Commands:
Command Action
MSG ″Click OK
to continue″
FONT Times 12 1
255 0 0
GET V1,4,5
File Commands
display message, wait for
click
change font to red 12point
Times bold
place the value of item
number 5 in section 4 into
the variable V1
SOUND beep.wav play the sound in the files
beep.wav
READMOL filename
WRITEMOL filename
WRITETEXT filename
READMOL and WRITEMOL operate on the
current molecule. These commands will work only
if there is at least one structure-related box
(structure, formula, or molweight) on the form, and
you are positioned to a valid entry in the database.
READMOL reads a specified structure file and
replaces the current molecule in the form.
WRITEMOL saves the current molecule to a
specified structure file; if the file doesn’t exist, it is
created, otherwise it is overwritten. For both
READMOL and WRITEMOL, the format of the file
is determined by its extension; for example,
benzene.cdx is a ChemDraw file.
WRITETEXT exports the current list as delimited
text with whatever delimiter is specified in the
Preferences dialog.
The table below shows examples of File
Commands:
Command Action
READMOL
benz.mol
WRITEMOL
saved.mol
WRITETEXT
hits.txt
read specified file to become
current molecule
write current molecule to
specified file
export current list to a text file
Database Commands
OPENDB [R / R / RE] dbname
CRETABLE tablename
DELTABLE tablename
SELTABLE tablename
CREFIELD fieldname
DELFIELD fieldname
SORT [D] fieldname
OPENDB opens a standard molecule database.
Specify a pathname to the .mdb file, or a name from
the ODBC Data sources list. You can specify the
mode of database opening:
• R—read-only
• E—exclusive
• RE—read-only and exclusive
CRETABLE creates tables in the current database.
DELTABLE deletes tables in the current database.
SELTABLE selects a table form the current database
and makes it the current working table for
subsequent field actions.
A-18 • CambridgeSoft
File Commands

CREFIELD creates fields in the current table in the
current database. You can specify the field type and
width in the CREFIELD command. The default text
field is 50 characters wide.
DELFIELD deletes fields in the current table in the
current database.
SORT sorts the database contents on the specified
field. The default sorts the database in ascending
order. You can specify descending order with D.
The table below shows examples of Database
Commands:
Command Action
CRETABLE MyTable
creates a new table
DELTABLE MyTable deletes a new table
Variable Commands
SETVAL [v] text
READVAL [v] filename
WRITEVAL [v] filename
INPUT [v] [prompt]
PASSWORD [v] [default]
GETDATA [v] box
PUTDATA box text
APPEND ON|OFF
APPENDVAL [v] [text]
INCREMENT [v]
DECREMENT [v]
LET v v op v
CAL has nine variables called V1, V2, ..., V9. These
are temporary storage locations you can use to move
information between form boxes and other data
sources.
Variable names can be substituted in any CAL
command. Any item shown in italics in a command
description may be replaced by the name of a
variable, prefixed with a dollar sign.
For example:
MSG messagemay be either:
MSG "An explicit message"
—a message explicitly coded into the script—or
MSG $V2
—a message taken from variable 2 at run time
You may concatenate variables, and variables and
literals together in CAL commands. You must add
both a leading and trailing dollar sign to the variable
name.
For example:
MSG$V2$$V1$
Displays a message box with the value of V2
immediately followed by the value of V1.
Most commands for manipulating variables take an
optional variable number as the first argument. If the
number is omitted, it is assumed to be 1.
SETVAL puts the specified text into a variable.
READVAL reads the contents of a text file into a
variable. WRITEVAL copies the contents of a
variable to a file.
INPUT displays a text input dialog, accepts data
from the user and stores it in a variable. An optional
prompt string is displayed in the box when it
appears.
PASSWORD is the same as INPUT, but displays all
characters as asterisks.
GETDATA retrieves the contents of a form box (as
long as it is not a structure) into a variable; see above
for how to identify a box. PUTDATA copies
ChemFinder 8 • A-19
Variable Commands

Administrator
specified text into a form box. Form names are casesensitive.
Be sure to use the same case as the form
box name into which you want to store data.
APPEND determines whether data in a storage
location is kept if other data is being moved there.
APPEND ON causes any subsequent data
movements to append new data to old; APPEND
OFF causes old data to be overwritten. This applies
to all variable commands except PUTDATA. The
default at program startup is APPEND OFF.
APPENDVAL is a shortcut designed to make it
easier to build string values. It is the same as setting
APPEND ON, doing a SETVAL, and then restoring
APPEND to its original state.
INCREMENT adds 1 to the value of a variable. Use
INCREMENT in loops.
DECREMENT subtracts 1 from the value of a
variable. Use DECREMENT in loops.
LET allows you to perform mathematical operations
on variables that contain integer or real-number
values. Only one operator per line is supported. It
recognizes the following operators:
• + for addition
• - for subtraction
• * for multiplication
• / for division
The table below shows examples of Variable
Commands:
Command Action
SETVAL "some
text"
SETVAL V2
"other text"
store text in V1
store text in V2
READVAL V9
tmpdata.txt
read text from file into V9
APPEND ON turn on append mode
WRITEVAL
output.txt
SETVAL V2
"append me"
Environment Variables
$INDEX
$RECNO
$NUM_RECS
$DTBA_NAME_LONG
$DTBA_NAME_SHORT
$FORM_NAME_LONG
$FORM_NAME_SHORT
$CFW_DIR
$FORM_DIR
append contents of V1 to
file
append text to contents of
V2
APPEND OFF turn off append mode
INPUT V2 "enter
new data"
GETDATA V3
molname
PUTDATA molname
″benzene″
prompt and get user input
to V2
copy data from molname
box to V3
store given string in
molname box
LET V3$V1+ $V4 sets V3 equal to the value
stored in V1 plus the value
stored in V4
A-20 • CambridgeSoft
Environment Variables

$SYSTEM_DIR
NOTE: To view a complete list of variables, click
Help on the Enter Cal Command dialog box.
ChemFinder provides several variables to allow you
to retrieve information about the current
ChemFinder environment. They cannot be set
directly, but are modified as a consequence of other
commands.
For example, the menu command:
Record Next
increments the current RECNO by 1.
The table below shows examples of Environment
Variables:
Command Action
SETVAL 1
$RECNO
SETVAL V1
$NUM_RECS
SETVAL V1
$DTBA_NAME_
LONG
SETVAL V1
$FORM_NAME_
SHORT
SETVAL V1
$SYSTEM_DIR
V1 now equals the number
of the current record
V1 now equals total
number of records in the
current list
V1 now equals, for
example
“c:\chemfinder\mydb.mdb
”
V1 now equals, for
example “mydb”
V1 now equals, for
example,
“c:\chemfndr\system”
Script-Only Commands
*text
:label
label:
GOTO label
IF v1 op v2 stmt
LOOP [count]
ENDLOOP
PAUSE [dseconds]
EXIT
INTERACTIVE ON / OFF
STEP ON / OFF
Script-only commands are useful only in script files,
not interactive CAL.
An asterisk (*) is used to mark a line as a comment
and not a command that should be executed.
Labels and GOTO give a mechanism for jumping
backwards in a script. A label may be any text string
starting or ending with a colon; it must appear prior
to any GOTO that references it.
IF is a standard conditional statement. It compares
two values according to an operator, and then
executes its final statement if the result is true. Valid
operators are:
= < > < >
LOOP begins a section of code that will execute
repeatedly, until ENDLOOP is reached. By default,
the number of times the code executes is equal to the
number of records in the current list, but you can
provide a specific count in the LOOP statement.
PAUSE temporarily stops the script from executing
for a specified number of tenths of a second. If no
number is given, the duration of the pause is 2
seconds.
EXIT ends the script immediately.
INTERACTIVE turns interactive mode on or off.
ChemFinder 8 • A-21
Script-Only Commands

Administrator
STEP toggles single-step (debugging) mode on and
off.
The table below shows examples of Script-Only
Commands:
Command Action
start: a label
IF $V1 = ""
MSG Empty
value!
PAUSE 100
GOTO start
provide an error message if the
variable V1 is empty
pause 10 seconds
go to specified label
LOOP 10 begin loop to repeat ten times
PAUSE
ENDLOOP
pause the default time: 2
seconds
return to LOOP statement until
done
NOTE: Script commands are subject to change.
See the Readme for up-to-date information.
A-22 • CambridgeSoft
Script-Only Commands

Appendix E: Technical Support
Overview
CambridgeSoft Corporation (CS) provides technical
support to all registered users of this software
through the World Wide Web (WWW), and through
our Technical Support department.
Our Technical Support pages on the WWW contain
answers to frequently asked questions (FAQs), in
addition to some general information about our
software. You can access our Technical Support
page using the following address:
http://www.cambridgesoft.com/support
If you don’t find the answers you need on the
WWW, please complete the following tasks before
contacting the Technical Support Department.
1. Check the ReadMe file for known limitations or
conflicts.
2. Check the system requirements for the software
at the beginning of this User’s Guide.
3. Read the Troubleshooting section of this
appendix and follow the possible resolution
tactics outlined there.
4. If all your attempts to resolve a problem fail, fill
out a CS Software Problem Report Form at:
www.cambridgesoft.com/support/mail
• Try to reproduce the problem before contacting
us. If you can reproduce the problem, please
record the exact steps that you took to do so.
• Record the exact wording of any error messages
that appear.
• Please record anything that you have tried to
correct the problem.
You can deliver your CS Software Problem Report
Form to Technical Support by the following
methods:
E-mail:
http://www.cambridgesoft.com/support/mail
or support@cambridgesoft.com
Fax: 617 588-9390
Mail:
CambridgeSoft Corporation
ATTN: Technical Support
100 CambridgePark Drive
Cambridge, MA 02140 USA
Serial Numbers
When contacting Technical Support, you must
always provide your serial number. This serial
number was on the outside of the original product
box and is the number that you entered when you
installed ChemFinder ChemOffice for the first time.
If you have thrown away your box and lost your
installation instructions, you can find the serial
number as follows:
• With ChemFinder launched, choose About CS
ChemFinder from the Help menu. The serial
number will appear at the middle left of the
About box.
Troubleshooting
This section describes steps you can take that affect
the overall performance of ChemFinder , as well as
steps to follow if your computer crashes when using
a CS software product.
ChemOffice 8 • A-23
Serial Numbers

Administrator
Performance
Below are some ways you can optimize the
performance of ChemFinder :
1. Install more physical RAM. The more you
have, the less ChemFinder will have to access
your hard disk to use Virtual Memory.
2. Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
your hard disk to be used as RAM. However,
the time for swapping between the application
and the hard disk is slower than swapping with
physical RAM. You can change VM for
Windows 95/98/NT 4.0 on the System control
panel, Performance tab.
System Crashes
should never crash, but below are the steps you
should go through to try to resolve issues that cause
computer crashes while using a CS software
product.
3. Restart Windows, then try to reproduce the
problem. If the problem does reoccur, keep
reading.
4. The most common conflicts for Windows users
concern Video Drivers, Printer Drivers, screen
savers, and virus protection. If you do end up
needing to contact us, be sure to determine what
type and version of drivers you are using.
Video Driver-related problems: If you are
having problems with the display of
ChemFinder , try switching to the VGA video
driver in the display Control Panel (or System
Setup) and retest the problems. If using a
different driver helps, your original driver may
need to be updated. Contact the maker of the
driver and obtain the most up-to-date driver. If
you still have trouble, contact us with the
relevant details about the original driver and the
resulting problem.
Printer Driver-related problems: Try using a
different printer driver. If using a different
driver helps, your original driver may need to
be updated-contact the maker of the driver and
obtain the most up-to-date driver. If you still
have trouble, contact us with the relevant details
about the original driver and the resulting
problem.
5. Try reinstalling the software. Before you
reinstall, uninstall the software and disable all
background applications, including screen
savers and virus protection. Use the
Add/Remove Control Panel.
6. If the problem still occurs, fax, e-mail, or use
the WWW at:
http://www.cambridgesoft.com/support/mai
l
to submit the details of the problem to Technical
Support.
A-24 • CambridgeSoft
Troubleshooting

