rdkit.Chem.rdfiltercatalog module¶

Module containing FilterCatalog functionality for filtering molecules based on structural patterns.

class rdkit.Chem.rdfiltercatalog.ExclusionList(self)¶

Bases: FilterMatcher

AddPattern(self, base: rdkit.Chem.rdfiltercatalog.FilterMatcher) → None¶: Add a FilterMatcherBase that should not appear in a molecule

SetExclusionPatterns(self, list: object) → None¶: Set a list of FilterMatcherBases that should not appear in a molecule

class rdkit.Chem.rdfiltercatalog.FilterCatalog(self)¶

class rdkit.Chem.rdfiltercatalog.FilterCatalog(self, pickle: bytes)

class rdkit.Chem.rdfiltercatalog.FilterCatalog(self, pickle: str)

class rdkit.Chem.rdfiltercatalog.FilterCatalog(self, params: rdkit.Chem.rdfiltercatalog.FilterCatalogParams)

class rdkit.Chem.rdfiltercatalog.FilterCatalog(self, catalogs: rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs)

Bases: object

AddEntry(self, entry: rdkit.Chem.rdfiltercatalog.FilterCatalogEntry) → None¶: Add a FilterCatalogEntry to the catalog

GetEntry(self, idx: int) → rdkit.Chem.rdfiltercatalog.FilterCatalogEntry¶: Return the FilterCatalogEntry at the specified index

GetEntryWithIdx(self, idx: int) → rdkit.Chem.rdfiltercatalog.FilterCatalogEntry¶: Return the FilterCatalogEntry at the specified index

GetFilterMatches(self, mol: rdkit.Chem.rdchem.Mol) → list[rdkit.Chem.rdfiltercatalog.FilterMatch]¶: Return every matching filter from all catalog entries that match mol

GetFirstMatch(self, mol: rdkit.Chem.rdchem.Mol) → rdkit.Chem.rdfiltercatalog.FilterCatalogEntry¶: Return the first catalog entry that matches mol

GetMatches(self, mol: rdkit.Chem.rdchem.Mol) → list[rdkit.Chem.rdfiltercatalog.FilterCatalogEntry]¶: Return all catalog entries that match mol

GetNumEntries(self) → int¶: Returns the number of entries in the catalog

HasMatch(self, mol: rdkit.Chem.rdchem.Mol) → bool¶: Returns True if the catalog has an entry that matches mol

RemoveEntry(self, obj: object) → bool¶: Remove the given entry from the catalog

Serialize(self) → bytes¶

class rdkit.Chem.rdfiltercatalog.FilterCatalogEntry¶

Bases: object

A filter catalog entry is an entry in a filter catalog. Each filter is named and is used to flag a molecule usually for some undesirable property.

For example, a PAINS (Pan Assay INterference) catalog entry be appear as follows:

>>> from rdkit.Chem.FilterCatalog import *
>>> params = FilterCatalogParams()
>>> params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
True
>>> catalog = FilterCatalog(params)
>>> mol = Chem.MolFromSmiles('O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2')
>>> entry = catalog.GetFirstMatch(mol)
>>> print (entry.GetProp('Scope'))
PAINS filters (family A)
>>> print (entry.GetDescription())
hzone_phenol_A(479)

__init__(self) -> None __init__(self, name: str, matcher: rdkit.Chem.rdfiltercatalog.FilterMatcher) -> None

ClearProp(self, key: str) → None¶

GetDescription(self) → str¶: Get the description of the catalog entry

GetFilterMatches(self, mol: rdkit.Chem.rdchem.Mol) → list[rdkit.Chem.rdfiltercatalog.FilterMatch]¶: Retrieve the list of filters that match the molecule

GetProp(self, key: str) → str¶

GetPropList(self) → list[str]¶

HasFilterMatch(self, mol: rdkit.Chem.rdchem.Mol) → bool¶: Returns True if the catalog entry contains filters that match the molecule

IsValid(self) → bool¶

Serialize(self) → bytes¶

SetDescription(self, description: str) → None¶: Set the description of the catalog entry

SetProp(self, key: str, val: str) → None¶

class rdkit.Chem.rdfiltercatalog.FilterCatalogParams(self)¶

class rdkit.Chem.rdfiltercatalog.FilterCatalogParams(self, catalogs: rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs)

Bases: object

Overloaded function.

