schrodinger.application.desmond.smarts module¶
SMARTS matching utility using MMPATTY. This utility is used in Desmond setup and should not be modified to use canvaslib due to the lack of support for zeor-order-bond patterns.
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schrodinger.application.desmond.smarts.
evaluate_matched_list
(matched_list)¶ Function to flatten and de-duplicate atoms matched in multiple SMARTS pattern. Atom indices are sorted in ascending values.
Parameters: matched_list (list) – List of atom sets each matches a SMARTS pattern Return type: list Returns: A list of non-duplicate atom indices representing the union of multiple SMARTS pattern.
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schrodinger.application.desmond.smarts.
evaluate_net_smarts
(structure, smarts_list, excl_smarts_list, verbose=False)¶ Search for substructures in
Structure
structure
matching the SMARTS patternsmarts_expression
.Returns a list of lists of ints. Each list of ints is a list of atom indices matching the SMARTS pattern while not in the exclusion SMARTS pattern
Parameters: - structure (
Structure
) – Structure to search for matching substructures. - smarts_list (list) – List of SMARTS strinsg used to match substructures.
- excl_smarts_list (list) – List of SMARTS strings whose matched atoms will be excluded from the returned match.
- verbose (bool) – If True, print additional progress reports from the C implementation.
Return type: list
Returns: A list of atom indices matching the SMARTS pattern and not in the exclusion SMARTS pattern.
- structure (