Index
- operator (in queries) 86
Symbols
% wildcard character 86
( operator in formula queries 87
* wildcard character 86
< operator in queries 86
= operator in queries 86, 87
> operator in queries 86
\ operator in queries 95
Numerics
3D searching 1, 91
3D structure display 1, 50
A
A (any atom type) A5
Access
attaching tables from 70
DAO 6
manipulating .mdbfiles 132
multi-user 66
Read-only 65
secured 66
using with ChemFinder 132
ActiveX control
Chem3D 1
ChemDraw 1, 35
ACX information, finding 136
ADD indicator
description 11
when displayed 12, 76
Add New Record command 76
Adding
data 76
data to database 112
fields 72, 132
menu to data box 51
multiple structures to forms 73
records 12, 76
scroll bars 51
structures 76
tables 82, 106, 132
Aligning objects 57
Anchored substring text queries 86
AND operator
hit lists 96
queries 86, 95
Annotations
showing 120
Anti-aromaticity A4
Append data 112
Append to existing data 113
Appending data on import 112
Aromaticity A4
ASCII file, exporting 118
Atom labels, colors 52
Atom lists 98, A5
Atom not-lists A5
Atom numbers, finding 85
Atom properties A5
Atom types
A (any) A5
in queries A1
link node 98
M (metal) A5
overview 98
Q (heteroatom) A5
special A5
X (halogen) A5
Atom-atom mapping
reaction queries 93
Attaching
non file-based databases 71
tables from file-based database 70
ChemFinder 8 Index • i

Administrator
B
tables from other applications 70
Backing up 75
Bitscreen A11
Bond length, uniform 120
Bond numbers, finding 85
Bond properties
in queries A7
ring/chain A8
Bond types
double either A2
in queries A1
overview 98
special A7
Boolean operations
in queries 86
on hit lists 96
Box creation commands, CAL A14
Box Manipulation commands, CAL A15
Boxes
changing styles 49
creating 44
deleting 56
font 52
hiding or showing 52
moving 55
properties 48
resizing 56
selecting 55
style 48
Bring to Front 57
Browsing
overview 7
with record tools 67
Btrieve 6, 70
Button
attaching to scripts 130
creating 47
C
CAL
execute with button 47
executing command with button 130
Help 129
overview 128
CambridgeSoft web site, accessing 137
Camsoft.com 137
Cells 6
cfs file extension 129, 131
cfw file extension 44, 132
Chain bonds A8
Change views 84
Changing box style 49
Charges in queries A2
Check valences 125
Chem3D
ActiveX control 1
Chem3D, viewing models 81
ChemClub.com 138
ChemDraw
ActiveX control 1, 8, 35
editing structures 79, 80
format, viewing in 49
ChemFinder
closing 17
overview 5
provided directories 5
starting 12
window components 9
ChemFinder Automation Language, see CAL A13
ChemFinder.com 135
Chemical markers, displaying 84
Chemicals, purchasing online 136
ChemNews.Com 137
ChemOffice SDK, accessing 138
ChemStore.com 136
Cleaning structures 79
Clearing forms 83
Closing ChemFinder 17
Color Preferences 121
Columns
adding in 132
changing formats 132
definition 6
Combined searching 95
Commit Changes command 77, 79, 80
Committing changes vs. saving 43
ii • Index ChemFinder

Communicating with other applications
using DDE 130
using OLE Automation 132
using scripts 130
Concurrent access 66
Connection Table files 109
Continuous forms 84
Conventions 2
Counterions 80
Create Database button 68
Create Table dialog box 69
Creating
boxes 44
button 47
data box menu 51
data boxes 45
database, overview 5
databases 68
form, overview 5
forms, automatically 42
forms, manually 44
forms, overview 39
multiple tables 82, 106
new form 44
picture boxes 47
scripts 129
subforms 103
tables 69
tabs 54
text 46
Creating frames 45
Current hit list, exporting 118
Current list
counter 12
description 11
exporting 117
retrieving all records 85
size 12
Current Mol as a Query command 91
Current record 11, 12
Customizing
fonts 52
numbers 53
text 52
toolbars 126
ChemFinder 8 Index • iii
D
Data
adding 76
committing 77, 82
deleting 82
displaying 44
editing 78
entering 76, 82
exporting 117
sorting 78
Data Box tool 44
Data boxes
creating 45
description 11
hiding or showing 52
Data items 6
Data Source
command 39, 70
ODBC 70
selecting 39, 70
Data Table
columns 101
description 11
displaying 67
moving columns 68
Page Setup 101
printing 100
resizing columns 68
resizing rows 68
sorting 78
subforms 106
Database commands, CAL A18
Database logon 66
Database size 12
Databases
adding structures119 74
backing up 75
cells 6
columns 6
compressing 132
creating 68
data items 6
fields 6

Administrator
flat-file 7, 68
management scheme 6
model 6
moving 75
multiple tables 71
non-chemical 70, 74
opening 39, 65
overview 5
read-only 12
records 6
resetting 79
rows 6
selecting 39
tables 7
vs. forms 7
Date fields 72
Dates
display preferences 87
queries 86
dBASE 6, 70
DDE, to communicate with other applications 130
Debugging scripts 129
Delete Record command 82
Deleting
boxes 56
contents of fields 82
data 82
fields 73
objects 56
records 82
tables 70
Delimited text files
exporting 118
headers 118
directories provided 5
Disabling security 63
Display preferences 119
Distributing objects 58
Documentation web page 137
Double either bond type A2
Duplicating records 77
E
Editing
data 78
fields 78
forms 55
forms, overview 39
labels 46
overview 7
redo 56
structures 79
structures with ChemDraw 80
undo 56
Editing form layout 58
Editing tabs 54
Element Editor 128
Element ranges in queries 87
Elements
colors 128
physical data 128
selecting 127
Enter Query command 83, 85
Enter Script Command dialog box 128
Enter the Label dialog box 47
Entering
data 76, 82
queries 12, 83
reaction queries 92
structures 76
Entering query 83
Environment Variables, CAL A20
Exact text match queries 86
Excel
communicating with using CAL 128
communicating with using DDE 131
Excel, security setting to export to 61
Exiting 17
Exporting
ASCII file 118
current hit list 96, 118
current list 117
data 117
delimited text files 118
Security settings 63
tables 132
iv • Index ChemFinder

F
FAQ
online, accessing 137
Technical support A23
Fields
adding 132
changing formats 132
date 72
deleting 73
deleting contents 82
editing 78
formula 69
illustration 6
integer 72
memo 72, 114
Mol_ID 69
molecular weight 69
picture 72
picture, description 72
real 72
structure 69
text 72, 114
width 114
File Commands, CAL A18
File extensions 75
File Formats
MDL A4
File formats, supported 109
File-based databases, attaching tables 70
Files, log 115
Find command 83
Find Current Molecule command 91
Find List 88
Find list 88
Find Text command 72
Finding atom and bond numbers 85
First Record command 67
Fit to box 120
Fixed labels 45, 50
Flat-file databases 7, 68
Fonts, customizing 52
Form permissions, change from earlier versions of
ChemFinder 61
Form toolbar 11, 44
Form tools 44
Forms
adding multiple structures 73
clearing 83
creating automatically 42
creating manually 44
editing 55
layout, changing 58
moving 75
multiple, for one database 7
overview 5
Page Setup commands 100
printing 100
saving 43
setting security 59
style 42
vs. databases 7
window 9
Formula field 69
Formula queries 87
Formulas
element ranges, in queries 87
input rules A9
parentheses in queries 87
query rules 87
sorting 78
FoxPro 6, 70
Frame tool 45
Framed Box tool 45
Framed Boxes
creating 46
description 11
Frames 45
Frames, creating 45
Framing pictures 121
Free sites, in queries A6
Frequently asked questions A23
Full Structure searching 90
ChemFinder 8 Index • v
G
General CAL commands A17
Generics hit only generics 124
Go To Record command 67

Administrator
Grid Tool 44
Grids
setting spacing 42
spacing 121
H
Headers, delimited text files 118
Help
CAL 129
Windows 2
Hiding annotations 120
Hiding data boxes 52
Hit any charge on carbon 123
Hit any charge on heteroatom 123
Hit lists
Boolean operations 96
current 12
intersecting 96
joining 97
replacing 96
restoring 96
saved as text files 96
saving 96
Home page, CambridgeSoft 137
How to use this guide 1
Hydrogens
added to structures 80
in queries A2
I
ID queries 88
Identity Searching 90
Implicit hydrogens
added to structures 80
in queries A7
Importing
append to existing data 113
appending 112
changing field definition 114
hit lists 96
log files 115
merging 112
overwriting 112
RDFiles 111–112
replace existing data 113
SDFiles 111–112
Security settings 63
skip entry 113
specifying location 116
tables 132
Importing structures 110
Integer fields 72
Integrated products 1
Intermediates
queries 94
searching 92
Internet, CambridgeSoft web site 137
Intersect with current list 96
ISIS/Graphic files 109
ISIS/Sketch files 109
Isotopes A3
vi • Index ChemFinder
J
Jet database engine 6
L
Lab supplies, purchasing online 136
Labels
buttons 130
editing 46
fixed 45, 50
fonts 52
live 50
Last Record command 67
Launching ChemFinder 12
Layout Tool 44
layout, form, changing 58
ldb file extension 132
Link Node 98
Linking subforms to main forms 103
Live labels 50
Locating atom and bond numbers 85
Log files 115
Logon, database 66

M
M (metal) A5
Main Form 11
Main toolbar 11, 44
Management scheme, databases 6
Mapping atoms in reaction queries 93
Margins 100
Match stereochemistry 124
Mathematical operators, in CAL command A20
mdb file extension 75, 132
MDL File Formats A4
MDL Molfiles 109
MDL RXNFiles 109
Memo fields 72, 114
Menu Bar 11
Menu commands, CAL A13
Menu, adding to data box 51
Merge data 112
Merging data on import 112
Microsoft Jet database engine 6
Models, viewing using Chem3D 81
Modifying data 78
Mol_ID field 69
Molecular formula queries 87
Molecular weight field 69
Moving
boxes 55
forms and databases 75
MS Access Workgroup information 59
msi file extension 75, 132
MSI Molfiles 109
mst file extension 75, 132
Multiple structures, adding to forms 73
Multi-step reactions 92
Multi-user access 66
N
New form, creating 44
New Record indicator 11
Next Record command 67
No implicit H on metals 125
Non file-based databases, attaching 71
Normalization, in queries A4
Numbers, customizing 53
Numeric format 53
Numerical queries 86
ChemFinder 8 Index • vii
O
Objects
aligning 57
distributing 58
spacing 58
Objects, deleting 56
ODBC
adding structures to existing sources 74
overview 6
selecting data sources 70
OLE Automation
communicating with other applications 132
overview 132
Online Help, see Help
Online Menu
Browse ChemStore.com 136
CambridgeSoft Home Page 137
ChemOffice SDK 138
CS Chem3D Technical Support 137
Lookup Suppliers on ChemStore.com 135
overview 135
Register online 138
Open Database button 39
Open last form on startup 126
Opening
ChemFinder 12
databases 39, 65
hit lists 96
pictures 47
Opening databases 65
Opening options 125
Operators, in CAL commands A20
OR operator
hit lists 97
queries 86
Oracle
attaching tables 70
driver 6
Other applications, attaching tables from 70

Administrator
Other applications, communicating with
using DDE 130
using OLE Automation 132
using scripts 130
Overriding security 63
Overwrite data 112
Overwriting data on import 112
P
Page Setup
forms 100
tables 101
Page Setup command 100
Paradox 6, 70
Password 60, 66
Periodic Table 127, A2
Permit extraneous fragments in full structure
searches 123
Picture boxes, creating 47
Picture fields, description 72
Picture tool 47
Pictures
cannot be edited 81
framing 121
not chemically significant 81
preferences 121
reading 47
saving 48
searching 81
storing ChemDraw drawing as 81
structures 81
updating 47
Plain Text tool 46
Portal database 76
Precision, numerical queries 86
Preferences
color 121
date display 87
display 119
grid spacing 121
open 125
picture display 121
Recent File List Size 126
registration 125
registration of structures 125
search details 122
search type 121
setting 119
stereochemistry 124
structure display 119
Previous Record command 67
Print command 100
Print Preview command 101
Printing
layout 100
margins 100
overview 100
scale to Fit 100
Products
queries 94
searching 92
Program Execution commands, CAL A16
Properties dialog box, opening 61
viii • Index ChemFinder
Q
Q (heteroatom) A5
QRY indicator 11, 12
Queries
anchored substring 86
atom lists 98, A5
atom not-lists A5
atom properties A1
atom properties in A5
atom types 98, A1
bond properties A7
bond types 98, A1
Booleans 86
charges A2
dates 86
entering 12, 83
exact structure 90
exact text match 86
finding current structure 91
formulas 87
free sites A6
Full Structure 90
hydrogens A2
ID 88

