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Administrator<br />

If an atom can be assigned to more than one atom<br />

type, atom types are assigned to atoms in the<br />

following order:<br />

1. Atom types whose bound-to types are<br />

specified and are not the same as their<br />

rectification types.<br />

2. Atom types whose bound-to types are<br />

specified and are the same as their rectification<br />

types.<br />

3. Atom types whose bound-to types are not<br />

specified.<br />

For example, in the model depicted above, O(4)<br />

could be one of several atom types. First, it could be<br />

an O Ether atom for which the bound-to type is<br />

unspecified (priority number 3, above).<br />

Alternatively, it could be an O Alcohol for which<br />

the bound-to type is the same as the rectification<br />

type, H Alcohol (priority number 2, above). A third<br />

possibility is O Carboxyl, for which the bound-to<br />

type is C Carbonyl and the rectification type is H<br />

Carboxyl (priority number 1). Because the<br />

characteristic of a specified bound-to type which is<br />

not the same as the rectification type (number 1 in<br />

the priority list above) is given precedence over the<br />

other two possibilities, the O Carboxyl atom type is<br />

assigned to the oxygen atom.<br />

Defining Atom Types<br />

If you need to define atom types, whether to add to<br />

the atom types table for building or to add to a file<br />

format interpreter for importing, here is the general<br />

procedure:<br />

To add or edit an atom type to the Atom Types<br />

table:<br />

1. From the View menu, point to Parameter<br />

Tables and choose Atom Types.<br />

The Atom Types table opens in a window.<br />

2. To edit an atom type, click in the cell that you<br />

want to change and type new information.<br />

3. Enter the appropriate data in each field of the<br />

table. Be sure that the name for the parameter<br />

is not duplicated elsewhere in the table.<br />

4. Close and Save the table.<br />

You now can use the newly defined atom type.<br />

616• Atom Types <strong>CambridgeSoft</strong><br />

Defining Atom Types

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