Using ChemFinder - CambridgeSoft

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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