Identity 90
implicit AND between fields 86, 95
implicit hydrogens A7
inequalities 86
intermediates 94
isotopes A3
multiple fields 95
multiple fragment 89
multiple substructures 99
normalization A4
numbers 86
overview 83
precision 86
products 94
progress display 88
radicals A2
ranges 86
reactants 94
reactions 92
refining 85
Similarity 90
similarity rules A11
special atom types in A5
special bond types A7
SQL 86, 95
stereochemistry 91, A3
stopping 84
structural similarity 90
structures 88
subforms 106
submitting 83
substituents A2, A5
substructure 89
text 86
unsaturation A7
using current structure 91
wildcards 86
Query fragments can overlap in target 123
Query properties
conflicting A1
overview A1
Questel F1D files 109
Questel F1Q files 109
Quick Reference Card, description 2
Quitting 17
ChemFinder 8 Index • ix
R
Radicals, in queries A2
Ranges, in queries 86
RDFiles
exporting 117
importing 111–112
Importing, Security settings 63
Reactants
queries 94
searching 92
Reaction centers
bond type A11
bond types A8, A9
display preferences 120
overview 92
Reaction queries 92
atom-atom mapping 93
creating 92
intermediates 94
overview 9
products 94
reactants 94
Reaction query must hit reaction center 93, 124
Reactions
centers 92
multiple-step 92
Read File command 47
READ indicator 11, 12
Read Structure command 110
Read-only access 65
Real fields 72
Recent file list size, setting 126
Record
toolbar, browsing with 67
toolbar, description 11
toolbar, illustration 65
Record Number dialog box 67
Record tool 67
Records
adding 12, 76
current 11, 12
deleting 82
duplicating 77

Administrator
illustration 6
moving between 67
retrieving all 85
Redo 56
Redo command 82
Refining queries 85
Registration of structures, preferences 125
Registration preferences 125
Registration, online 138
Relational databases 7, 71, 103
Relative stereochemistry 1
Relative Tetrahedral Stereochemistry 125, A3
Renaming tabs 55
Replace current list 96
Replace existing data 113
Requirements
Windows 3
Resetting database 79
Resetting the database 85
Resizing boxes 56
Resonance, forms A4
Restore List command 96
Restore Previous List command 85
Restoring changes 56
Results, viewing 84
Reversing changes 56
Ring bonds A8
Rows 6
S
Sample code, SDK web site 138
Sample directory 5
Save command
effect on changes 43
not needed when editing data 77
Save dialog box 43
Save List command 96
Save Structure command 109
Saving
changes to forms 17
forms 43
hit lists 96
pictures 48
subform 43
vs. committing119 43
Scale to Fit, when printing 100
Scaling structures 120
Script-Only Commands, CAL A21
Scripts
attaching to buttons 130
communicating with other applications 130
debugging 129
executing 129
using in subforms 106
writing 129
Scroll bars, adding 51
SDFiles
exporting 117
importing 111–112
Importing, Security settngs 63
SDK Online, accessing 138
SDK, www address 128
Search details preferences 122
Search toolbar 11, 83
Search Type preferences 121
Searching
3D 1
see also Queries
for numbers 86
online for chemical information 135
overview 83
Secured access 66
Securing forms 59
Security
disabling 63
MS Access Workgroup information 59, 60
options 60
overriding 63
setting options 59
Selecting
a database 39
boxes 55
Selection tool 55
Send to Back 57
Serial number A23
Setting
box properties 48
numeric format 53
Setting alerts 125
x • Index ChemFinder

Setting preferences 119
Shortcut menu 11
Show opening dialog 126
Show reaction centers 120
Showing
data boxes 52
Showing annotations 120
Similarity searching 90
rules A11
Skip entry 113
SMD files 109
Sorting
data table 78
fields 78
formulas 78
in languages 79
permanently 132
structures 78
text 78
Sorting data 78
Special atom types, list of A5
SQL 95
SQL Server 6
Starting ChemFinder 12
Status Bar 11, 12
Stereochemistry
allenic, not supported A3
cis/trans double bonds A3
octahedral, not supported A3
overview 91
queries A3
relative tetrahedral 125, A3
search preferences 124
square planar, not supported A3
tetrahedral A3
trigonal bipyrimidal, not supported A3
Stopping a query 84
Structure columns 73
Structure display
3D 1
Structure display preferences 119
Structure field 69
Structures
adding 76
adding to non-chemical database 74
checking chemistry 80
chemically-significant text 80
cleaning 79
editing 79, 80
entering 80, 125
file formats 109
importing 110
pictures 81
queries 88
query properties A1
red highlighting in queries 89
registration 125
scaling 120
sorting 78
Style, box, changing 49
Styled text 81
Subforms
creating 103
data table 106
description 12
linking 103
linking fields 103
overview 103
searching 106
switching between forms and data tables 106
Tutorial 36–38
using scripts 106
Submitting query 83
Substituents, in queries A2, A5
Substructure searching 89
Substructure searching, overview 89
Supplier, finding online 135
Support, technical A23
Supported file formats 109
Switch views 84
System directory 5
System requirements 3
ChemFinder 8 Index • xi
T
Table header 12
Table view 84
Tables
adding 82, 106, 132
changing names 132

Administrator
creating 69
definition 7
deleting 70
exporting 132
importing 132
Tabs
creating and editing 54
renaming 55
Tanimoto
coefficient A12
equation A11
similarity as search criteria 7
Tanimoto similarity A11
Technical support A23
Temporary database 76
Tetrahedral stereo center hits 124
Text
as structures 80
creating 46
customizing 52
queries 86
sorting 78
Text fields 72, 114
Text Format toolbar 52, 81
Text, styled 81
Title Bar 12
Toolbars
customizing 126
description 11
text 81
Tools
Data Box 44
Frame 45
Framed box 45
Grid 44
Layout 44
Picture 47
Plain Text 46
record 67
Transferring information to other computers 75
Troubleshooting
guidelines A23
online 137
xii • Index ChemFinder
U
Undo 56
Undo Changes command 77, 79, 82
Uniform bond length 120
Union with current list 97
Unsaturation, in queries A7
User’s guide, online 137
Username 60, 66
V
Valence
charged atoms A2
non-standard state 125
unfilled A2
Valences, check 125
Variable Commands, CAL A19
View format for structures, selecting 49
Viewing
chemical markers 84
continuous forms 84
switching views 84
table 84
Viewing models using Chem3D 81
Viewing results 84
Visual Basic 6, 132
W
Web site, CambridgeSoft, accessing 137
Width of fields 114
wildcard
% 86
* 86
Windows Help 2
Windows metafiles 44, 47, 48
wmf 48
X
X (halogen) A5

Desktop Software
Enterprise Solutions
Research & Discovery
Applied BioInformatics
Knowledge Management
Chemical Databases

ChemOffice WebServer
Oracle Cartridge
E-Notebook Enterprise
Document Manager
Discovery LIMS
21CFR11 Compliance
Desktop
E-Notebook
Enterprise
Document
Manager
Enterprise
Discovery
LIMS
21CFR11
Compliance
CAMBRIDGESOFT
ChemOffice Desktop to
ChemOffice
E-Notebook
ChemDraw
Chem3D
ChemFinder
ChemInfo
KNOWLEDGE
MANAGEMENT
RESEARCH &
DISCOVERY
Registration
System
Formulations
& Mixtures
DESKTOP SOFTWARE
Success begins at the desktop, where scientists use ChemDraw and ChemOffice to
pursue their ideas and communicate with colleagues using the natural language of
chemical structures, models, and information. In the lab, scientists capture their
results by organizing chemical information, documents, and data with E-Notebook.
Chem3D modeling and ChemFinder information retrieval integrate smoothly with
ChemOffice and Microsoft Office to speed day-to-day research tasks.
ENTERPRISE SOLUTIONS
Just as ChemOffice supports the daily work of the individual scientist,
enterprise solutions and databases, built on ChemOffice WebServer, and Oracle
Cartridge help organizations collaborate and share information.
KNOWLEDGE MANAGEMENT
Inventory
Manager
WebServer
Research organizations thrive when information is easily captured, well organized,
and available to others who need it. E-Notebook Enterprise streamlines daily record
keeping with rigorous security and efficient archiving, and facilitates searches by text
and structure. Document Manager organizes procedures and reports for archiving
and chemically-intelligent data mining. Discovery LIMS tracks laboratory requests, and
21CFR11 Compliance implements an organization’s regulatory compliance processes.

SOLUTIONS
Enterprise Solutions
CombiChem
Enterprise
Oracle Cartridge
or SQL DB
Registration System
Formulations & Mixtures
Inventory Manager
CombiChem Enterprise
BioAssay HTS
BioSAR Browser
ChemACX Database
ChemSAR Properties
The Merck Index
Chemical Databases
Consulting Development
Support & Training
APPLIED
BIOINFORMATICS
BioAssay
HTS
BioSAR
Browser
ChemACX
Database
ChemSAR
Properties
CHEMICAL
DATABASES
The Merck
Index
Chemical
Databases
RESEARCH & DISCOVERY
Managing the huge data streams of new lab technology is a key challenge.
Registration System organizes information about new compounds according to an
organization's business rules, while Inventory Manager works with Registration System
and chemical databases for complete management of chemical inventories.
CombiChem Enterprise and Formulations & Mixtures are also important parts of
research data management.
APPLIED BIOINFORMATICS
Finding structural determinants of biological activity requires processing masses of
biological assay data. Scientists use BioAssay HTS and BioSAR Browser to set up
biological models and visualize information, to generate spreadsheets correlating
structure and activity, and to search by structure.
CHEMICAL DATABASES
Good research depends on reference information, starting with the structure-searchable
ChemACX Database of commercially available chemicals. The Merck Index 13th
Edition and other databases provide necessary background about chemicals, their
properties, and reactions.
CONSULTING & SERVICES
CambridgeSoft's scientific staff has the industry experience, and chemical and
biological knowledge to maximize the effectiveness of your information systems.

Software
Applications & Features
Databases
ChemDraw/Spotfire Win
*BioAssay Pro Win
Purchase/Excel Win
CombiChem/Excel Win
ChemFinder/Office Win
ChemDraw/Excel Win
Name=Struct Win/Mac
Struct=Name Win/Mac
ChemNMR Win/Mac
CLogP/ChemDraw Win/Mac
BioArt Win/Mac
Structure Clean Up Win/Mac
Polymer Draw Win/Mac
LabArt Win/Mac
ChemSAR/Excel Win
3D Query Win
MOPAC/Chem3D Win
GAMESS Client Win
Gaussian Client Win
Tinker/Chem3D Win
*CAMEO/ChemDraw Win
*The Merck Index Win
*ChemACX Ultra Win
ChemSCX Win
ChemMSDX Win
*ChemINDEX Ultra Win
ChemRXN Win
NCI & AIDS Win
*Available Separately
CS ChemOffice
Software Suites
ChemOffice Ultra
Includes
*ChemDraw Ultra Win/Mac
*ChemDraw Pro Win/Mac
*ChemDraw Std Win/Mac
*ChemDraw Plugin Pro Win/Mac
*Chem3D Ultra Win
*Chem3D Pro Win
Chem3D Std Win
*Chem3D Plugin Pro Win
*E-Notebook Ultra Win
ChemFinder Pro Win
ChemFinder Std Win
ChemOffice Pro
ChemDraw Ultra
ChemDraw Pro
ChemDraw Std
Chem3D Ultra
E-Notebook Ultra

