medchem.utils

medchem.utils.smarts

SMARTSUtils

Collections of utils to build complex SMARTS query more efficiently for non experienced user

aliphatic_chain(min_size=6, unbranched=False, unsaturated_bondtype=None, allow_hetero_atoms=True) classmethod

Returns a query that can match a long aliphatic chain

Parameters:

Name	Type	Description	Default
min_size	int	minimum size of the long chain	6
unbranched	bool	whether the chain should be unbranched	False
unsaturated_bondtype	Optional[str]	additional unsaturated bond type to use for the query. By default, Any bond type (~) is used. Single bonds ARE always allowed and bondtype cannot be aromatic	None
allow_hetero_atoms	bool	whether the chain can contain hetero atoms	True

Example

to build a query for a long aliphatic chain of a least 5 atoms (e.g: 'CCC(C)CCC')

SMARTSUtils.aliphatic_chain(min_size=5)

Returns:

Name	Type	Description
smarts	str	smarts pattern matching a long aliphatic chain

atom_in_env(*smarts_strs, include_atoms=False, union=False) classmethod

Returns a recursive/group smarts to find an atom that fits in the environments defined by all the input smarts

Parameters:

Name	Type	Description	Default
smarts_strs	str	list of input patterns defining the environment the atom must fit in. The first atom of each pattern should be the atom we want to match to, unless include_atoms is set to True, then [*:99] will be added at the start of each pattern	()
include_atoms	bool	whether to include an additional first atom that needs to be in the required environment or not	False
union	bool	whether to use the union of the environments or the intersection	False

Example

you can use this function to construct a complex query if you are not sure about how to write the smarts for example, to find a carbon atom that is both in a ring or size 6, bonded to an ethoxy and have a Fluorine in meta

SMARTSUtils.atom_in_env("[#6;r6][OD2][C&D1]", "[c]aa[F]", union=False) # there are alternative way to write this

Returns:

Name	Type	Description
smarts	str	smarts pattern matching the group/environment

meta(smarts_str1, smarts_str2, aromatic_only=False) classmethod

Returns a recursive smarts string connecting the two input smarts in meta of each other. Connection points needs to be through single or double bonds.

Parameters:

Name	Type	Description	Default
smarts_str1	str	first smarts pattern defining the first functional group	required
smarts_str2	str	second smarts pattern defining the second functional group	required
aromatic_only	bool	whether the ring needs to be aromatic or not	False

Example

to build a smarts for a methyl group in meta to an oxygen (e.g: 'c1c(C)cc(O)cc1')

SMARTSUtils.meta('[#6;!R]', '[#8]')

Returns:

Name	Type	Description
smarts	str	smarts pattern connecting the two input smarts in meta of each other

ortho(smarts_str1, smarts_str2, aromatic_only=False) classmethod

Returns a recursive smarts string connecting the two input smarts in ortho of each other. Connection points needs to be through single or double bonds.

Parameters:

Name	Type	Description	Default
smarts_str1	str	first smarts pattern defining the first functional group	required
smarts_str2	str	second smarts pattern defining the second functional group	required
aromatic_only	bool	whether the ring needs to be aromatic or not	False

Example

to build a smarts for a methyl group in ortho to an oxygen (e.g: 'C1CC(C)C(O)CC1')

SMARTSUtils.ortho('[#6;!R]', '[#8]')

Returns:

Name	Type	Description
smarts	str	smarts pattern connecting the two input smarts in ortho of each other

para(smarts_str1, smarts_str2, aromatic_only=False) classmethod

Returns a recursive smarts string connecting the two input smarts in para of each other. Connection points needs to be through single or double bonds.

Parameters:

Name	Type	Description	Default
smarts_str1	str	first smarts pattern defining the first functional group	required
smarts_str2	str	second smarts pattern defining the second functional group	required
aromatic_only	bool	whether the ring needs to be aromatic or not	False

Example

to build a smarts for a methyl group in para to an oxygen (e.g: 'c1(C)ccc(O)cc1')

SMARTSUtils.para('[#6;!R]', '[#8]')

Returns:

Name	Type	Description
smarts	str	smarts pattern connecting the two input smarts in para of each other

standardize_attachment(smiles, attach_tokens='[*:1]') classmethod

Standardize an attachment point in a smiles

Parameters:

Name	Type	Description	Default
smiles	str	SMILES string	required
attach_tokens	str	Attachment point token to use as standard token	'[*:1]'

---

medchem.utils.loader

get_data_path(filename, module='medchem.data') cached

Return the filepath of an internal data file.

get_grammar(grammar=None, as_string=False)

Return the default lark grammar file for the medchem query system

Parameters:

Name	Type	Description	Default
grammar	Optional[Union[PathLike, str]]	The path to the grammar file. If None, the default medchem grammar file is used.	None
as_string	bool	If True, return the grammar as a string. Defaults to False.	False

---

medchem.utils.graph

automorphism(mol, standardize=True, node_attrs=DEFAULT_NODE_ATTR, edge_attrs=DEFAULT_EDGE_ATTR)

Compute automorphism in a molecular graph

Parameters:

Name	Type	Description	Default
mol	Union[str, Mol]	input molecular graph	required
standardize	bool	whether to standardize the compound or not	True
node_attrs	List[str]	list of categorical atom attributes/properties to consider for node matching	DEFAULT_NODE_ATTR
edge_attrs	List[str]	list of categorical bond attributes/properties to consider for edge matching	DEFAULT_EDGE_ATTR

score_symmetry(mol, exclude_self_mapped_edged=False, **automorphism_kwargs)

Provide a symmetry score for a given input molecule

Note

This is an heuristic and our definition of symmetry is pretty loose. We define symmetry according to any (set of) plans dividing the molecule into two very similar subgraph. We include both edge and vertex transitivity. For example the star-molecular graph (e.g neopentane) is symmetrical here, although it's not vertex-transitive.

Parameters:

Name	Type	Description	Default
mol	Union[Mol, str]	inputs molecules	required
exclude_self_mapped_edged	bool	Whether to exclude edges that matches to themselves in automorphism.	False
automorphism_kwargs	Any	keyword for determining automorphism	{}