aizynthfinder.context.scoring package

Submodules

aizynthfinder.context.scoring.collection module

Module containing classes used to score the reaction routes.

class aizynthfinder.context.scoring.collection.ScorerCollection(config)

Bases: aizynthfinder.context.collection.ContextCollection

Store scorer objects for the aizynthfinder interface.

The scorers can be obtained by name with simple indexing

scorers = ScorerCollection()
scorer = scorers['state score']

Scorers defined in this module and that does not require any other argument to initialize than the config are auto-loaded.

Parameters

config (Configuration) – the configuration of the tree search

Return type

None

create_default_scorers()

Setup the scores that only need the config as their input.

Return type

None

load(scorer)

Add a pre-initialized scorer object to the collection

Parameters

scorer (aizynthfinder.context.scoring.scorers.Scorer) – the item to add

Return type

None

load_from_config(**scorers_config)

Load one or several scorers from a configuration dictionary

The keys are the name of scorer class. If a scorer is not defined in the aizynthfinder.context.scoring module, the module name can be appended, e.g. mypackage.scoring.AwesomeScore.

The values of the configuration is passed directly to the scorer class along with the config parameter.

Raises

ScorerException – if module or class could not be found

Parameters

scorers_config (Any) –

Return type

None

make_subset(subset_names)

Make a new scorer collection by taking a subset of this collection. The scorer instances will be shared between the collections

Parameters

subset_names (List[str]) – the scorers to copy over

Returns

the newly formed collection

Return type

ScorerCollection

names()

Return a list of the names of all the loaded scorers

Return type

List[str]

objects()

Return a list of all the loaded scorer objects

Return type

List[Scorer]

score_vector(item)

For the given item, score it with all selected scorers and return a vector

Parameters

item (_Scoreable) – the item to be scored

Returns

the vector with the scores

Return type

Sequence[float]

weighted_score(item, weights)

For the given item, score it with all selected scorers and return a weighted sum of all the scores.

If weights is not the same length as the number of scorers an exception is raised.

If no scorers are selected this will raise an exception

Parameters

  • item (_Scoreable) – the item to be scored

  • weights (Sequence[float]) – the weights of the scorers

Returns

the weighted sum

Return type

float

aizynthfinder.context.scoring.scorers module

Module containing classes used to score the reaction routes.

class aizynthfinder.context.scoring.scorers.SquashScaler(slope, xoffset, yoffset)

Bases: object

Squash function loosely adapted from a sigmoid function with parameters to modify and offset the shape

Parameters

  • slope (float) – the slope of the midpoint

  • xoffset (float) – the offset of the midpoint along the x-axis

  • yoffset (float) – the offset of the curve along the y-axis

Return type

None

slope: float
xoffset: float
yoffset: float
class aizynthfinder.context.scoring.scorers.MinMaxScaler(min_val, max_val, reverse, scale_factor=1)

Bases: object

Scaling function that normalises the value between 0 - 1, the reverse variable controls the direction of scaling, reverse should set to be true for rewards that need to be minimised the scale_factor could be used to adjust the scores when they are too small or too big

Parameters

  • val – the value that is being scaled

  • min_val (float) – minimum val param val could take

  • max_val (float) – maximum val param val could take

  • scale_factor (float) – scaling factor applied to the minmax scaled output

  • reverse (bool) –

Return type

None

min_val: float
max_val: float
reverse: bool
scale_factor: float = 1
class aizynthfinder.context.scoring.scorers.Scorer(config=None, scaler_params=None)

Bases: abc.ABC

Abstract base class for classes that do scoring on MCTS-like nodes or reaction trees.

