schrodinger.application.matsci.mlearn.features module¶
Classes and functions to deal with ML features.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.matsci.mlearn.features.
avg_atomic_vol
(struct)¶ Get average atomic volume.
Parameters: struct ( schrodinger.structure.Structure
) – Structure to be used for feature calculationReturn type: float Returns: Average atomic volume (A^3)
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schrodinger.application.matsci.mlearn.features.
get_distance_cell
(struct, cutoff, cell, pbc)¶ Create an infrastructure Distance Cell. Struct MUST have the Chorus box properties.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: schrodinger.structure.Structure
, ,schrodinger.infra.structure.DistanceCell
,schrodinger.infra.structure.PBC
Returns: Supercell, an infrastructure Distance Cell that accounts for the PBC, and the pbc used to create it.
Raise: ValueError if struct is missing PBCs
- struct (
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schrodinger.application.matsci.mlearn.features.
elemental_generator
(struct, element, is_equal=True)¶
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schrodinger.application.matsci.mlearn.features.
avg_neighbor_count
(struct, element, cutoff, cell=None, pbc=None)¶ Get average neighbor count.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the count
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average neighbor count
- struct (
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schrodinger.application.matsci.mlearn.features.
std_neighbor_count
(struct, element, cutoff, cell=None, pbc=None)¶ Get standard deviation of neighbor count.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the count
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average neighbor count
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_element_neighbor_count
(struct, cutoff, element, cell=None, pbc=None)¶ Get average element neighbor count.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - cutoff (float) – The cutoff for finding nearest neighbor atoms
- element (str) – Element for which to compute the average
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average number of bonds per element
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_sublattice_neighbor_count
(struct, element, cutoff, cell=None, pbc=None)¶ Get average sublattice neighbor count.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average sublattice neighbor count
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_neighbor_ion
(struct, element, cutoff, cell=None, pbc=None)¶ Get average neighbor ionicity.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average neighbor ionicity
- struct (
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schrodinger.application.matsci.mlearn.features.
std_neighbor_ion
(struct, element, cutoff, cell=None, pbc=None)¶ Get standard deviation of neighbor ionicity.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average neighbor ionicity
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_sublattice_neighbor_ion
(struct, element, cutoff, cell=None, pbc=None)¶ Get average sublattice neighbor ionicity.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Average sublattice neighbor count
- struct (
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schrodinger.application.matsci.mlearn.features.
get_anion
(struct)¶ Get the most electronegative element in the structure (anion).
Parameters: struct ( schrodinger.structure.Structure
) – Input structureReturn type: str, float, int Returns: Element, it’s electronegativity, number of anions in the cell
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schrodinger.application.matsci.mlearn.features.
vol_per_anion
(struct)¶ Get volume per anion.
Parameters: struct ( schrodinger.structure.Structure
) – Input structureReturn type: float Returns: Volume per anion
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schrodinger.application.matsci.mlearn.features.
avg_anion_anion_short_distance
(struct, supercell)¶ Get average anion anion shortest distance.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - struct – Supercell input structure
Return type: float
Returns: Average anion anion shortest distance
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_element_anion_short_distance
(struct, element, supercell)¶ Get average element anion shortest distance.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- struct – Supercell input structure
Return type: float
Returns: Average element anion shortest distance
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_element_element_short_distance
(struct, element, supercell)¶ Get average element element shortest distance.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - element (str) – Element for which to compute the average
- struct – Supercell input structure
Return type: float
Returns: Average element element shortest distance
- struct (
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schrodinger.application.matsci.mlearn.features.
anion_frame_coordination
(struct, supercell)¶ Get anion framework coordination.
Parameters: - struct (
schrodinger.structure.Structure
) – Input structure - struct – Supercell input structure
Return type: float
Returns: Anion framework coordination
- struct (
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schrodinger.application.matsci.mlearn.features.
avg_sublattice_eneg
(struct, element)¶ Get average sublattice electronegativity.
Parameters: - struct (schrodinger.structure.Structure) – Input structure
- element (str) – Element which to exclude from lattice
Return type: float
Returns: Average sublattice electronegativity
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schrodinger.application.matsci.mlearn.features.
packing_fraction
(struct, cutoff, cell=None, pbc=None)¶ Get packing fraction of the crystal.
Parameters: - struct (schrodinger.structure.Structure) – Input structure
- cutoff (float) – The cutoff for finding nearest neighbor atoms
- cell (
schrodinger.infra.structure.DistanceCell
) – Distance cell object for the struct - pbc (
schrodinger.infra.structure.PBC
) – PBC object for the struct
Return type: float
Returns: Packing fraction
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class
schrodinger.application.matsci.mlearn.features.
LatticeFeatures
(element='Li', cutoff=4.0)¶ Bases:
schrodinger.application.matsci.mlearn.base.BaseFeaturizer
Class to generate lattice-based features.
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transform
(structs)¶ Get numerical features from structures. Also sets features names in self.labels. See parent class for more documentation.
Parameters: structs (list( schrodinger.structure.Structure
)) – List of structures to be featurizedReturn type: numpy array of shape [n_samples, n_features] Returns: Transformed array
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