__init__(self) -> None
__init__(self, catalogs: rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs) -> None

Construct from a FilterCatalogs identifier (i.e. FilterCatalogParams.PAINS)

AddCatalog(self, catalogs: rdkit.Chem.rdfiltercatalog.FilterCatalogParams.FilterCatalogs) → bool¶

class FilterCatalogs(*values)¶

Bases: IntEnum

ALL = 16382¶

BRENK = 16¶

CHEMBL = 16256¶

CHEMBL_BMS = 512¶

CHEMBL_Dundee = 256¶

CHEMBL_Glaxo = 128¶

CHEMBL_Inpharmatica = 4096¶

CHEMBL_LINT = 8192¶

CHEMBL_MLSMR = 2048¶

CHEMBL_SureChEMBL = 1024¶

NIH = 32¶

PAINS = 14¶

PAINS_A = 2¶

PAINS_B = 4¶

PAINS_C = 8¶

ZINC = 64¶

class rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher(self)¶

class rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher(self, matcher: rdkit.Chem.rdfiltercatalog.FilterMatcher)

Bases: FilterMatcher

Hierarchical Filter

basic constructors:: FilterHierarchyMatcher( matcher ) where can be any FilterMatcherBase (SmartsMatcher, etc)
FilterHierarchyMatcher’s have children and can form matching: trees. When GetFilterMatches is called, the most specific ( i.e. lowest node in a branch) is returned.
n.b. A FilterHierarchicalMatcher of functional groups is returned: by calling GetFunctionalGroupHierarchy()

>>> from rdkit.Chem import MolFromSmiles
>>> from rdkit.Chem.FilterCatalog import *
>>> functionalGroups = GetFunctionalGroupHierarchy()
>>> [match.filterMatch.GetName()
...     for match in functionalGroups.GetFilterMatches(
...         MolFromSmiles('c1ccccc1Cl'))]
['Halogen.Aromatic', 'Halogen.NotFluorine.Aromatic']

Overloaded function.

__init__(self) -> None
__init__(self, matcher: rdkit.Chem.rdfiltercatalog.FilterMatcher) -> None

Construct from a filtermatcher

AddChild(self, hierarchy: rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher) → rdkit.Chem.rdfiltercatalog.FilterHierarchyMatcher¶: Add a child node to this hierarchy.

SetPattern(self, matcher: rdkit.Chem.rdfiltercatalog.FilterMatcher) → None¶: Set the filtermatcher pattern for this node. An empty node is considered a root node and passes along the matches to the children.

class rdkit.Chem.rdfiltercatalog.FilterMatch(self, filter: rdkit.Chem.rdfiltercatalog.FilterMatcher, atomPairs: collections.abc.Sequence[tuple[int, int]])¶

Bases: object

Object that holds the result of running FilterMatcherBase::GetMatches

filterMatch holds the FilterMatchBase that triggered the match

atomPairs holds the [ (query_atom_idx, target_atom_idx) ] pairs for the matches.

Note that some matches may not have atom pairs (especially matches that use FilterMatchOps.Not

property atomPairs¶: (self) -> list[tuple[int, int]]

property filterMatch¶: (self) -> RDKit::FilterMatcherBase

class rdkit.Chem.rdfiltercatalog.FilterMatcher(self, name: str)¶

Bases: object

Base class for matching molecules to filters.

A FilterMatcherBase supplies the following API - IsValid() returns True if the matcher is valid for use, False otherwise - HasMatch(mol) returns True if the molecule matches the filter - GetMatches(mol) -> [FilterMatch, FilterMatch] returns all the FilterMatch data

that matches the molecule

print( FilterMatcherBase ) will print user-friendly information about the filter Note that a FilterMatcherBase can be combined from many FilterMatcherBases This is why GetMatches can return multiple FilterMatcherBases. >>> from rdkit.Chem.FilterCatalog import * >>> carbon_matcher = SmartsMatcher(‘Carbon’, ‘[#6]’, 0, 1) >>> oxygen_matcher = SmartsMatcher(‘Oxygen’, ‘[#8]’, 0, 1) >>> co_matcher = FilterMatchOps.Or(carbon_matcher, oxygen_matcher) >>> mol = Chem.MolFromSmiles(‘C’) >>> matches = co_matcher.GetMatches(mol) >>> len(matches) 1 >>> print(matches[0].filterMatch) Carbon