The actual scoring is done be calling an instance of a scorer class with a Node or ReactionTree object as only argument.

scorer = MyScorer()
score = scorer(node1)

You can also give a list of such objects to the scorer

scorer = MyScorer()
scores = scorer([node1, node2])
Parameters

  • config (Optional[Configuration]) – the configuration the tree search

  • scaler_params (Optional[StrDict]) – the parameter settings of the scaler

Return type

None

scorer_name = 'base'
sort(items)

Sort nodes or reaction trees in descending order based on the score

Parameters

items (_Scoreables) – the items to sort

Returns

the sorted items and their scores

Return type

Tuple[_Scoreables, Sequence[float], Sequence[int]]

class aizynthfinder.context.scoring.scorers.StateScorer(config, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the state score

Parameters

  • config (Configuration) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'state score'
class aizynthfinder.context.scoring.scorers.MaxTransformScorerer(config=None, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the maximum transform

Parameters

  • config (Optional[Configuration]) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'max transform'
class aizynthfinder.context.scoring.scorers.FractionInStockScorer(config, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the fraction in stock

Parameters

  • config (Configuration) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'fraction in stock'
class aizynthfinder.context.scoring.scorers.NumberOfReactionsScorer(config=None, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the number of reaction it took to get to a node

Parameters

  • config (Optional[Configuration]) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'number of reactions'
class aizynthfinder.context.scoring.scorers.NumberOfPrecursorsScorer(config=None, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the number of pre-cursors in a node or route

Parameters

  • config (Optional[Configuration]) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'number of pre-cursors'
class aizynthfinder.context.scoring.scorers.NumberOfPrecursorsInStockScorer(config, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes based on the number of pre-cursors in stock a node or route

Parameters

  • config (Configuration) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'number of pre-cursors in stock'
class aizynthfinder.context.scoring.scorers.AverageTemplateOccurrenceScorer(config=None, scaler_params=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring the nodes based on the average occurrence of the templates used to get to a node

Parameters

  • config (Optional[Configuration]) –

  • scaler_params (Optional[StrDict]) –

Return type

None

scorer_name = 'average template occurrence'
class aizynthfinder.context.scoring.scorers.PriceSumScorer(config, scaler_params=None, default_cost=1.0, not_in_stock_multiplier=10)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Scorer that sums the prices of all pre-cursors

Parameters

  • config (Configuration) –

  • scaler_params (Optional[StrDict]) –

  • default_cost (float) –

  • not_in_stock_multiplier (int) –

Return type

None

scorer_name = 'sum of prices'
class aizynthfinder.context.scoring.scorers.RouteCostScorer(config, scaler_params=None, reaction_cost=1, average_yield=0.8, default_cost=1, not_in_stock_multiplier=10)

Bases: aizynthfinder.context.scoring.scorers.PriceSumScorer

Score based on the cost of molecules and reactions. From Badowski et al. Chem Sci. 2019, 10, 4640

Parameters

  • config (Configuration) –

  • scaler_params (Optional[StrDict]) –

  • reaction_cost (int) –

  • average_yield (float) –

  • default_cost (int) –

  • not_in_stock_multiplier (int) –

Return type

None

scorer_name = 'route cost'
class aizynthfinder.context.scoring.scorers.ReactionClassMembershipScorer(config, reaction_class_set, in_set_score=1.0, not_in_set_score=0.1)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Scorer that checks if the reaction classes are in a specified set

The score is calculated as product over each reaction. For each reaction the reaction classification is checked if it is in a given list of classes.

Parameters

  • config (Configuration) –

  • reaction_class_set (Sequence[str]) –

  • in_set_score (float) –

  • not_in_set_score (float) –

Return type

None

class aizynthfinder.context.scoring.scorers.StockAvailabilityScorer(config, source_score, default_score=0.1)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Scorer that computes score based on the stock availability of the starting material

The score is calculated as a product of a stock score per starting material. The stock score for each molecule is based on the source of the stock, or a default value if the molecule is not in stock.

Parameters

  • config (Configuration) –

  • source_score (StrDict) –

  • default_score (float) –

Return type

None

class aizynthfinder.context.scoring.scorers.CombinedScorer(config, scorers, weights=None)

Bases: aizynthfinder.context.scoring.scorers.Scorer

Class for scoring nodes and reaction trees by combining weighted scores from a list of scorers

If no weights are provided as input, the scorer provides default weights that are equal for all input scorers.

The CombinedScorer cannot be instantiated from the config file as it requires the names of the scorers to combine as input.

Parameters

  • config (Configuration) –

  • scorers (Sequence[str]) –

  • weights (Optional[Sequence[float]]) –

Return type

None

Module contents

Sub-package containing scoring routines