medchem.catalogs

medchem.catalogs.list_named_catalogs()

List all available named catalogs. This list will not report chemical groups !

Tip

For a list of chemical groups that can be queried using NamedCatalog.chemical_groups, use medchem.groups.list_default_chemical_groups

medchem.catalogs.merge_catalogs(*catalogs)

Merge several catalogs into a single one

Returns:

Name	Type	Description
catalog	FilterCatalog	merged catalog

medchem.catalogs.catalog_from_smarts(smarts, labels=None, mincounts=None, maxcounts=None, entry_as_inds=False)

Load catalog from a list of smarts

Parameters:

Name	Type	Description	Default
smarts	Union[Sequence[str], ndarray, Series]	list of input smarts to add to the catalog	required
labels	Optional[Union[Sequence[str], ndarray, Series]]	list of label for each smarts	None
mincounts	Optional[Union[Sequence[int], ndarray, Series]]	minimum count before a match is recognized	None
maxcounts	Optional[Union[Sequence[int], ndarray, Series]]	maximum count for a match to be valid	None
entry_as_inds	bool	whether to use index for entry id or the label	False

Returns:

Name	Type	Description
catalog	FilterCatalog	filter catalog built from the input smarts

medchem.catalogs.NamedCatalogs

Holder for substructure matching catalogs. This class provides several popular and custom catalog that can be used for substructure matching.

All the catalogs are cached using functools.lru_cache to avoid reloading them every time.

Note

A filter catalog is a collection of substructures and molecular patterns (SMARTS) used to flag molecules with (un)desirable structural properties.

alerts(subset=None) staticmethod

Common alerts filter catalogs commonly used in molecule filtering

Parameters:

Name	Type	Description	Default
subset	Optional[Union[List[str], str]]	subset of alert providers to consider	None

Returns:

Name	Type	Description
catalog	FilterCatalog	filter catalog

bredt() cached staticmethod

Bredt Filter Rules: a catalog for filtering unstable molecules, ideal for molecules generated by deep learning models or chemical space enumeration. See example of usage by surge

chemical_groups(filters='medicinal') cached staticmethod

Chemical group filter catalogs

Parameters:

Name	Type	Description	Default
filters	Union[str, List[str]]	list of tag to filter the catalog on.	'medicinal'

nibr() cached staticmethod

Catalog from NIBR

Warning

This will return all the compounds in the catalog, regardless of their severity (FLAG, EXCLUDE, ANNOTATION). You likely don't want to use this for blind prioritization.

tox(pains_a=True, pains_b=True, pains_c=False, brenk=True, nih=False, zinc=False) cached staticmethod

Common toxicity and interference catalog

Parameters:

Name	Type	Description	Default
pains_a	bool	whether to include PAINS filters (assay A)	True
pains_b	bool	whether to include PAINS filters (assay B)	True
pains_c	bool	whether to include PAINS filters (assay C)	False
brenk	bool	whether to include BRENK filters, also known as Dundee filters	True
nih	bool	whether to include NIH filters	False
zinc	bool	whether to include ZINC filters	False

unstable_graph(severity_threshold=5) cached staticmethod

Unstable molecular graph to filter out, ideal for generated de novo molecules.

Warning

This method returns problematic patterns and thus patterns with higher severity than the threshold.

Parameters:

Name	Type	Description	Default
severity_threshold	int	minimum severity for a pattern to be returned.	5