Desktop to Enterprise Solutions
ChemOffice Ultra includes it all, providing
ChemDraw Ultra, Chem3D Ultra, E-Notebook
Ultra, ChemFinder, CombiChem, BioAssay and
The Merck Index, for a seamlessly integrated suite
for chemists.Use ChemDraw/Excel and ChemFinder/
Word for Microsoft Office integration. Predict spectra,
use Name=Struct, and visualize 3D molecular surfaces
and orbitals with MOPAC. Use the ChemDraw and
Chem3D Plugins to publish your work or to query
databases on the web.
ChemOffice WebServer enterprise solutions and databases help
organizations collaborate on shared information with ChemDraw webbased
interface and Oracle Cartridge security.
Knowledge Management with E-Notebook Enterprise streamlines
daily record-keeping with rigorous security and efficient archiving.
Document Manager indexes chemical structure content of documents
and folders.
Research & Discovery efforts are improved with Registration System
by organizing new compound information, while Inventory Manager
works with chemical databases for complete management of chemical
inventories.
Applied BioInformatics scientists use BioAssay HTS and BioSAR
Browser to set up biological models and visualize information, to generate
spreadsheets correlating structure and activity, and to search by structure.
Chemical Databases include the ChemACX Database of commercially
available chemicals, The Merck Index 13th edition, and other databases.
Consulting & Services includes consulting development, technical
support, and education training for pharmaceutical, biotechnology, and
chemical customers, including government and education, by
CambridgeSoft’s experienced staff.
ChemOffice WebServer
Enterprise Solutions & Databases
• Oracle Cartridge & Database Webserver
Knowledge Management
• E-Notebook Enterprise, Document Mgr,
Discovery LIMS & 21CFR11 Compliance
Research & Discovery
• Registration System, Formulations & Mixtures,
Inventory Manager & CombiChem Enterprise
Applied BioInformatics
• BioAssay HTS & BioSAR Browser
Chemical Databases
• The Merck Index, ChemACX & ChemSAR Properties
ChemOffice Ultra
Ultimate Drawing, Modeling & Information
• Adds The Merck Index, E-Notebook, CombiChem,
MOPAC, BioAssay & ChemACX to Office Pro
ChemOffice Pro
Premier Drawing, Modeling & Information
• Includes ChemDraw Ultra, Chem3D Pro,
ChemSAR/Excel, ChemFinder Pro,
ChemINDEX & ChemRXN databases
Also Available Separately…
ChemDraw Ultra
Ultimate Drawing, Query & Analysis
• Adds ChemDraw/Excel, ChemNMR, Name=Struct,
AutoNom & ChemFinder /Word to ChemDraw Pro
• ChemNMR, Stereochemistry, Polymers & BioArt
ChemDraw Pro
Premier Drawing & Database Query
• Define complex database queries
• ISIS/Draw & Base compatible via copy/paste
• Structure CleanUp and Chemical Intelligence
Chem3D Ultra
Ultimate Modeling, Visualization & Analysis
• Adds MOPAC, CLogP, Tinker, ChemProp,
ChemSAR & Chem3D Plugin to Chem3D Pro
• Advanced modeling & molecular analysis tool
E-Notebook Ultra
Ultimate Journaling & Information
• E-Notebook, ChemDraw Std, Chem3D Std,
ChemDraw/Excel & CombiChem/Excel
• Includes ChemFinder, ChemFinder/Word,
ChemINDEX & ChemRXN databases
Some features are Windows only.
All specifications subject to change without notice.

CS E-Notebook
Electronic Journal Journal
and Information
E-Notebook Ultra streamlines daily record keeping tasks of research scientists, maintains live chemical
structures and data, and saves time documenting work and retrieving chemical information. E-Notebook combines
all of your notebooks into one and sets up as many project notebooks as you need, organized the way you
work. Notebook pages include ChemDraw documents, Excel spreadsheets, Word documents and spectral data.
E-Notebook automatically performs stoichiometry calculations on ChemDraw reaction pages. Search by structure,
keyword, dates and other types of data. Maintain required hardcopy archives by printing out pages.
Information cannot be accidentally modified. Spectral controls from Thermo Galactic are available.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
BioAssay Pro, available in ChemOffice Ultra, allows for flexible storage and retrieval of biological data. It
is designed for complex lead optimization experiments and supports almost any biological model.
Scanned Images in
Notebook Pages
Automatic
Stoichiometric
Calculations
DESKTOP

SOFTWARE
E-Notebook Ultra
Ultimate Journaling & Information
• Advanced search and structure query features
• Stores structures and models for easy retrieval
• Stores physical and calculated data
• Search by substructure, including stereochemistry,
using ChemDraw
• Search and store chemical reaction data
• CombiChem/Excel combinatorial libraries
• Integration with ChemDraw and Chem3D
• Import/export MDL SD & RD files
CombiChem/Excel
Combinatorial Chemistry in Excel
• Generate combinatorial libraries
•Choose starting materials & reaction schemes
•View structures & track plate/well assignments
ChemFinder Pro
Premier Searching & Information
• Advanced search & structure query features
• Stores structures & reactions along with calculated data & associated information
• Search by substructure including stereochemistry using ChemDraw
• Integration with ChemDraw & Chem3D
•Import/export MDL SD & RD files
ChemInfo Std
Reference & Reaction Searching
• ChemINDEX for small molecule information
• ChemRXN for reaction databases
BioAssay Pro
Biological Assay Structure Activity
• Set up biological models & visualize information
• Search data by structure to isolate key structural determinants of biological activity
•Tabulate & analyze structure-activity relationships with spreadsheet templates
•Available in ChemOffice Ultra
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CS ChemDraw
Chemical Structure Drawing Standard
DESKTOP
ChemDraw Ultra adds ChemDraw/Excel, ChemNMR, Name=Struct, Beilstein’s AutoNom, CLogP and
ChemFinder/Word to ChemDraw Pro. With rich polymer notation, atom numbering, BioArt templates, and
modern user interface, ChemDraw is more powerful than ever before. Create tables of structures, identify and
label stereochemistry, estimate NMR spectra from a ChemDraw structure with structure-to-spectrum
correlation, obtain structures from chemical names, assign names from structures, and create multi-page
documents and posters.
ChemDraw Pro will boost your productivity more than ever. Draw publication-quality structures and
reactions. Publish on the web using the ChemDraw Plugin. Create precise database queries by specifying atom
and bond properties and include stereochemistry. Display spectra, structures, and annotations on the same
page. Use the Online Menu to query ChemACX.Com by structure, identify available vendors, and order online.
Structure-to-Spectrum
NMR Correlation
Stereochemistry

SOFTWARE
ChemDraw Ultra
Ultimate Drawing, Query & Analysis
• Adds ChemDraw/Excel, ChemNMR, Name=Struct,
AutoNom & ChemFinder/Word to ChemDraw Pro
• Name=Struct/AutoNom creates structures from
names & vice versa
• ChemNMR predicts 1 H & 13 C NMR line spectra
with peak-to-structure correlation
• Polymer notation based on IUPAC standards
• ChemDraw/Excel brings chemistry to Excel
ChemDraw Pro
Premier Drawing & Information Query
• Query databases precisely by specifying atom & bond properties, reaction centers,
substituent counts, R-groups & substructure
• Read ISIS files with Macintosh/Windows cross-platform compatibility
• Structure Clean Up improves poor drawings
• Display spectra from SPC and JCAMP files
• Chemical intelligence includes valence, bonding & atom numbering
• Right-button menus speed access to features
ChemDraw Std
Publication Quality Structure Drawing
• Draw and print structures & reactions in color,
and save as PostScript, EPS, GIF, SMILES & more
• Collections of pre-defined structure templates
• Large choice of bonds, arrows, brackets, orbitals, reaction symbols & LabArt
• Style templates for most chemical journals
• Compatible with Chem3D, ChemFinder, ChemInfo, E-Notebook & Microsoft Office
ChemDraw Plugin
Advanced WWW Structure Client
• Embed live ChemDraw documents in WWW pages
•Works with Netscape & Internet Explorer
• Included with ChemDraw Ultra & Pro
SYSTEMS & LANGUAGES
Windows & Macintosh English, Japanese, French, German
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-10.1
Some features are Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CS Chem3D
Molecular Modeling and Analysis
Chem3D Ultra includes MOPAC, Tinker and set-up/control interfaces for optional use of GAMESS and
Gaussian. Estimate advanced physical properties with CLogP and ChemProp, and create SAR tables using
property servers to generate data for lists of compounds. Use ChemSAR/Excel to explore structure activity
relationships and use add-on Conformer for conformational searching. Publish and view models on the web
using the Chem3D Plugin.
Chem3D Pro brings workstation quality molecular visualization and display to your desktop. Convert
ChemDraw and ISIS/Draw sketches into 3D models. View molecular surfaces, orbitals, electrostatic potentials,
charge densities and spin densities. Use built-in extended Hückel to compute partial atomic charges. Use MM2
to perform rapid energy minimizations and molecular dynamics simulations. ChemProp estimates physical
properties such as logP, boiling point, melting point and more. Visualize Connolly surface areas and
molecular volumes.
Large Molecular
Visualization
Molecular Modeling & Analysis
DESKTOP

SOFTWARE
Chem3D Ultra
Ultimate Modeling, Visualization & Analysis
• Adds MOPAC, CLogP, Tinker, ChemProp,ChemSAR
& Chem3D Plugin to Chem3D Pro
•Includes GAMESS & Gaussian client interfaces
• ChemSAR/Excel builds SAR tables
Chem3D Pro
Premier Modeling, Visualization & Analysis
•Create 3D models from ChemDraw or ISIS Draw, accepts output from other modeling packages
• Model types: space filling CPK, ball & stick, stick, ribbons, VDW dot surfaces & wire frame
• Compute & visualize partial charges, 3D
surface properties & orbital mapping
• Polypeptide builder with residue recognition
• ChemProp—Basic property predictions with Connolly volumes & surface areas
• MM2 minimization & molecular dynamics, extended Hückel MO calculations
• Supports: PDB, MDL Molfile, Beilstein ROSDAL, Tripos SYBYL MOL, EPS, PICT, GIF, 3DMF, TIFF, PNG & more
MOPAC/Chem3D
Advanced Semi-Empirical Computation
• Calculate ∆Hf, solvation energy, dipoles, charges, UHF & RHF spin densities, MEP, charge densities & more
• Optimize transition state geometries
• AM1, PM3, MNDO & MINDO/3 methods
CAMEO/ChemDraw
Synthetic Reaction Prediction
• Expert system predicts and displays products
• ChemDraw creates starting materials when you choose reaction conditions; sold separately
Chem3D Plugin
Advanced WWW Model Client
•Works with Microsoft Internet Explorer
•Visualize 3D molecules on ChemFinder.Com
SYSTEMS & LANGUAGES
Windows & Macintosh English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-9.2.X
Some features are Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CS ChemFinder
Searching and Information Integration
ChemFinder Pro is a fast, chemically intelligent, relational database search engine for personal, group or
enterprise use. Extended integration with Microsoft Excel and Word adds chemical searching and database
capability to spreadsheets and documents.
An ever-increasing number of chemical databases are available in ChemFinder format. Compatibility with MDL
ISIS databases is provided by SDfile and RDfile import/export. ChemFinder provides network server workgroup
functionality when used with ChemOffice WebServer.
ChemFinder/Word is an extension of Microsoft Excel and Word for Windows. Create structure searchable
spreadsheets and index documents with embedded ChemDraw structures.
ChemDraw/Excel adds chemical intelligence to Microsoft Excel for Windows. Show structures in spreadsheet
cells, tabulate chemical calculations and analyze data with Excel functions and graphs.
Purchase/Excel uses ChemDraw/Excel to manage reagent lists and track purchasing information.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
Search Chemical
Databases
ChemDraw/Excel
DESKTOP

