schrodinger.application.matsci.rdpattern_gui module¶

GUI elements to generate and evaluate Smiles/SMARTS pattern for both CG and all atomic structure using RDKIT

class schrodinger.application.matsci.rdpattern_gui.GuiPattern(struct, *, is_cg=None, sanitize=True, include_stereo=True, fall_back=False)¶

Bases: schrodinger.application.matsci.rdpattern.Pattern, schrodinger.ui.qt.widgetmixins.basicmixins.MessageBoxMixin

This class describes a pattern that can be used by graphical user interface.

evaluateSmarts(smarts, **kwargs)¶: Overwrite parent class to reload rdmol to obey stereochemistry in case smarts has stereo and current rdmol does not.

PROTECTED_PATTERN_BIT = ['D', 'R', 'r', 'v', 'x', 'X', 'H']¶

__init__(struct, *, is_cg=None, sanitize=True, include_stereo=True, fall_back=False)¶

Initiate Pattern class

Parameters

struct (schrodinger.structure.Structure) – Structure for which patterns need to be selected
is_cg (bool or None) – Whether structure is CG. If None, perform a check
sanitize (bool) – Whether RDKit sanitization should be performed. This option is not applicable for coarsegrained structures.
include_stereo (bool) – Whether the stereochemistry of the structure should be translated into the RDKit mol. Setting to False can speed this up substantially.
fall_back (bool) – Ignored if sanitize=False. If sanitize=True, will fall back to using a non-sanitized structure if sanitization fails.

clearCache()¶: Clear cache

error(*args, **kwargs)¶: Shows a popup error message box. For parameter documentation see messagebox.MessageBox.

evaluateSmiles(**kwargs)¶

forgetMessageBoxResponse(key)¶

Forgets any previously saved response that was stored via a save_response_key.

Parameters: key – the key for the response to forget

getMoleculeSmarts()¶

Get SMARTS for each molecule in the structure

Returns: The dictionary where the key is the molecule number and the value is the corresponding SMARTS pattern
Return type: dict

getMoleculeSmiles()¶

Get SMILES for each molecule in the structure

Returns: The dictionary where the key is the molecule number and the value is the corresponding SMILES pattern
Return type: dict

getPattern(atom_ids=None, is_smiles_requested=False, isomeric=True)¶

Get SMILES/SMARTS for full structure or for substructure of given atom ids.

Parameters

atom_ids (list) – list of atom indices
is_smiles_requested (bool) – return Smiles pattern if True else Smarts
isomeric (bool) – include information about stereochemistry in the SMILES/SMARTS

Return type

str

Returns

SMILES pattern for the atom ids provided

getUniqueMolNums(use_smarts=False)¶

Get the unique representative molecules in the structure. This function can be upto 50 times slower than extracting molecules individually for small molecules like water.

Parameters: use_smarts (bool) – If true the unique molecules will share the same SMARTS pattern. If false the unique molecules will share the same SMILES pattern.
Return type: list
Returns: list of molecule numbers that are unique

info(*args, **kwargs)¶: Shows a popup information message box. For parameter documentation see messagebox.MessageBox.

loadMol()¶: Load rdkit mol in the pattern

particleNameToProxy(smarts)¶

If the structure is a coarse grain structure convert the SMARTS pattern of coarse grain particle name to proxy element name. Does nothing for atomistic structures

Parameters: smarts (str) – The SMARTS pattern
Returns: The translated SMARTS pattern
Return type: str

static patternTranslate(s_pattern, mapper)¶

Replace passed SMARTS/SMILES such that the mapper key values are replaced by

Parameters

s_pattern (str) – The SMARTS/SMILES pattern to change
mapper (dictionary where the key is the element name to find in the pattern and value is the name to replace it with) – The mapper used to convert the SMARTS/SMILES pattern

Returns

the converted SMARTS/SMILES pattern

Return type

str

proxyToParticleName(smarts)¶

If the structure is a coarse-grained structure convert the SMARTS pattern of proxy elements to coarse grain particle name. Does nothing for atomistic structures

Parameters: smarts (str) – The SMARTS pattern
Returns: The translated SMARTS pattern
Return type: str

question(*args, **kwargs)¶: Shows a popup question message box. For parameter documentation see messagebox.QuestionMessageBox.

property sanitized¶

Get whether the structure was sanitized or not

Returns: sanitization status of the structure
Return type: bool

showMessageBox(*args, **kwargs)¶: Shows a popup message box. For parameter documentation see messagebox.MessageBox.

property smarts¶

Get the SMARTS for the passed structure

Returns: SMARTS pattern for the passed structure
Return type: str

property smiles¶

Get the SMILES for the passed structure

Returns: SMILES pattern for the passed structure
Return type: str

toRdIndices(particle_indices)¶

Convert list of Schrodinger structure particle indices to RDMol atom indices

Parameters: particle_indices (tuple) – tuple of Schrodinger structure particle indices
Return type: list
Returns: list of RDMol atom indices

toSmarts(**kwargs)¶

toSmiles(**kwargs)¶

toStIndices(particle_indices)¶

Convert list of RDMol atom indices to Schrodinger structure particle indices

Parameters: particle_indices (tuple) – tuple of RDMol atom indices
Return type: list
Returns: list of Schrodinger structure particle indices

validateSmarts(smarts)¶

Validate the passed smarts pattern

Parameters: smarts (str) – SMARTS to validate
Return type: str or None
Returns: Error message on error, None if SMARTS is valid

warning(*args, **kwargs)¶: Shows a popup warning message box. For parameter documentation see messagebox.MessageBox.