`medchem.query`¶

`medchem.query.QueryFilter` ¶

Query filtering system based on a custom query grammar

`call(mols, scheduler='processes', n_jobs=-1, progress=True)` ¶

Call the internal chemical filter that has been build

Parameters:

Name	Type	Description	Default
`mols`	`List[Union[str, Mol]]`	list of input molecules to filter	required
`n_jobs`	`int`	whether to run jobs in parallel and number of jobs to consider.	`-1`
`scheduler`	`str`	joblib scheduler to use.	`'processes'`
`progress`	`bool`	whether to show job progress.	`True`

`init(query, grammar=None, parser='lalr')` ¶

Constructor for query filtering system

Parameters:

Name	Type	Description	Default
`query`	`str`	input unparsed query	required
`grammar`	`Optional[str]`	path to grammar language to use. Defaults to None, which will use the default grammar.	`None`
`parser`	`str`	which Lark language parser to use. Defaults to "lalr".	`'lalr'`

`medchem.query.QueryOperator` ¶

A class to hold all the operators that can be used in queries

`AVAILABLES_PROPERTIES = list_descriptors()` `class-attribute` `instance-attribute` ¶

Default list of available properties in medchem's query system

`AVAILABLE_CATALOGS = list_named_catalogs()` `class-attribute` `instance-attribute` ¶

Default list of available catalogs in medchem's query system

`AVAILABLE_FUNCTIONAL_GROUPS = list_functional_group_names()` `class-attribute` `instance-attribute` ¶

Default list of available functional groups in medchem's query system

`AVAILABLE_RULES = RuleFilters.list_available_rules_names()` `class-attribute` `instance-attribute` ¶

Default list of available rules in medchem's query system

`getprop(mol, prop)` `staticmethod` ¶

Compute the molecular property of a molecule. This is an alternative to the hasprop function, that does not enforce any comparison.

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`prop`	`str`	molecular property to apply as filter on the molecule	required

Returns:

Name	Type	Description
`property`	`float`	computed property value

`hasalert(mol, alert)` `staticmethod` ¶

Check if a molecule match a named alert catalog. The alert catalog needs to be one supported by the medchem package.

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`alert`	`str`	named catalog to apply as filter on the molecule	required

Returns:

Name	Type	Description
`has_alert`	`bool`	whether the molecule has a given alert

`hasgroup(mol, group)` `staticmethod` ¶

Check if a molecule has a specific functional group.

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`group`	`str`	functional group to check on the molecule.	required

Returns:

Name	Type	Description
`has_group`	`bool`	whether the molecule has the given functional group

`hasprop(mol, prop, comparator, limit)` `staticmethod` ¶

Check if a molecule has a property within a desired range

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`prop`	`str`	molecular property to apply as filter on the molecule	required
`comparator`	`Callable`	operator function to apply to check whether the molecule property matches the expected value	required
`limit`	`float`	limit value for determining whether the molecule property is within desired range	required

Returns:

Name	Type	Description
`has_property`	`bool`	whether the molecule has a given property within a desired range

`hassubstructure(mol, query, is_smarts=False, operator='min', limit=1)` `staticmethod` ¶

Check if a molecule has the substructure provided by a query

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`query`	`str`	input smarts query	required
`is_smarts`	`bool`	whether this is a smarts query or not	`False`
`operator`	`Optional[str]`	one of min or max to specify the min or max limit	`'min'`
`limit`	`int`	limit of substructures to be found	`1`

Returns:

Name	Type	Description
`has_substructure`	`bool`	whether the query is a subgraph of the molecule

`hassuperstructure(mol, query)` `staticmethod` ¶

Check if a molecule has a superstructure defined by a query. Note that a superstructure cannot be a query (SMARTS)

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`query`	`str`	input smarts query	required

Returns:

Name	Type	Description
`has_superstructure`	`bool`	whether the molecule is a subgraph of the query

`like(mol, query, comparator, limit)` `staticmethod` ¶

Check if a molecule is similar or distant enough from another molecule using tanimoto ECFP distance.

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`query`	`Union[Mol, str]`	input molecule to compare with	required
`comparator`	`Callable[[float, float], bool]`	operator function to apply to check whether the molecule property matches the expected value. Takes computed_similarity and `limit` as arguments and returns a boolean.	required
`limit`	`float`	limit value for determining whether the molecule property is within desired range	required

Returns:

Name	Type	Description
`is_similar`	`bool`	whether the molecule is similar or distant enough from the query

`matchrule(mol, rule)` `staticmethod` ¶

Check if a molecule match a druglikeness rule

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`rule`	`str`	druglikeness rule check on the molecule.	required

Returns:

Name	Type	Description
`match_rule`	`bool`	whether the molecule match the given rule

`similarity(mol, query)` `staticmethod` ¶

Compute the ECFP tanimoto similarity between two molecules. This is an alternative to the like function, that does not enforce any comparison, and lets python handles the binary comparison operators.

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`query`	`Union[Mol, str]`	input query molecule to compute similarity against	required

Returns:

Name	Type	Description
`similarity`	`float`	computed similarity value between mol and query

`medchem.query.EvaluableQuery` ¶

Parser of a query into a list of evaluable function nodes

`call(mol, exec=True)` ¶

Evaluate a query on an input molecule

Parameters:

Name	Type	Description	Default
`mol`	`Union[Mol, str]`	input molecule	required
`exec`	`bool`	whether to interpret the resulting query or not	`True`

Returns:

Type	Description
`str`	query string or boolean value corresponding to the query result

`init(parsed_query, verbose=False)` ¶

Constructor for query evaluation

Parameters:

Name	Type	Description	Default
`parsed_query`	`Union[str, ParseTree]`	query that has been parsed and transformed	required
`verbose`	`bool`	whether to print debug information	`False`

`medchem.query.QueryParser` ¶

Bases: Transformer

Query parser for the custom query language for molecule. This parses the input language, build a parseable and evaluable representation. The trick for lazy evaluation is to define custom guard with 'fn(*)' around expression that needs to be evaluated.

Note that you SHOULD NOT HAVE TO INTERACT WITH THIS CLASS DIRECTLY.

Example

import medchem
import lark
QUERY_GRAMMAR = medchem.utils.loader.get_grammar(as_string=True)
QUERY_PARSER = Lark(QUERY_GRAMMAR, parser="lalr", transformer=QueryParser())
# see how the string needs to be "quoted". This builds on the json quote requirements to avoid dealing with unwanted outcomes
example = """(HASPROP("tpsa" > 120 ) | HASSUBSTRUCTURE("c1ccccc1")) AND NOT HASALERT("pains") OR HASSUBSTRUCTURE("[OH]", max)"""
t = QUERY_PARSER.parse(example)
print(t)
((((`fn(getprop, prop='tpsa')` > 120.0) or `fn(hassubstructure, query='c1ccccc1', operator='None', limit=None, is_smarts=None)`) and not `fn(hasalert, alert='pains')`) or `fn(hassubstructure, query='[OH]', operator='max', limit=None, is_smarts=None)`)

`bool_expr(bool_term, *others)` ¶

Define how boolean expressions should be parsed

`bool_term(bool_factor, *others)` ¶

Define how boolean terms should be parsed