SOFTWARE
ChemFinder/Word
• Search structures in documents & folders
ChemDraw/Excel
• Add chemical intelligence to spreadsheets
Purchase/Excel
•Organize chemical purchasing information
ChemFinder Pro
Premier Searching & Information
• Advanced search and structure query features
• Stores structures and reactions along with calculated data and associated information
• Search by substructure including stereochemistry using ChemDraw
• Import/export MDL SD and RD files
• Integration with ChemDraw and Chem3D
ChemFinder/Word
Searching Word, Excel & More
• Searches documents for embedded structures
• Indexes structures and source locations
• Searches specified folders and whole hard drives
ChemDraw/Excel
Searching & Calculating in Excel
• Displays ChemDraw structures in spreadsheet cells
• Adds chemical calculations to Excel functions
• Useful for graphing and analyzing chemical data
Purchase/Excel
High Throughput Purchasing
• Finds vendor and price information from ChemACX Database or ChemACX.Com
• Search for suppliers and purchase online
• Maintains lists of compounds
CombiChem/Excel
Combinatorial Chemistry in Excel
• Generate combinatorial libraries
•Choose starting materials and reaction schemes
•View structures and track plate/well assignments
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CS ChemInfo
Reference and Chemical Databases
DESKTOP
The Merck Index is an encyclopedia of chemicals, drugs, and biologicals, with over 10,000 monographs
covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses
and more.
ChemACX Pro includes 500,000 chemical products from 300 supplier catalogs, searchable with a single
query by structure, substructure, name, synonym, partial name, and other text and numeric criteria.
ChemACX-SC is a compilation of searchable catalogs from leading screening compound suppliers.
ChemACX.Com is the ChemACX web site with full search capabilities and convenient online ordering
from major suppliers.
ChemINDEX includes 100,000 chemicals, public NCI compounds, and more.
ChemRXN is a collection of 30,000 fully atom-mapped reactions selected and refined from the chemical
literature. It includes reactions from InfoChem’s ChemSelect database and ISI’s ChemPrep database.
ChemMSDX provides material safety data sheets for 7,000 pure compounds.
ChemFinder.Com is the award-winning web site with information and WWW links for over 100,000
chemicals. Search by name or partial name, view structure drawings, or use the ChemDraw Plugin for structure
and substructure searches. View live ChemDraw files on Windows and Macintosh clients.
ChemINDEX database on
ChemFinder.Com
ChemRXN database
on CD-ROM

SOFTWARE
The Merck Index
• Encyclopedic chemical reference
ChemACX Pro
• Chemical searching & buying
The Merck Index
Chemistry’s Constant Companion
• Over 10,000 monographs of chemicals, drugs & biologicals
ChemACX Pro
Chemical Searching & Buying
• Database of commercially available chemicals: 300 catalogs with 500,000 chemical products
• ChemACX-SC database with 500,000 structures from leading screening compound suppliers
ChemACX.Com
WWW Chemical Searching & Buying
• Search by text, structure or substructure and order online from major catalogs
ChemINDEX
Reference Searching & Information
• NCI database of over 200,000 molecules, with anti-HIV & anti-cancer assay data
ChemRXN
Reaction Searching & Information
•Includes ChemSelect with reactions from InfoChem GmbH & ISI’s ChemPrep
ChemMSDX
Safety Data Searching & Information
•Provides full Material Safety Data Sheets for over 7,000 pure compounds
ChemFinder.Com
WWW Reference Searching & Info
• WWW links for over 100,000 compounds
• Enter text queries or use ChemDraw Plugin for structure & substructure searching
•Works with Netscape & MS Internet Explorer
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
CD-ROM software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

ENTERPRISE
ChemOffice WebServer
Enterprise Solutions, Applications and Databases
ChemOffice WebServer
ChemOffice WebServer is the leading solution platform for enterprise, corporate intranet, and Internet scientific
information applications. Compatible with major databases including Oracle, SQL Server, and Microsoft
Access, ChemOffice WebServer is the development and deployment platform for custom applications and those
listed below.
ChemOffice Browser
ChemOffice Browser, including ChemDraw Java, ActiveX, and the ChemDraw and Chem3D Plugins, brings the
power and chemical intelligence of ChemOffice to Internet and intranet applications.
User Friendly & IT Ready
User-friendly and IT ready ChemOffice WebServer and Browser enterprise solutions, applications and databases
are easier and faster for users to learn and the IT staff to deploy. Using ChemOffice WebServer technology,
along with familiar browser technology, overall costs are lowered and less time is required for implementation.
Enterprise Solutions
Enterprise solutions built upon ChemOffice WebServer, including Oracle Cartridge, help workgroups and
organizations collaborate and share information, just as ChemOffice supports the daily work of the scientist.
Easy Management
of Search Results
Browse Detailed
Compound Information

SOLUTIONS
•Development and deployment platform for workgroup
and enterprise chemical information applications
•Webserver and browser components facilitate
application deployment to desktops with minimal
impact and training
• Enterprise Solution applications address areas of
Knowledge Management, Research & Discovery,
Applied BioInformatics and Chemical Databases
Knowledge Management
Knowledge Management applications organize and distribute chemical information. E-Notebook Enterprise
streamlines daily record keeping with rigorous security and efficient archiving, and facilitates information
retrieval by structure and text searching. Document Manager indexes the chemical structure content of documents,
Discovery LIMS tracks laboratory requests, and 21CFR11 Compliance implements an organization’s regulatory
compliance processes.
Research & Discovery
Research and discovery applications include Registration System for managing proprietary compound information,
Inventory Manager for reagent tracking needs, and chemical databases for complete management of chemical
inventories. Formulations & Mixtures and CombiChem Enterprise also provide tailored approaches to managing
chemical data.
Applied BioInformatics
BioAssay HTS and BioSAR Browser applications process biological assay data to pinpoint the structural determinants
of biological activity. BioAssay HTS supports low, high, and ultra-high throughput workflow, including
sample and plate management, while BioSAR Browser probes structural details within assay data.
Chemical Databases
The Merck Index and ChemACX Database provide reference information, property estimations, and searchable
compilations of commercially available chemicals.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

Oracle Cartridge
Enterprise Infrastructure for Database Security
WebServer Oracle Cartridge
In scientific applications, the ability to store and manipulate chemical information is essential. By using
CambridgeSoft’s Oracle Cartridge, you add chemical knowledge to your Oracle platform and automatically
take advantage of Oracle’s security, scalability, and replication without any other external software or programs.
You can search the chemical data by structure, substructure, and similarity, including options for stereo-selectivity,
all through extensions to Oracle’s native SQL language. Tools like PowerBuilder, Visual Basic and Visual
C++ readily lend themselves as database clients. With the addition of the ChemDraw ActiveX control in the client,
your end users can be structure-searching in no time.
Chemical Data Formats
CambridgeSoft recognizes that there is an enormous amount of legacy data out there in a myriad of formats,
and most users have no desire to make wholesale changes to their chemical data generation or storage. To this
end, Oracle Cartridge supports all major data types without translation or modification. In addition to CDX,
it supports CDXML, MolFile, Rxn, and SMILES formats. Moreover, there are built-in extensions to SQL that
allow you to extract data in all supported formats. Due to the variety of data formats supported, Oracle
Cartridge is easily deployed even within existing applications. Since no manipulation of the data is needed, new
records are automatically added to the index for searching.
Web Based
Architecture
Simple Client-Server
Architecture
ENTERPRISE

SOLUTIONS
•Adds chemical data types to Oracle, linking chemical
applications to enterprise software systems without
special programming
• Confers Oracle’s security and scalability, simplifying
large-systems’ architectural considerations
•Makes legacy chemical data, such as MDL ISIS,
accessible to ChemOffice WebServer applications
WebServer Enterprise Solutions
Even if you’re not developing your own applications, or interested in the advanced data portability aspects of
the Oracle Cartridge, CambridgeSoft’s strategy will have a positive benefit for your IT infrastructure.
CambridgeSoft’s enterprise solutions are available in Oracle Cartridge versions, including E-Notebook Enterprise,
Document Manager, Registration System, Inventory Manager, and BioAssay HTS. By utilizing Oracle Cartridge,
you can deal with issues such as scalability and security entirely through the database layer, simplifying largesystems’
architectural considerations. Oracle Cartridge has the side benefit of providing a database-level interface
to key applications, so developers can integrate CambridgeSoft’s solution platform with in-house IT solutions
without tinkering with the business tier. Communicating with Oracle Cartridge is as simple as learning a few
extensions to SQL.
Systems & Support
Support extends to include a variety of UNIX operating systems in addition to Windows servers. Oracle
Cartridge has been deployed by large pharmaceutical companies with Oracle 8i and 9i.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

KNOWLEDGE
E-Notebook Enterprise
Desktop to Enterprise Knowledge Management
E-Notebook
E-Notebook provides a smooth web-based interface designed to replace paper laboratory notebooks, with a fully
configurable, secure system for organizing the flow of information generated by your organization. You can enter
reactions, Microsoft Word documents, spectra and other types of data, and then search this data by text, substructure
or meta-data. You can organize your electronic pages by projects, experiments or any other classification
that conforms to your workflow.
Desktop to Enterprise
E-Notebook allows organization of notebook pages at either the personal or enterprise level. Enterprise groups can
organize and store notebook pages in a central data repository, allowing colleagues to take advantage of each
other’s work. All access to data is subject to granular security. E-Notebook works with Oracle Cartridge and SQL
Server, for departments or entire enterprises, and Microsoft Access, for individuals or small groups.
ChemDraw & Stoichiometry Calculations
While not quantum theory, stoichiometric calculations remain long and tedious. E-Notebook tackles this troublesome
problem. First, draw your reaction directly in the page. Then, simply enter the mass, volume and den-
Scanned Images in
Notebook Pages
Automatic Stoichiometric Calculations

MANAGEMENT
•Custom organization of notebook pages at personal
or enterprise levels with links to chemical registration
•Notebook pages include ChemDraw reaction schemes,
Microsoft Word and Excel documents, and spectral
data using the Galactic Spectral Control
• Oracle Cartridge provides detailed security and data
integrity; SQL Server also available
sity, volume and molarity, and other factors of the limiting reagent and specify the number of equivalents of the
other reactants. The notebook will do everything except calculate the experimental yield. To do that, you still
have to run the experiment!
Microsoft Office & Galactic Spectra
E-Notebook manages all the other kinds of data chemists store in their notebooks. For free-form data, you can
include Microsoft Word or Excel documents. For spectral data, you can take advantage of the Galactic Spectral
Control embedded in the notebook that allows for analysis and storage of hundreds of kinds of spectra files.
Inventory Manager
E-Notebook includes an inventory of common reactants and reagents. If you have one of these common components
loaded into the inventory application, all you have to do is click the Add Reactant button in
E-Notebook. From here, you navigate to the desired compound and include it in your stoichiometry calculations.
The enterprise edition of E-Notebook integrates with procurement and inventory management systems.
Not only does this provide a useful way to know what compounds you have in stock and where they are located,
it also saves time entering data.
Registration System
E-Notebook can be integrated into the entire chemical workflow of enterprise organizations. For example, once
you record a reaction in your notebook, you can click a button to forward the products of the reaction to your
compound registration system. These kinds of workflow enhancements increase productivity for the entire
organization.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

Document Manager
Desktop to Enterprise Document Searching
Document Manager
Everyone produces reports electronically, but searching information located in these reports has always been
difficult. Thousands of Microsoft Word, Excel, PowerPoint, and other documents reside on file servers or individual
computers, with no way to globally search them for information. Certainly, no easy way exists to search
for the chemistry contained in these documents. Document Manager solves this problem, and requires no
change in how you write and distribute reports.
Easy to Use
Document Manager manages a repository of new documents. These can be Microsoft Word, Excel, PowerPoint,
or many other document types. When a new document is added, Document Manager automatically builds a
free-text index of the document, and automatically extracts the chemical information into a chemically-aware,
substructure searchable database. Chemical information can be both ChemDraw and ISIS/Draw. Finding information
in reports is now as simple as entering a query through your web browser.
Unattended Data Indexing
As new documents are added they are automatically indexed and chemical information is extracted. Similarly, if
a document is modified, it is re-indexed. No administration of the server is necessary other than routine back-up.
Search Documents
by Structure
Unattended Data
Repository Indexing
KNOWLEDGE

MANAGEMENT
• Indexes chemical structure information in documents and
compiles a structure-searchable database
• Monitors designated folders or drives and automatically
indexes new documents as they appear
• Documents are searchable by structure and free text
Free Text Searching
Documents are searchable by free text, including Boolean expressions, proximity operators, or simple queries.
For example “author near Saunders” finds all Word documents where the word “author” appears near the word
“Saunders”.
Advanced Chemical Searching
Since the chemical information is automatically extracted, documents can be queried by structure, substructure,
similarity, molecular weight and formula. Chemical queries also support atom lists, Boolean operations
on structures, superatoms, functional groups and many others. Queries can also be refined after an initial
search, extending the power of the query language.
Structured Document Support
Structured documents, including documents created with Word templates or XML, are also supported.
Information in structured documents is extracted and stored in specific fields of the database for more precise
searching.
ChemFinder/Word
ChemFinder/Word, the desktop version, searches Word documents, Excel spreadsheets, ChemDraw files,
ChemFinder databases, SD files, MDL molfiles, and more. Unlike other Microsoft Find facilities,
ChemFinder/Word lets you work with the results you’ve located. Once you have a hit list, you can browse,
search, refine, or export it to any destination.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

