gt4sd.properties.scores.core module

Implementation of scorers.

Summary

Classes:

CombinedScorer
DistanceScorer
IsomerScorer
QEDScorer
RDKitDescriptorScorer
SMARTSScorer
TanimotoScorer
TargetValueScorer

Functions:

distance_to_score

calculating exponential for a given distance

Reference

distance_to_score(distance, beta)

calculating exponential for a given distance

Parameters

distance (float) – A float.

Return type

float

Returns

An exponential score value for a given SMILES

class DistanceScorer(beta=1e-08)

Bases: ScoringFunction

__init__(beta=1e-08)

DistanceScorer is used to call a partial copy of distance_to_score function.

Parameters

beta (float) – A float value used for getting an exponential score value

get_distance(smile_distance)

Generates a partial copy of distance_to_score function

Parameters

smiles – SMILES.

Return type

float

Returns

An exponential score value for a given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class TargetValueScorer(target, scoring_function)

Bases: DistanceScorer

__init__(target, scoring_function)

Scoring function which is used to generate a score based on a taget and a scoring function.

Parameters

• target (float) – target score that will be used to get the distance to the score of the SMILES

• scoring_function (Callable[[str], float]) – an instance of a scoring class

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

score_list(smiles_list)

Generates a list of scores for a given SMILES List

Parameters

smiles_list (List[str]) – A List of SMILES.

Return type

List[float]

Returns

A List of scores

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class CombinedScorer(scorer_list, weights=None)

Bases: object

__init__(scorer_list, weights=None)

Scoring function which generates a combined score for a SMILES as per the given scoring functions.

Parameters

• scorer_list (List[Type[Any]]) – A list of the scoring functions

• weights (Optional[List[float], None]) – A list of weights

_normalize_weights(weights=None)

It is used for normalizing weights.

Parameters

weights – A list of weights.

Return type

List[float]

Returns

Sum of all the scores generated by the given scoring functions

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Returns

Sum of all the scores generated by the given scoring functions

score_list(smiles_list)

Generates a list of scores for a given SMILES List

Parameters

smiles_list (List[str]) – A List of SMILES.

Return type

List[float]

Returns

A List of scores

__dict__ = mappingproxy({'__module__': 'gt4sd.properties.scores.core', '__init__': <function CombinedScorer.__init__>, '_normalize_weights': <function CombinedScorer._normalize_weights>, 'score': <function CombinedScorer.score>, 'score_list': <function CombinedScorer.score_list>, '__dict__': <attribute '__dict__' of 'CombinedScorer' objects>, '__weakref__': <attribute '__weakref__' of 'CombinedScorer' objects>, '__doc__': None, '__annotations__': {}})

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

__weakref__

list of weak references to the object (if defined)

class RDKitDescriptorScorer(target, modifier='gaussian_modifier', descriptor='num_rotatable_bonds')

Bases: TargetValueScorer

__init__(target, modifier='gaussian_modifier', descriptor='num_rotatable_bonds')

Scoring function wrapping RDKit descriptors.

Parameters

• target (float) – target score that will be used to get the distance to the score of the SMILES

• modifier (str) – score modifier

• descriptor (str) – molecular descriptors

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class TanimotoScorer(target, target_smile, fp_type='ECFP4', modifier='gaussian_modifier')

Bases: TargetValueScorer

__init__(target, target_smile, fp_type='ECFP4', modifier='gaussian_modifier')

Scoring function that looks at the fingerprint similarity against a target molecule.

Parameters

• target (float) – target score that will be used to get the distance to the score of the SMILES

• target_smile (str) – target molecule to compare similarity

• fp_type (str) – fingerprint type

• modifier (str) – score modifier

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class IsomerScorer(target, target_smile)

Bases: TargetValueScorer

__init__(target, target_smile)

Scoring function for closeness to a molecular formula.

Parameters

• target (float) – target score that will be used to get the distance to the score of the SMILES

• target_smile (str) – targeted SMILES to compare closeness with

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class SMARTSScorer(target, target_smile, inverse=True)

Bases: TargetValueScorer

__init__(target, target_smile, inverse=True)

Scoring function that looks at the fingerprint similarity against a target molecule.

Parameters

• target (float) – target score that will be used to get the distance to the score of the SMILES

• target_smile (str) – The SMARTS string to match

• inverse (bool) – If True then SMARTS is desired else it is not desired in the molecules

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'

class QEDScorer(target)

Bases: TargetValueScorer

__init__(target)

Scoring function that calculates the weighted sum of ADS mapped properties using QED module of rdkit

Parameters

target (float) – target score that will be used to get the distance to the score of the SMILES

score(smiles)

Generates a score for a given SMILES

Parameters

smiles (str) – SMILES.

Return type

float

Returns

A score for the given SMILES

__annotations__ = {}

__doc__ = None

__module__ = 'gt4sd.properties.scores.core'