schrodinger.application.matsci.smartsutilsgui module

GUI elements for working with SMARTS patterns

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.smartsutilsgui.SMARTSNameValidator(*args, **kwargs)

Bases: AtomNameLabelValidator

Ensures that the line edit contains only valid SMARTS name characters

VALID_LABEL_PUNCTUATION = '_-()[]'
schrodinger.application.matsci.smartsutilsgui.populate_smarts_edit(smarts_edit, maestro, warning, append=False, delim=' ', canvas_api=False, use_rdkit=False, fall_back=False, check_connectivity=True, allow_intermolecular=False)

Populates the smarts edit with smarts pattern grabbed from WS. If append is true then the smarts pattern is appended to smarts_edit with delim (space as default) as delimiter else smarts_edit is replaced with the given smarts pattern.

Parameters:

  • smarts_edit (swidgets.SMARTSEdit) – The smarts edit on which population of smarts pattern is to be done

  • maestro (schrodinger.maestro.maestro) – maestro provides structure and selected atom index

  • warning (function) – prints warning message

  • append (bool) – If flag is true then smarts is appended to smarts_edit with delim as delimiter else smarts_edit is replaced with smarts

  • delim (str) – The delimiter used when append is true.

  • canvas_api (bool) – whether to use deprecated_pattern.generate_smarts or deprecated_pattern.generate_smarts_canvas

  • use_rdkit (bool) – Whether to use rdkit

  • fall_back (bool) – whether to fall back on using deprecated_pattern.generate_smarts if canvas/rdkit fails, used only if canvas_api is True

  • check_connectivity (bool) – If True, check for whether the atoms given are connected and raise a ValueError if they are not. SMARTS generation will give bogus results for unconnected atoms.

  • allow_intermolecular (bool) – If check_connectivity is False this controls whether matches must be intramolecular or allowed to be intermolecular

schrodinger.application.matsci.smartsutilsgui.get_smarts_from_ws(maestro, warning, canvas_api=False, use_rdkit=False, fall_back=False, check_connectivity=True, allow_intermolecular=False)

Get the SMARTS pattern for the selected atoms in the workspace and insert it into the SMARTS entry

Parameters:

  • maestro (schrodinger.maestro.maestro) – maestro provides structure and selected atom index

  • warning (function) – prints warning message

  • canvas_api (bool) – whether to use deprecated_pattern.generate_smarts or deprecated_pattern.generate_smarts_canvas

  • use_rdkit (bool) – Whether to use rdkit

  • fall_back (bool) – whether to fall back on using deprecated_pattern.generate_smarts if canvas/rdkit fails, used only if canvas_api is True

  • check_connectivity (bool) – If True, check for whether the atoms given are connected and raise a ValueError if they are not. SMARTS generation will give bogus results for unconnected atoms.

  • allow_intermolecular (bool) – if check_connectivity is False this controls whether matches must be intramolecular or allowed to be intermolecular

Return type:

str or None

Returns:

smarts pattern selected from workspace or None if any of the validation fails