KNOWLEDGE
21CFR11 Compliance
Electronic Records and Signatures Regulations
The Challenge
Large and growing enterprises are facing a challenge to their core missions of developing and producing new
products including food, therapeutic pharmaceuticals, medical devices, cosmetics or other health enhancing
items. The complexity lies in complying with government regulations designed to protect public health and
safety. The most notable of these is Title 21 of the Code of Federal Regulations governing Electronic Records
and Signatures (21CFR11). Although 21CFR11 has been in the draft stage for almost a decade, final regulations
have recently been created. Enforcement of these regulations is beginning to take place and enterprises are
responding with a wide variety of initiatives, both within individual organizations and across industry sectors.
Integrated Software
CambridgeSoft applications, such as E-Notebook Enterprise and Document Manager, are at the leading edge of
the integration of corporate knowledge management with 21CFR11 Compliance. These products are designed so
that as your organization reviews its internal processes for 21CFR11 Compliance, the software can be configured
to support these internal processes. Major requirements of 21CFR11, such as electronic signatures, audit trails,
and long-term archiving, are incorporated within the routine workflow to generate the critical information
required by research, development and production. In addition, E-Notebook Enterprise and Document Manager
can be integrated with existing critical data systems.
E-Notebook Data Capture
Document and
Record Management

MANAGEMENT
• E-Notebook Enterprise and Document Manager
integrate corporate knowledge with regulatory
compliance
• Consulting teams analyze and adapt existing
procedures to comply with new regulations
• Systems include authentication and digital signatures
and adapt to changing regulations and demands
Analysis
As your enterprise develops the operating procedures that you will need to adopt for 21CFR11 Compliance,
CambridgeSoft’s consulting team can provide invaluable assistance in analyzing your current operating procedures,
adapting your existing procedures to comply with new regulations, and validating the software and the
operating procedures that you will use. CambridgeSoft’s consulting teams consist of individuals who have
extended experience in deploying systems used by large pharmaceutical companies, emerging biotechs, and
major enterprises worldwide.
Implementation
Once you have determined how your enterprise will comply with these new regulations, implementing those
decisions needs to be done quickly, efficiently and with the understanding that the rules for compliance are in
flux. In order to succeed, you must be able to respond to change. CambridgeSoft’s 21CFR11 Compliance consulting
has both the tools and the expertise to provide complete solutions, carry out integration with your existing
systems, and help you execute the process as quickly as your organization demands. Since ongoing monitoring
is a part of business for regulated industries, you can be confident that, as regulations evolve and your
requirements change, your systems can adapt. With CambridgeSoft, you can take advantage of the knowledge
that has helped dozens of businesses, large and small, gain control over their business processes, their
intellectual capital, and their material resources.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

RESEARCH &
Registration System
Chemical and Biological Registration
Registration System
Registration System includes a robust data model for pure compounds, batches, salt management, automatic
duplicate checking and unique ID assignments. Compounds may be entered individually or with SD files. The
data model resides entirely in Oracle and uses Oracle’s security and transaction framework. For companies
intending to modify or construct their own registration system, ChemOffice WebServer includes a powerful
Software Developer’s Kit (SDK) to add custom functionality. Instead of inventing a proprietary language,
ChemOffice WebServer SDK extends the Microsoft and Oracle platforms, allowing information scientists to use
the industry’s most powerful development tools.
ChemDraw Plugin & WebServer
Registration System is easily adapted in almost any work environment. Its web-based, industry standard
ChemDraw interface, makes ChemOffice WebServer the best choice for your corporate scientific information.
User Friendly Chemical Registration
New compounds are entered through a web form, and chemical, along with non-chemical, data is kept in a
temporary storage area. When the compound is registered, it is compared for uniqueness via a configurable,
stereoselective duplicate check, and assigned a registry number. All information about the compound, including
its test data and other syntheses, is tracked by the registry number.
Search for a Compound
Display & Format Results

DISCOVERY
• Accessed through your favorite web browser, the
system uses Oracle with robust data model to manage
chemical products and their properties
• Checks for uniqueness during registration and optionally
registers duplicates as batches of existing substance
• User administration and data entry are done through
simple, easy-to-learn web forms; highly configurable
system avoids tedious and expensive customization
Duplicate Checking with Override
When compounds are registered, the structure is checked for novelty. If a duplicate already exists in the database,
the user can elect to register the information as a new batch of the existing compound, or assign it a
unique registry number.
Oracle Cartridge
Registration System is the only true n-tiered application of its kind that is designed around thin clients and thin
servers. This translates into ultimate flexibility on both the client and server side. Oracle is supported as a host,
both with native security, on a variety of platforms and operating systems. The chemical information is directly
stored in the Oracle tables.
Web Based User Interface
While the business logic of Registration System is complex, its user interface is clean and simple. Web browser
support for Netscape Navigator and Internet Explorer, plus a choice of ChemDraw Plugin, ActiveX or Java
client tools are provided. This significantly reduces training time and cost of client maintenance.
Advanced Chemistry Features
Duplicate checking is stereochemically aware. Batch data is maintained separately from compound data.
Registration numbers support multiple sequences, including one for synthesized and one for procured.
Compounds can be tracked by project and notebook reference, and registered in batches from SD files or other
sources of molecular information.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

Inventory Manager
Chemical and Biological Inventory Integration
Database Technology
Inventory Manager is a ChemOffice WebServer based application designed to manage the reagent tracking needs of
chemical and pharmaceutical research centers. The system manages data associated with both commercially
and internally produced chemical substances. Although Inventory Manager is a stand-alone application, it can
be tightly integrated with CambridgeSoft’s Registration System and chemical procurement ChemACX Database.
Inventory Manager is designed for a range of sizes from large workgroups to enterprises, and captures both
stockroom and reagent needs as well as high-throughput discovery.
Cascading Location Model
Inventory Manager has a fully cascading location model. This means that laboratories can decide for themselves
the granularity of their locations. Some labs may define locations as wells on plates residing on shelves inside
refrigerators, which, in turn, are found in laboratories. Another lab may decide to track reagents at the bench
or cabinet level. Still, in other settings, it may suffice to track chemicals on a lab-by-lab basis. The moving of
chemical inventories is greatly helped by this model. For example, if an entire refrigerator is relocated, all of its
containers move along with it. There is no need to re-catalog or reconcile, which saves a great deal of time.
Viewing Information
by Container
Substructure Search
Form
RESEARCH &

DISCOVERY
• Integrated with Registration System and ChemACX
for procurement and life cycle chemical tracking
• Cascading location model allows different labs to track
reagents at different levels (stockroom, refrigerators)
• Designed for tracking reagents, high-throughput
discovery libraries, and true HTS plate management
at multiple levels
Discovery, Reagents & Stockroom
Inventory Manager integrates fully with CambridgeSoft’s ChemACX Database of available chemicals and
Registration System. It also functions completely as a stand-alone application. Through this architecture,
CambridgeSoft’s enterprise solutions are truly plug-and-play. There are no added system integration costs, and
the applications can live on different servers in different parts of the world.
Flexibility
The flexibility of the location model allows Inventory Manager to accommodate both reagent and discovery
inventories in the same system. Each container in the system can be configured to track quantities in increasingly
small values. A reagent bottle, for instance, can be measured as “full” or “empty”, while wells in a 96-well
plate can be measured in microliters. By moving such settings and preferences down to the container level,
rather than system-wide or custom programming, Inventory Manager can accommodate both worlds in a
single instance.
Integration with Purchasing & Registration
Inventory records are created directly from ChemACX Database of available chemicals, as well as from
Registration System. For substances that do not exist in either database, Inventory Manager has its own chemically
aware user interface. By tightly coupling with ChemACX Database and Registration System, the need for
duplicate data entry is virtually eliminated. Once a product is ordered, its chemical information is stored and
it is given an “on order” status, reducing duplicate ordering of popular reagents.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CombiChem Enterprise
Desktop to Enterprise Combinatorial Chemistry
Benefits of Combinatorial Chemistry
Combinatorial chemistry, in particular the technique of parallel synthesis, has become an essential element of
the drug discovery process. This is true both at the point of finding new leads as well as optimizing a promising
lead. By using parallel synthesis techniques, chemists are able to multiply their productivity by a factor of
between 5 and 100. This increase in productivity creates data management challenges. CombiChem Enterprise
has been developed to provide the software tools required by the combinatorial chemist to manage and
document parallel synthesis experiments. The software models real-world workflow as much as possible.
Starting Out
To start, the user simply draws a generic reaction step in a ChemDraw ActiveX control directly embedded in
the notebook environment. Multiple reactants and products are supported. Points of variability on the molecules
are indicated by the traditional “R” designation. Furthermore, query features can be used to precisely define
the intended molecules. After drawing the reaction, the software analyzes the generic
reaction, determines the role of each molecule, and creates pages for managing the lists of real reagents to be
used in the actual parallel synthesis experiment.
Library in
Spreadsheet View
Reaction Based
Library Generation
RESEARCH &

DISCOVERY
• Reagent lists can be drawn from varied sources
• Reaction based library generation allows for
evaluation by product or reagent
• Data management is simplified and library
specifications are available to others on the network
Finding Reagents
Flexibility is the key when dealing with databases of chemical compounds. CombiChem Enterprise can use
reagent lists from a variety of different sources: SD files, ChemFinder databases, ChemFinder hit lists, ChemOffice
WebServer hit lists, ChemACX Database, or directly from the user via ChemDraw. Regardless of the source,
CombiChem Enterprise produces a list of reagents which match a particular generic reactant. The chemist then
chooses which of the compounds to use for generating products.
Getting Results
Once the chemist has given CombiChem Enterprise a set of reagents for each of the generic reactants in the
reaction scheme, the software generates the set of products which would result from running the experiment.
CombiChem Enterprise evaluates the products using several in silico methods, and the chemist can then choose
which compounds to keep and which ones to reject. After the products have been generated, the software
provides product information for each of the reagents. The chemist can use that information, for example, to
trim away reagents having few or no products which pass the Lipinski Rule of Five test. Finally, the products
are laid out on plates based on user-definable plate layouts.
Integration with E-Notebook
Keeping track of compound library data can be a challenge: which reagents led to this product, which
product goes with that spectrum, what was in the mixture used in this thin layer chromatography? CombiChem
Enterprise provides ways to organize the data and navigation is simple. When used with E-Notebook Enterprise,
the data for a library of shared compounds, and the entire experiment, is automatically documented and made
available to the entire organization.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

BioAssay HTS
Biological Assay and High Throughput Screening
BioAssay HTS
BioAssay HTS provides scientists with an effective way of managing test results for biological and other kinds
of experiments intended to assess the efficacy of compounds. Suitable for both plate-based high throughput
screening assays and smaller-scale lead optimization experiments, BioAssay HTS provides researchers with
simple tools for setting up their models in a database, uploading data, automating calculations and reporting
on their findings.
User Friendly Assay Management
Even for the most basic protein assays, the independent and dependent variables used by the biologist to quantify
efficacy can vary substantially from assay to assay. The underlying requirement that follows from this variability
is for a flexible data management system that can adapt quickly to different assays and biological models.
With BioAssay HTS, researchers or IT support staff simply define the observables and calculations that
make up the assay. The database does the rest. Users can set up unlimited levels of drill-down. This allows users,
for example, to click an IC50 and see a graph of percent inhibition versus concentration. Click again, and the
software displays the original triplicate results, with outliers marked. The software even supports complex in
vivo models.
Flexible Assay
Definition Tools
Automated Curve
Fitting & Data Analysis
RESEARCH &

