medchem.groups

medchem.groups.list_default_chemical_groups(hierarchy=False)

List all the available chemical groups.

Note

chemical groups defines how a collection of patterns are organized. They do not correspond to individual pattern name.

Parameters:

Name	Type	Description	Default
hierarchy	bool	whether to return the full hierarchy or the group name only	False

Returns:

Type	Description
list	List of chemical groups

medchem.groups.list_functional_group_names(unique=True)

List common functional group names

Parameters:

Name	Type	Description	Default
unique	bool	whether to return only unique names	True

Returns:

Type	Description
list	List of functional group names

medchem.groups.get_functional_group_map() cached

Map functional groups to their corresponding SMARTS string.

Returns:

Type	Description
dict	List of functional group names

medchem.groups.ChemicalGroup

Build a library of chemical groups using a list of structures parsed from a file

The default library of structure has been curated from https://github.com/Sulstice/global-chem and additional open source data.

Note

For new chemical groups, please minimally provide the 'smiles'/'smarts', 'name' and "group" and optional 'hierarchy' columns

Warning

The SMILES and SMARTS used in the default list of substructures do not result in the same matches. Unless specified otherwise, the SMILES will be used in the matching done by this class, whereas due to RDKit's limitation, the SMARTS will be used in the matching done by the generated catalog.

dataframe property

Get the dataframe of the chemical groups

mol_adjusted property

Get the Molecules object of the SMILES, adjusted for stricter match for the chemical groups in this instance

mol_smarts property

Get the SMARTS of the chemical groups in this instance

mols property

Get the Molecule object of the SMILES for the chemical groups in this instance

name property

Get the Name of the chemical groups in this instance

smarts property

Get the SMARTS of the chemical groups in this instance

smiles property

Get the SMILES of the chemical groups in this instance

__init__(groups=None, n_jobs=None, groups_db=None)

Build a chemical group library

Parameters:

Name	Type	Description	Default
groups	Optional[Union[str, List[str]]]	List of groups to use. Defaults to None where all functional groups are used	None
n_jobs	Optional[int]	Optional number of jobs to run in parallel for internally building the data. Defaults to None.	None
groups_db	Optional[Union[PathLike, str]]	Path to a file containing the dump of the chemical groups. Default is internal dataset	None

filter(names, fuzzy=False)

Filter the group to restrict to only the name in input

Parameters:

Name	Type	Description	Default
names	List[str]	list of names to use for filters	required
fuzzy	bool	whether to use exact or fuzzy matching	False

get_catalog(exact_match=True)

Build an rdkit catalog from the current chemical group data

Parameters:

Name	Type	Description	Default
exact_match	bool	whether to adjust the queries for a more stringent match	True

get_matches(mol, use_smiles=True, exact_match=False, terminal_only=False)

Get all the functional groups in this instance that matches the input molecule

Parameters:

Name	Type	Description	Default
mol	Union[Mol, str]	input molecule	required
use_smiles	bool	whether to use the smiles representation of the catalog or the smarts	True
exact_match	bool	whether to use exact matching by adjusting the query	False
terminal_only	bool	ensure whether the matches to the functional group are terminal, meaning that any subgraph matching should not be in the middle of the molecules.	False

has_match(mol, exact_match=False, terminal_only=False)

Check whether the input molecule has any functional group in this instance

Parameters:

Name	Type	Description	Default
mol	Union[Mol, str]	input molecule	required
exact_match	bool	whether to use exact matching by adjusting the query	False
terminal_only	bool	ensure the matches to the functional group are terminal	False

list_groups()

List all the chemical groups available

list_hierarchy_groups()

List all the hierarchy in chemical groups available. To get the full hierarchy on each path, split by the . character.