GetMatches(self, mol: rdkit.Chem.rdchem.Mol) → list[rdkit.Chem.rdfiltercatalog.FilterMatch]¶: Returns the list of matching subfilters mol matches any filter

GetName(self) → str¶

HasMatch(self, mol: rdkit.Chem.rdchem.Mol) → bool¶: Returns True if mol matches the filter

IsValid(self) → bool¶: Return True if the filter matcher is valid, False otherwise

rdkit.Chem.rdfiltercatalog.FilterMatcherBase¶: alias of FilterMatcher

rdkit.Chem.rdfiltercatalog.PythonFilterMatcher¶: alias of FilterMatcher

class rdkit.Chem.rdfiltercatalog.SmartsMatcher(self, name: str)¶

class rdkit.Chem.rdfiltercatalog.SmartsMatcher(self, rhs: rdkit.Chem.rdchem.Mol)

class rdkit.Chem.rdfiltercatalog.SmartsMatcher(self, name: str, mol: rdkit.Chem.rdchem.Mol, minCount: int = 1, maxCount: int = 4294967295)

class rdkit.Chem.rdfiltercatalog.SmartsMatcher(self, name: str, smarts: str, minCount: int = 1, maxCount: int = 4294967295)

Bases: FilterMatcher

Smarts Matcher Filter

basic constructors:

SmartsMatcher( name, smarts_pattern, minCount=1, maxCount=UINT_MAX ) SmartsMatcher( name, molecule, minCount=1, maxCount=UINT_MAX )

note: If the supplied smarts pattern is not valid, the IsValid() function will: return False

>>> from rdkit.Chem.FilterCatalog import *
>>> minCount, maxCount = 1,2
>>> carbon_matcher = SmartsMatcher('Carbon', '[#6]', minCount, maxCount)
>>> print (carbon_matcher.HasMatch(Chem.MolFromSmiles('CC')))
True
>>> print (carbon_matcher.HasMatch(Chem.MolFromSmiles('CCC')))
False
>>> carbon_matcher.SetMinCount(2)
>>> print (carbon_matcher.HasMatch(Chem.MolFromSmiles('C')))
False
>>> carbon_matcher.SetMaxCount(3)
>>> print (carbon_matcher.HasMatch(Chem.MolFromSmiles('CCC')))
True

Overloaded function.

__init__(self, name: str) -> None
__init__(self, rhs: rdkit.Chem.rdchem.Mol) -> None

Construct from a molecule

__init__(self, name: str, mol: rdkit.Chem.rdchem.Mol, minCount: int = 1, maxCount: int = 4294967295) -> None

Construct from a name, molecule, minimum and maximum count

__init__(self, name: str, smarts: str, minCount: int = 1, maxCount: int = 4294967295) -> None

Construct from a name, smarts pattern, minimum and maximum count

GetMaxCount(self) → int¶: Get the maximum times pattern can appear for the filter to match

GetMinCount(self) → int¶: Get the minimum times pattern must appear for the filter to match

GetPattern(self) → rdkit.Chem.rdchem.Mol¶

IsValid(self) → bool¶: Returns True if the SmartsMatcher is valid

SetMaxCount(self, count: int) → None¶: Set the maximum times pattern can appear for the filter to match

SetMinCount(self, count: int) → None¶: Set the minimum times pattern must appear to match

SetPattern(self, pat: rdkit.Chem.rdchem.Mol) → None¶

SetPattern(self, pat: str) → None

Overloaded function.

SetPattern(self, pat: rdkit.Chem.rdchem.Mol) -> None

Set the pattern molecule for the SmartsMatcher

SetPattern(self, pat: str) -> None

Set the smarts pattern for the Smarts Matcher (warning: MinimumCount is not reset)

rdkit.Chem.rdfiltercatalog module¶

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