DISCOVERY
•Effectively manages data from complex biological
assays involved with lead optimization
• Adapts quickly and flexibly to different assays and
biological models
• Closely integrated with Microsoft Excel, ChemOffice
and ChemDraw
Easily Manage Large Volumes of Data
BioAssay HTS offers an easy way to capture large volumes of data from automated laboratory equipment and
store it securely in Oracle. Scheduled data import means you can set up an import template once, and all future
data will appear in the system as it is gathered. BioAssay HTS contains a complete plate inventory system that tracks
plates and compound groups across plates. It easily manages daughter plate creation, barcoding, and freeze/thaw
cycle tracking. Since it is integrated with your assay data, you can instantly view compound information and
visualize results plate-wise to detect anomalies before they become a problem.
Automated Calculations & Curve Fitting
Once the database is configured for an assay, calculations are performed automatically whenever new data is
entered or imported. Calculations can be quite complex, built from multi-step procedures. For an IC50 assay in
triplicate, the software can average your triplicate results, take control values into account, and perform a
sigmoidal dose-response curve fit according to your specifications. It is now as easy to do for 10,000
compounds as it is for ten.
Find Structure-Activity Relationships
Users can visualize data for multiple assays with BioSAR Browser, which is specifically designed for viewing
structures and alphanumerics side-by-side. Other components of the ChemOffice product line provide
additional ways to analyze structural and biological data and perform structure searches. Both ChemFinder and
ChemOffice WebServer make it easy to create customized forms for viewing data. Users can export data to Excel
or Spotfire for further analysis and reporting.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

BioSAR Browser
RESEARCH &
Biological and Chemical Meta Data Catalog
BioSAR Browser
BioSAR Browser, a strategic must for any discovery organization interested in serious data mining, is a data-dictionary
driven structure-activity analysis program. Users may choose among assays registered in the dictionary or
search for assays of interest.
Providing Catalog Capabilities
The power of BioSAR Browser lies in the researcher’s freedom from dependence on IT support. Once an assay
is registered into the data-dictionary it is automatically included in the powerful analysis framework. By reducing
the time between question and answer, BioSAR Browser gives researchers the freedom to explore new
ideas—the bottom line for discovery information systems. Systems that provide answers after questions have
become irrelevant are of no use. BioSAR Browser avoids this by placing application development in the
researcher’s control.
Forms & Tables in a Unified Interface
While most SAR tools provide only a table-based interface, BioSAR Browser provides a forms-based interface in
addition to a tabular view. Researchers have demonstrated that both form and tabular views are essential. Forms
provide highly detailed information about one compound, whereas tabular views make comparisons between
Data Dictionary
Organizes Reports
Form and Table Views

DISCOVERY
• Catalog driven data mining and analysis operation
• Both form and table views available within simple
web interface; ChemDraw for Spotfire
• Role based security specifies operations allowed for
administrators, publishers and browsers
compounds more feasible. There is often a tradeoff between power and simplicity, and most SAR tools opt for
the former at the expense of the latter. BioSAR Browser, however, merges the sophistication of a powerful data
catalog technique with knowledge gained through years of working closely with users. The result is a SAR
application that is as intuitive as it is powerful.
Security & Convenience
Security within BioSAR Browser is highly granular. Different roles exist for administrators, publishers, and
browsers. Administrators may add assays to the data catalog engine, publishers may create reports and publish
them, and browsers may use data query and analysis. Most data mining tools provide a mechanism to store
queries, but the interface for creating queries is too complex. With BioSAR Browser, each set of assays is a complete
report with a query form, a view form, and a table view, combining the convenience of a ChemFinder or
ISIS application with the power and flexibility of a data catalog-driven mining program.
ChemDraw for Spotfire
ChemDraw for Spotfire is a powerful add-in for the Spotfire DecisionSite software. Spotfire makes industry
standard applications for high-dimensional visual data analysis, and is used to explore large biological datasets.
ChemDraw for Spotfire adds chemistry to DecisionSite, providing structure visualization and searching services.
Highlight a spot in Spotfire’s DecisionSite, and a structure is displayed directly in the window. If you draw
a structure and click Search, the matching records are displayed right in the Spotfire window. The structures
are retrieved from a chemical database such as Registration System, ChemFinder, or Oracle Cartridge, and are
returned directly over the network. In this way, structures can be linked by registry number, CAS number, or
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CHEMICAL
ChemACX Database
Available vailable Chemicals and Screening Compounds
ChemACX Database
Sifting through chemical catalogs is a poor use of time for any researcher. The Available Chemicals Xchange
database, ChemACX Database, provides a complete tool for research chemical sourcing and purchasing. The
database can be accessed from both desktop and enterprise environments and boasts an impressive list of major
suppliers, from Alfa Aesar and Aldrich, to TCI and Zeneca with hundreds in between. The enterprise procurement
solution for ChemACX saves time by streamlining the entire purchasing process. Use ChemACX to
build an internal requisition, print the form on your company template, fill it out and submit it to purchasing.
ChemACX-SC
ChemACX-SC is an additional fully structure searchable database containing the catalogs of leading screening
compound suppliers, including ChemBridge, Maybridge, Sigma-Aldrich’s Rare Chemical Library and others.
Data Quality
Over 500,000 products from 300 research chemical and biological catalogs have been selected to have their
product catalogs prepared for electronic delivery. The data provided by the suppliers is enriched by editors who
add searchable chemical structures, physical and chemical properties, and incorporate a comprehensive
chemical synonym dictionary. All substances and supplier catalog numbers are cross-referenced, making it easy
to locate alternate sources for back ordered or discontinued items.
ChemACX on CD-ROM
ChemACX on the Web

DATABASES
• Fully structure-searchable database of 500,000 products
from 300 chemical catalogs; separate ChemACX-SC
database contains screening compounds
• Search by name, synonym, partial name, formula, and
other criteria, as well as structure and substructure
• Shopping cart system works with requisition forms
and purchasing systems, such as SAP, Ariba and
Commerce1, to streamline chemical purchasing
Data Currency
A premium is placed on the accuracy and currency of the ChemACX Database. Many suppliers listed in the
database are also currently selling their products online through the ChemACX.Com web site, and therefore
have a vested interest in ensuring that their data remains complete, accurate and up-to-date. You won’t find a
sourcing database with more frequently updated content and current pricing than ChemACX.
Data Accessibility
The same way that Internet users can publicly access ChemACX.Com, enterprise users can access their private
ChemACX Database via a standard web browser. There is no need to configure or install any additional software.
ChemDraw users can either use the ChemDraw Plugin to draw chemical structures directly in the browser’s
search page, or alternatively submit queries to the database server directly from ChemDraw. ChemFinder
users can access their own copy of the database right from their local hard drive.
Electronic Requisitions
Traditional sourcing databases were conceived merely as reference tools. ChemACX Database, however, goes
one step further by including the ability to collect products into an electronic shopping cart and export its contents
into electronic requisition forms or purchasing systems. This time-saving feature has proven to be one of
the most popular advantages of ChemACX among scientists and purchasing agents alike. Users can readily
export data from the shopping cart into Excel and Word templates used as departmental requisition forms.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

The Merck Index
Chemistry’s Constant Companion
CHEMICAL
Industry Standard
Among printed chemical reference works, one that stands out for its integrity, detail and longevity is The Merck
Index. This encyclopedia of chemicals, drugs and biologicals has 10,250 monographs, 446 named reactions and
23 additional tables. Merck & Co., Inc., the publisher of The Merck Index, has chosen CambridgeSoft to produce
the complete contents of the 13th edition in a fully searchable ChemOffice format.
Detailed Monographs
The subjects covered include human and veterinary drugs, biologicals and natural products, agricultural chemicals,
industrial and laboratory chemicals, and environmentally significant compounds. What makes The
Merck Index so valuable is its extensive coverage. The information provided includes chemical, common and
generic names, trademarks, CAS registry numbers, molecular formulas and weights, physical and toxicity data,
therapeutic and commercial uses, and literature citations. In addition to the standard searches, compound
monographs can now be searched by ChemDraw structure as well as substructure. Moving this information to
the fully searchable ChemOffice format makes it easier and faster to search and get results. Instead of consulting
the auxiliary indices and then turning to the actual monograph, all searching can be done from a single form.
Query Search Form
Organic Name Reactions

DATABASES
• Encyclopedic reference for over 10,000 chemicals,
drugs, and biologicals
• Fully searchable by ChemDraw structure, substructure,
names, partial names, synonyms and other data fields
• Available in desktop, enterprise and online formats
Integrated Information
Having The Merck Index in ChemOffice format confers another valuable benefit: integration with other information
sources. For example, after locating a substance in The Merck Index, it is a simple matter to copy the
name, structure or other data elements to search ChemACX Database to find out whether there are commercial
suppliers of the substance. The structures could also be used as input to Chem3D to obtain three-dimensional
models and to perform electronic structure and physical property calculations. Information can also be brought
into any ChemOffice desktop or enterprise solution, including ChemDraw/Excel, ChemFinder/Word, E-Notebook
and Registration System.
ChemOffice Formats
The Merck Index is available in two ChemOffice compatible formats. The desktop edition is a CD-ROM in a
ChemFinder database format, for use by an individual researcher. The enterprise edition, designed for workgroups
and larger user communities, is served by ChemOffice WebServer to connected users. The Merck Index thus adds
to the growing set of reference databases served by ChemOffice WebServer. Just as ChemOffice integrates the
desktop edition of The Merck Index with the scientist’s everyday activities, the enterprise edition becomes an integral
part of the applications deployed on ChemOffice WebServer.
Web Versions
The complete contents of The Merck Index are also available online through your favorite web browser. To
meet your specific needs, single user subscriptions, corporate extranet subscriptions and intranet webservers are
all available.
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All other trademarks are the property of their respective holders. All specifications subject to change without notice.

CHEMICAL
Chemical Databases
Reference, Chemicals, Reactions, Patents Patents
and MSDS
Databases
ChemOffice WebServer provides a full range of compound and reaction databases essential for research.
Databases are available at ChemFinder.Com, or over corporate intranets.
Reference
The Merck Index contains encyclopedic references for over 10,000 chemicals, drugs and biologicals.
ChemINDEX includes 100,000 chemicals, public NCI compounds and others.
World Drug Index (WDI) from Derwent contains over 58,000 compounds with known biological activity.
WDI classifies compounds according to type of biological activity, mechanism, synonyms, trade names,
references and more.
Chemicals
ChemACX and ChemACX-SC, Available Chemicals Xchange, is a large and growing source for information
on compound availability. It lists compounds from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds
in between, including 500,000 products from 300 catalogs. ChemACX-SC is a library of screening compounds.
Derwent Patents
ISI Reactions

DATABASES
• Extensive collection of chemical reference information
in fully searchable database format
• Includes information on commercial availability;
properties; biological activity; organic reactions; material
safety data sheets; and patent or development status
• Developed by CambridgeSoft in partnership with the
leading chemical database publishers
Reactions
Organic Syntheses is the electronic version of the annual and collective volumes of trusted, peer reviewed synthesis
procedures published since 1921 by Organic Syntheses.
Current Chemical Reactions (CCR) from ISI is both a current awareness and a data mining application used to
design chemical syntheses. Renowned for its quality, CCR contains information from over 300,000 articles
reporting the complete synthesis of molecules. Updated daily, CCR is an excellent way to stay on top of recent
developments.
ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 2.5 million reactions
through an automated process of reaction classification. With over 390,000 reaction types, ChemReact is for
expert synthetic chemists designing novel syntheses. Entries in ChemSynth are further refined to those with over
50% yield and at least two literature references.
ChemRXN is a refined selection of over 29,000 fully atom-mapped reactions. Including carefully selected reactions
from InfoChem’s ChemSelect database and ISI’s ChemPrep database, ChemRXN is a terrific combination of utility.
Patents
World Drug Alerts (WDA) from Derwent is a current awareness application providing information on patents,
new biologically active compounds, new methods for synthesizing drugs, and other data. It is a requirement for
effective decision making in all stages of drug design.
Investigational Drugs Database (ID db) from Current Drugs is the world’s leading competitor intelligence
service on drug R&D. Updated weekly, it covers all aspects of drug development world wide, from first patent to
launch or discontinuation.
Safety MSDS
ChemMSDX provides over 7,000 material safety datasheets.
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CONSULTING &
Consulting & Services
Development, Installation & Training Training
Services
Managing Information
Today’s businesses are facing many complex issues. Among them are the overloads of disparate types of information,
unmanaged proliferation of valuable research data, virtual projects in many locations, uncontrolled
research data, compliance, certification and regulation. Technological solutions to these issues require careful
planning and management. CambridgeSoft now offers the following professional services to assist businesses
in fully utilizing the power of technology.
Decision Making
CambridgeSoft believes that successful technology utilization begins with the assessment and decision making
process. Our experts can assist clients with:
· Readiness Assessment: Identify the scope, requirements, and deliverables for your project. Assure critical IP
is incorporated. Allow end-users to capitalize on existing scientific and technology resources.
· Strategic Planning: Conduct formal analysis of scientific, technical, operational, and process environments
to determine the necessary approach to customization and deployment.
· Prototypes and Proof of Concept: Prototypes allow you to test the technical feasibility of solutions. This
activity can provide a baseline for the future roll-out of the solution, and can also gather user feedback so
requirements can be refined.
DECISION
MAKING
Readiness
Assessment
Strategic
Planning
Prototype or
Proof of Concept
Business Case
Development
CUSTOM
DEVELOPMENT
Custom
Application
Development
Data
Integration
Installation &
Customization
of Applications
DEPLOYMENT &
TRAINING
Application
Development
Beta &
Pre-Release
Programs
Controlled
Pilots
Training
MANAGE
THE PROCESS

