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)[source]¶

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)[source]¶: 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.

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

evaluateSmiles(smiles, uniquify=True, use_chirality=True, max_matches=1000000000)¶

Get the list of matches for the passed SMILES pattern in the reference structure

Parameters

smiles (str) – SMILES pattern to find
uniquify (bool) – if True, return only unique sets of matching atoms
use_chirality (bool) – enables the use of stereochemistry in the matching
max_matches (int) – the maximum number of matches to return

Return type

list or None

Returns

list of list atom indices with matching SMILES.

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(atom_ids=None, isomeric=True)¶

Get SMARTS for subset of atom ids

Parameters

atom_ids (iterable) – atom indices
isomeric (bool) – include information about stereochemistry in the SMARTS

Return type

str

Returns

SMARTS pattern for the atom ids provided

toSmiles(atom_ids=None, isomeric=True)¶

Get SMILES for subset of atom ids

Parameters

atom_ids (iterable) – atom indices
isomeric (bool) – include information about stereochemistry in the SMILES

Return type

str

Returns

SMILES pattern for the atom ids provided

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.