schrodinger.application.matsci.smartsutils module¶

Utilities for working with SMARTS patterns

class schrodinger.application.matsci.smartsutils.SMARTSGroupData(number, name, pattern, indexes)¶

Bases: tuple

__contains__(key, /)¶: Return key in self.

__len__()¶: Return len(self).

count(value, /)¶: Return number of occurrences of value.

index(value, start=0, stop=9223372036854775807, /)¶

Return first index of value.

Raises ValueError if the value is not present.

indexes¶: Alias for field number 3

name¶: Alias for field number 1

number¶: Alias for field number 0

pattern¶: Alias for field number 2

schrodinger.application.matsci.smartsutils.defines_integer_atom_props(st)¶

Return True if the given structure has SMARTS-related integer atom properties defined. These properties were originally used when each atom was forced to belong to a single SMARTS group. That condition has been relaxed but these properties are kept for backwards compatibility.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: bool
Returns: True if such properties are defined

schrodinger.application.matsci.smartsutils.get_group_names(atom)¶

Return a list of group names for the given atom.

Parameters: atom (schrodinger.structure._StructureAtom) – the atom
Return type: list
Returns: group names

schrodinger.application.matsci.smartsutils.get_group_atom_indices(atom)¶

Return a list of group atom indices for the given atom.

Parameters: atom (schrodinger.structure._StructureAtom) – the atom
Return type: list
Returns: group atom indices

schrodinger.application.matsci.smartsutils.get_group_numbers(atom)¶

Return a list of group numbers for the given atom.

Parameters: atom (schrodinger.structure._StructureAtom) – the atom
Return type: list
Returns: group numbers

schrodinger.application.matsci.smartsutils.append_property(atom, key, value)¶

Append the given property to the atom.

Parameters

atom (schrodinger.structure._StructureAtom) – the atom
key (str) – the property key
value (str) – the property value

schrodinger.application.matsci.smartsutils.validate_name(name)¶

Make sure name has the correct set of characters

Parameters: name (str) – The string to check
Return type: bool
Returns: True if name has no invalid characters, False if any characters are invalid

exception schrodinger.application.matsci.smartsutils.SMARTSGroupError¶

Bases: Exception

Class for exceptions related to SMARTS group finding

__init__(*args, **kwargs)¶

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.matsci.smartsutils.delete_group_properties(struct)¶

Delete all SMARTS group properties (structure and atom) from the structure

Parameters: struct (schrodinger.structure.Structure) – The structure to delete properties from

schrodinger.application.matsci.smartsutils.find_group_data(struct)¶

Find an SMARTS group data on the structure

Parameters: struct (schrodinger.structure.Structure) – The structure to find groups on
Return type: dict
Returns: A dictionary. Keys are smarts group numbers, values are SMARTSGroupData named tuples for the SMARTS group with that number
Raises: SMARTSGroupError – If something in the data is not consistent

schrodinger.application.matsci.smartsutils.get_rdkit_atoms(smarts)¶

Return a collection of rdkit atoms for the given SMARTS. The return value has the length of a potential match group, for example for ‘cc’ this length is 2, for ‘[$([NH]([CH2])[CH2])]C’ it is 2, for [n-0X2].[n-0X2] it is 2, etc., even though there might be any number of matches if the pattern was matched.

Parameters: smarts (str) – the SMARTS pattern
Raises: RuntimeError – if rdkit has a problem with the SMARTS
Return type: rdkit.Chem.rdchem._ROAtomSeq
Returns: the rdkit atoms

schrodinger.application.matsci.smartsutils.is_smarts_bonding_pair(smarts)¶

Return True if the given SMARTS would match a bonding pair, False otherwise.

Parameters: smarts (str) – the SMARTS pattern
Return type: bool
Returns: True if the SMARTS would match a bonding pair, False otherwise

class schrodinger.application.matsci.smartsutils.SMARTSGroup(name, pattern, logger=None)¶

Bases: object

Handles matching and record-keeping for a SMARTS patter

__init__(name, pattern, logger=None)¶

Create a SMARTSGroup object

Parameters

name (str) – The name of this SMARTS group
pattern (str) – The SMARTS pattern for this group

Raises

ValueError – If name has invalid characters
ValueError – If the SMARTS is invalid

nextNumber(numbers_used)¶

Get the next unused group number

Parameters: numbers_used (set) – Each member is a number that has already been used for a group and is unavailable. The number returned by this function is added to the numbers_used set.
Return type: int
Returns: The lowest available number. This number will have been added to the numbers_used set.

prioritizeBackbone(matches, backbone_atoms)¶

Prioritize matches that are in backbone of the molecule

Parameters

matches (list) – List of list containing the smart pattern matches
backbone_atoms (dict) – dictionary with key as molecule number and backbone atoms index ordered in a list

Returns

List of list containing the smart pattern matches where the matches in the backbone appears first

Return type

list

prioritizeSameMonomers(struct, matches)¶

Prioritize matches that belong to same (or least) number of unique monomers.

Parameters

struct (schrodinger.structure.Structure) – The structure to find SMARTS pattern match in
matches (list) – List of list containing the smart pattern matches

Returns

List of list containing the smart pattern matches where the matches that belong to same (or least) number of unique monomers appear first

Return type

list

orderedMatches(struct, backbone_atoms)¶

Evaluate the smarts pattern matches, where matches are ordered to follow network sequence. Consider backbone atoms matches first in the sequence and the side chain matches are then ordered according to atom index.

Parameters

struct (schrodinger.structure.Structure) – The structure to delete properties from
backbone_atoms (dict) – dictionary with key as molecule number and backbone atoms index ordered in a list

Return list(list)

List of list containing the smart pattern matches

getSmartsDictData(struct, match, allow_partial_overlap)¶

Gets the smarts dictionary data for the passed match

Parameters

struct (schrodinger.structure.Structure) – The structure to which the SMARTS match belongs to
match (list) – The list of atom indices that belong to the SMARTS match
allow_partial_overlap (bool) – Whether partial overlap is allowed

Returns

Dictionary where the key is a SMARTSGroupData and the value is the list of atom indices that belong to the group

Return type

dict

Raises

ValueError – If overlapping is not supported due to backwards incompatibility

isAlreadyMatched(match, smarts_group_matches)¶

Check if atoms have already been matched to the same SMARTS pattern. This allows creating a group from some atoms already matched to some group and other atoms already matched to some other group but prevents creating a group that is a sub-group of another group

Parameters

match (list) – The list of atom indices that belong to the SMARTS match
smarts_group_matches (dict) – Dictionary where the key is a unique SMARTS pattern and the value is the list of atom indices that belong to the group

Return type

bool

Returns

Whether the match has already been matched to same SMARTS

onlyDifferByAHydrogen(struct, match, smarts_group_matches)¶

Check all atoms except a single H atom have already been matched to the same SMARTS group. This prevents matching a terminal methyl 3 times as is the case for a polymer head or tail monomer with a terminating hydrogen

Parameters

struct (schrodinger.structure.Structure) – The structure to which the SMARTS match belongs to
match (list) – The list of atom indices that belong to the SMARTS match
smarts_group_matches (dict) – Dictionary where the key is a unique SMARTS pattern and the value is the list of atom indices that belong to the group

Return type

bool

Returns

Whether all atoms except a single H atom have already been matched

isOverlapAllowedInMatch(struct, match, smarts_group_data_dict)¶

Determines if overlap is allowed for the current match.

Parameters

struct (schrodinger.structure.Structure) – The structure to which the SMARTS match belongs to
match (list) – The list of atom indices that belong to the SMARTS match
smarts_group_data_dict (dict) – Dictionary where the key is a SMARTSGroupData and the value is the list of atom indices that belong to the group

Return type

bool

Returns

Whether overlapping is allowed for the current match

addMatchToAtoms(struct, numbers_used, match)¶

Adds match information to structure atom property

Parameters

struct (schrodinger.structure.Structure) – The structure to which the SMARTS match belongs to
numbers_used (set) – Each member is a number that has already been used for a group and is unavailable. The number returned by this function is added to the numbers_used set.
match (list) – The list of atom indices from the match

log(msg)¶

Log message if logger is present

Parameters: msg (str) – The message to log

match(struct, numbers_used, backbone_atoms, allow_partial_overlap=False)¶

Find all the SMARTS groups matching the SMARTS pattern and mark them with the appropriate properties

Parameters

struct (schrodinger.structure.Structure) – The structure to find SMARTS pattern match in
numbers_used (set) – A set of all the group numbers that have been used and are unavailable
backbone_atoms (dict) – dictionary with key as molecule number and backbone atoms index ordered in a list
allow_partial_overlap (bool) – whether atoms can belong to multiple groups

class schrodinger.application.matsci.smartsutils.SMARTSComplexity(smarts)¶

Bases: object

Class that holds SMARTS pattern and allows to compare complexity of SMARTS pattern

__init__(smarts)¶

Constructs a new instance of SMARTSComplexity

Parameters: smarts (str) – The SMARTS pattern