SERVICES
· Business Case Development: Business cases help define a clear and purposeful solution based on well-defined
and documented business needs. Having a business case helps to justify good projects, stop bad projects
before they are started, and provides the basis for ongoing measurements after project completion to make
sure that the business is getting the results they wanted.
· Operational Planning: In order to effect change on complex environments, it is necessary for organizations
to develop operational plans. These plans minimize the risks associated with large technology deployments.
Plans may incorporate key business processes and workflows, and help to identify any operational constraints.
Custom Development
Your organization requires solutions that meet you unique needs. CambridgeSoft consultants can assist with:
· Custom Application Development: Assess business needs, document specifications, and create custom webbased
solutions for your enterprise.
· Data Integration: Create interfaces with other data management systems to incorporate your data into an
enterprise system.
· Installation and Customization: Customize your solution to your specifications. Make certain that all technical
and logistical installation processes are managed.
Deployment & Training
Develop a comprehensive road map for deployment of technology solutions across the enterprise. Our experts
help you plan and deploy your solutions by:
· Application Deployment: Document, define and execute all of the actions required to support end user
acceptance. Manage the deployment process to assure a smooth roll-out to the end-users
· Beta and Pre-Release Programs: Beta and pre-release programs involve a limited deployment to a small set
of users in order to identify deployment readiness or logistical issues that must be addressed prior to a largescale
deployment. When early release programs are employed, the success rate of large scale deployments
is greatly increased and end users are more likely to adopt the new technology.
· Controlled Pilots: Controlled pilots involve deploying a pre-production system to a small group of users to
evaluate it's functional, usability, technical, and operational characteristics in a real-world environment
prior to the completion of final system development. A controlled pilot helps identify and correct showstopper
technology or operational issues before a final roll out program is implemented.
· Training: Develop customized training materials for users, system administrators, and help desk personnel.
If you choose to outsource training management, CambridgeSoft can schedule and conduct training for
all users and stakeholders.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.

Administrator

ChemOffice.Com ®
CS ChemFinder ®
for Windows Quick Reference
SCREEN ELEMENTS
Menu Bar
Text Format
Toolbar
Form Toolbar
Record Toolbar
Status Bar
TOOLBARS
Main Toolbar
Layout Database
New Save Copy Undo Print Tool Wizard
Open Cut Paste Redo About Switch Views
ChemFinder
Enter Find Current Save Current Hit List
Query Find Molecule Restore Previous List
Retrieve All Display Previous Over Current List
Records Query Restore Saved Hit List
Search Toolbar
Shortcut Menu
Current List Size
Current Record Total Database Size
Subscript
Bold Underline Align Left
Font Font Size Italic Color Align Right
Superscript Align Center
Subform
Frame Text Button Grid
Selection Tool Tool Tool Tool Tool
Minimize Button
Maximize Button
Close Box
Table Header
Go To Last Undo
First Record Record Record Changes Delete Record
Previous Record Next Add New Commit Omit
Record Changes Changes Record
Data Box Tool Framed Picture Subform Tool
Box Tool Tool
Bullets
Scroll Bar
Framed Data Box
Main Form
Data Box

MENUS
Create a new, blank form.
Close the active form.
Save a copy of the active form in another
location or file format.
Create database automatically.
Export the current data set as an SDFile,
RDFile, or as Delimited Text.
Specify what should appear in the header
and footer of a table.
Preview the selected print task.
Specify settings for the application.
Close and exit CS ChemFinder.
Clear active form for entering
search query.
Stop current search.
Display previous search query.
Select current molecule as the
structure in a search query.
Restrict structural query to
an exact match.
Retrieve stored list of query results
for current database.
Restore hit list before last search.
Specify preferences for how searches are
performed and results are displayed.
Display contents of the help file.
Display a topic on how
to use the help file.
Display the tutorial
topics in the help file.
Display a window with information
about CS ChemFinder.
Choose a form to open.
Saves changes to the form.
Open the Database
Properties dialog to work
with databases and fields.
Import data to the active
form from a Structure Data
File or Reaction Data file.
Specify settings for
the printed page.
Specify printer and paper
options for printing.
Most recently
opened databases.
Execute
search query.
Restore all records in the opened
database back into the active form.
Display the dialog
for entering
ChemFinder
Automation
Language (CAL)
commands.
Print the form based on Print
and Page Setup settings.
Specify character format
of text selection.
Search for the current structure according
to the restrictions chosen below.
Restrict structural query to a
substructure match.
Save current query results to a file.
Search current hit list.
Search by Database ID field.
Choose a size to apply
to text selection.
Justify text so all is aligned
to the center of a data box.
Create bulleted list.
Zoom in and edit
structure.
Execute the automated
browse script.
Arrange icons at the bottom of
the window.
Arrange windows so that they
overlap.
Justify text so all is aligned
to the right of a data box.
Justify text so all is aligned
to the left of a data box.
Choose a font style to apply
to text selection.

Display the first record
in the opened database.
Display the next record
in the opened database.
Specify a record
number to display
in the database.
Make a copy of the
current record and add
it to the database.
Register changes to
the current record.
Remove current record
from list.
Multiple undo effect of
the last commands.
Remove selection to
the Clipboard.
Past information from
the Clipboard.
Select all objects in
the active form.
Align two or
more objects.
Shortcut Menu
Display the preceding
record in the database.
Display the last record
in the database.
Add a new record in
the current database.
Permanently remove
the current record.
Undo unsaved changes
to the current record.
Multiple redo effect of the
last commands.
Copy selection to
the Clipboard.
Delete selection (not
to the Clipboard).
Undo unsaved changes to
the current record.
Space objects evenly.
Display this menu by right-clicking a data box. The contents of the menu varies depending on the
contents of the data box. This context menu was displayed for a data box containing a structure.
Display Box Properties
for changing properties
of selected databox.
Display Preferences
dialog box.
Sort the records based
on the field to which
you are pointing.
Change the source of the data for
the form that contains the data
box at which you are pointing.
Specify or create a field to link
to the data box at which you
are pointing.
List the currently available fields
in the form. Choosing a field
links the data box to that field.
Display records in tabular
format in a new window.
Display Records in
Form View.
Display the Periodic Table
(for elemental data and
entering formula queries.
Display chemical
indicators.
Toggle the status bar
display and
customization options.
Display the Tool bars dialog for
tool bar display.
Alternate between Form View
and Table Views.
Toggle the grid matrix display in
the active form.
Display the Tool bars dialog for
tool bar display.
Browse ChemOffice SDK
Browse Online Resources.
Find Structure Information and Resources.

QUICK START
The following instructions are intended to give you a quick start using CS ChemFinder. For more detailed instructions, see the
CS ChemFinder User’s Guide.
Creating a Database
1. Create a form with a data box for each field you want to
display.
2. Right-click a data box and choose Data Source.
3. Click Create Database.
4. Name your database (.MDB file), and click OK. Click the
OK button in the Box Properties dialog box.
Structure fields are created automatically.
To create other fields, see Creating New Fields below.
Adding Records and Entering Data
1. On the Record toolbar, click the Add Record button. The
form is cleared.
2. To enter structures: right-click on the Structure Data Box
and choose Edit Structure. Draw your structure in
ChemDraw and click on the ChemFinder window when
you are done.
3. To enter alphanumeric data: click on the data box and type
the new data.
4. When you are finished, click Commit Changes or Undo
Changes. If you have more than two records, you can
Commit Changes by moving to another record using the
Record tools.
Searching
1. On the Search toolbar, click the Enter Query button. The
form is cleared.
2. To enter a structural query: right-click on the Structure
Data Box and choose Edit Structure. Draw your query in
ChemDraw and click on the ChemFinder window when
you are done.
3. To enter an alphanumeric query: click the data box you
want to search and type the query in the data box.
4. On the Search menu, choose the type of search you want.
5. On the Search toolbar, click the Search button.
6. On the Search toolbar, click the Retrieve All button to
browse the full database.
US 1 617 588-9300 FAX 1 617 588–9390 WWW www.cambridgesoft.com
EU 00 800 875 20000 FAX +44 1223 464990 EMAIL info@cambridgesoft.com
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
IWE 05061 0304
Importing Data from SDFiles
1. Open an existing or blank form. From the File menu, point
to Import, and choose SDFile.
2. Choose your .SDF file. Click OK.
3. Select your import options (Overwrite, Append, or Merge).
4. To edit a field, double-click its name in the left pane.
5. Click OK.
Creating a Form
1. Open a blank form and click the Layout tool.
2. Click a tool button on the Form toolbar.
3. Click and drag in the form to create data boxes. Type box
labels when requested.
4. Use the Selection tool on the Form toolbar to edit size and
position of data boxes.
5. From the File menu, choose Save to save your form as a
.CFW file.
Using Your Form with an Existing Database
1. Right-click on a data box, and choose Data Source.
2. Click Open Database.
3. Choose a database (.MDB file) and click Open.
4. In the left pane of the Database tab, click the field you
want to assign to the data box you selected in Step 3.
5. Click OK.
6. To assign fields to other data boxes: right-click on a data
box and choose a field.
Creating New Fields
1. Right-click on an unassigned data box and choose Field.
2. On the Field tab of the Box Properties dialog box, click
Create Field.
3. Type a field name, type, and width. Click OK.
4. To assign the new field: right-click on the appropriate data
box and choose the field.

✁
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CS Software Problem Report
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www.cambridgesoft.com/support/mail
USER INFORMATION (Please Print Legibly)
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Title
Firm
Street
City
Country
State Zip
Tel
Email
Fax
DETAILS OF THE PROBLEM
ATTEMPTED SOLUTION
SYSTEM CONFIGURATION
Submit this form via…
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EMAIL support@cambridgesoft.com
FAX 1 617 588–9360
MAIL CambridgeSoft, 100 CambridgePark Dr.
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SOFTWARE
Version Number
Serial Number
SYSTEM
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Windows (version)
ChemOffice ChemDraw Chem3D E-Notebook ChemFinder ChemDraw
Plugin
Chem3D
Plugin
Other
MacOs (version) PRINTER
Web Browser(s) (version) Printer Type
CPU Type Printer Driver Name
RAM (in MB) Driver Version Number
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US 1 617 588-9300 FAX 1 617 588–9390 WWW www.cambridgesoft.com
EU 00 800 875 20000 FAX +44 1223 464990 EMAIL info@cambridgesoft.com
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA

CS ChemOffice
®
Desktop to Enterprise Solutions
ChemOffice Ultra includes it all,
with ChemDraw Ultra, Chem3D Ultra and
E-Notebook Ultra for a seamlessly integrated
suite. Draw reaction mechanisms for publication
and visualize 3D molecular surfaces, orbitals
and molecular properties. Features include
The Merck Index, ChemACX, CombiChem/Excel,
ChemSAR/Excel, ChemDraw/Excel, ChemFinder/Office,
and BioAssay. Bring your work to the web or query
online databases with the ChemDraw Plugin.
ChemOffice WebServer serves chemical databases
over your intranet with the Oracle Cartridge using the
ChemDraw Plugin. Enterprise applications include E-Notebook,
Document Mgr, Discovery LIMS, 21CFR11, Registration System,
Formulations & Mixtures, Inventory Manager, CombiChem,
BioAssay HTS, BioSAR Browser and Drug Degradation. Databases
include, The Merck Index and ChemACX database of 500,000 products
from 300 catalogs including Sigma-Aldrich.
US 1 617 588-9300 FAX 1 617 588–9390 WWW www.cambridgesoft.com
EU 00 800 875 20000 FAX +44 1223 464990 EMAIL info@cambridgesoft.com
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA