Mutation Module

Contains tools for determining substitution probability of different species and for mutating instances of SmactStructure to predict new structures.

Tools for handling ion mutation.

class smact.structure_prediction.mutation.CationMutator

Bases: object

Handles cation mutation of SmactStructures based on substitution probability.

Based on the algorithm presented in:

Hautier, G., Fischer, C., Ehrlacher, V., Jain, A., and Ceder, G. (2011) Data Mined Ionic Substitutions for the Discovery of New Compounds. Inorganic Chemistry, 50(2), 656-663. doi:10.1021/ic102031h

complete_cond_probs()

Generate a DataFrame with all the conditional substitution probabilities.

complete_pair_corrs()

Generate a DataFrame with all the pair correlations.

complete_sub_probs()

Generate a DataFrame with all the substitution probabilities.

cond_sub_prob(s1: str, s2: str) → float

Calculate the probability of substitution of one species with another.

cond_sub_probs()

Calculate the probabilities of substitution of a given species.

Calculates probabilities of substitution of given species with all others in the lambda table.

static from_json(lambda_json: ~typing.Optional[str] = None, alpha: ~typing.Optional[~typing.Callable[[str, str], float]] = <function CationMutator.<lambda>>)

Create a CationMutator instance from a DataFrame.

Parameters

• lambda_json (str, optional) – JSON-style representation of the lambda table. This is a list of entries, containing pairs and their associated lambda values. Each entry is a list of [species1, species2, lambda]. If not supplied, defaults to the lambda table included with pymatgen.

• alpha – See __init__().

Returns

A CationMutator instance.

get_lambda(s1: str, s2: str) → float

Get lambda values corresponding to a pair of species.

Parameters

• s1 (str) – One of the species.

• s2 (str) – The other species.

Returns

The lambda value, if it exists

in the table. Otherwise, the alpha value for the two species.

Return type

lambda (float)

get_lambdas()

Get all the lambda values associated with a species.

Parameters

species (str) – The species for which to get the lambda values.

Returns

A pandas Series, with index-labelled lambda entries.

pair_corr(s1: str, s2: str) → float

Determine the pair correlation of two ionic species.

same_spec_cond_probs()

Calculate the same species conditional substiution probabilities.

same_spec_probs()

Calculate the same species substiution probabilities.

sub_prob(s1: str, s2: str) → float

Calculate the probability of substitution of two species.

sub_probs()

Determine the substitution probabilities of a species with others.

Determines the probability of substitution of the species with every species in the lambda table.

unary_substitute(structure: SmactStructure, thresh: Optional[float] = 1e-05) → Generator[Tuple[SmactStructure, float], None, None]

Find all structures with 1 substitution with probability above a threshold.

Parameters

• structure – A SmactStructure instance from which to generate compounds.

• thresh (float) – The probability threshold; discard all substitutions that have a probability to generate a naturally-occuring compound less than this.

Yields

Tuples of (SmactStructure, probability).