def __init__(self, exclude=None):
super(StructureFeaturizers, self).__init__(exclude=exclude)
self._fast_featurizers = [
sf.DensityFeatures(),
sf.GlobalSymmetryFeatures(),
sf.EwaldEnergy(),
sf.SineCoulombMatrix(flatten=True)
]
ssf = sf.SiteStatsFingerprint
self._slow_featurizers = [
ssf.from_preset('CrystalNNFingerprint_ops'),
ssf.from_preset("BondLength-dejong2016"),
ssf.from_preset("BondAngle-dejong2016"),
ssf.from_preset("Composition-dejong2016_SD"),
ssf.from_preset("Composition-dejong2016_AD"),
ssf.from_preset("CoordinationNumber_ward-prb-2017"),
ssf.from_preset("LocalPropertyDifference_ward-prb-2017"),
sf.ChemicalOrdering(),
sf.StructuralHeterogeneity(),
sf.MaximumPackingEfficiency(),
sf.XRDPowderPattern(),
sf.Dimensionality(),
sf.OrbitalFieldMatrix(flatten=True),
sf.JarvisCFID(),
]
# Prevent import errors
self._require_external = []
if torch and cgcnn:
self._require_external.append(sf.CGCNNFeaturizer())
if dscribe:
self._require_external.append(sf.SOAP())
self._need_fitting_featurizers = [
sf.PartialRadialDistributionFunction(),
sf.BondFractions(),
sf.BagofBonds(coulomb_matrix=sf.CoulombMatrix()),
sf.BagofBonds(coulomb_matrix=sf.SineCoulombMatrix()),
]
self._matrix_featurizers = [
sf.CoulombMatrix(flatten=False),
sf.RadialDistributionFunction(), # returns dict
sf.MinimumRelativeDistances(), # returns a list
sf.ElectronicRadialDistributionFunction()
]
# these are the same as _need_fitting_featurizers
self._many_features_featurizers = [
sf.PartialRadialDistributionFunction(),
sf.BondFractions(approx_bonds=False),
sf.BagofBonds(coulomb_matrix=sf.CoulombMatrix()),
sf.BagofBonds(coulomb_matrix=sf.SineCoulombMatrix()),
sf.OrbitalFieldMatrix(flatten=True),
sf.JarvisCFID()
]
def all(self):
fs = [
# Vector
self.ssf.from_preset('CrystalNNFingerprint_ops'),
self.ssf.from_preset("BondLength-dejong2016"),
self.ssf.from_preset("BondAngle-dejong2016"),
self.ssf.from_preset("Composition-dejong2016_SD"),
self.ssf.from_preset("Composition-dejong2016_AD"),
self.ssf.from_preset("CoordinationNumber_ward-prb-2017"),
self.ssf.from_preset("LocalPropertyDifference_ward-prb-2017"),
sf.BondFractions(approx_bonds=False),
sf.BagofBonds(coulomb_matrix=sf.CoulombMatrix()),
sf.BagofBonds(coulomb_matrix=sf.SineCoulombMatrix()),
sf.CoulombMatrix(flatten=True),
sf.BondFractions(),
# Non vector
sf.CoulombMatrix(flatten=False), # returns matrix
sf.SineCoulombMatrix(flatten=False), # returns matrix
sf.RadialDistributionFunction(), # returns dict
sf.MinimumRelativeDistances(), # returns a list
sf.ElectronicRadialDistributionFunction(), # returns ??
sf.PartialRadialDistributionFunction(), # returns ??
]
fs += self.heavy
return self._get_featurizers(fs)
def need_fit(self):
fs = [
sf.PartialRadialDistributionFunction(),
sf.BondFractions(),
sf.BagofBonds(coulomb_matrix=sf.CoulombMatrix()),
sf.BagofBonds(coulomb_matrix=sf.SineCoulombMatrix()),
]
return self._get_featurizers(fs)
def __init__(self, exclude=None):
super(StructureFeaturizers, self).__init__(exclude=exclude)
self._fast_featurizers = [
sf.DensityFeatures(),
sf.GlobalSymmetryFeatures(),
sf.EwaldEnergy()
]
self._slow_featurizers = [
sf.SiteStatsFingerprint.from_preset('CrystalNNFingerprint_ops'),
sf.ChemicalOrdering(),
sf.StructuralHeterogeneity(),
sf.MaximumPackingEfficiency(),
sf.XRDPowderPattern(),
sf.Dimensionality(),
sf.OrbitalFieldMatrix(flatten=True)
]
self._need_fitting_featurizers = [
sf.PartialRadialDistributionFunction(),
sf.BondFractions(),
sf.BagofBonds()
]
self._matrix_featurizers = [
sf.RadialDistributionFunction(), # returns dict
sf.CoulombMatrix(), # returns a matrix
sf.SineCoulombMatrix(), # returns a matrix
sf.OrbitalFieldMatrix(flatten=False), # returns a matrix
sf.MinimumRelativeDistances(), # returns a list
sf.ElectronicRadialDistributionFunction()
]
# these are the same as _need_fitting_featurizers
self._many_features_featurizers = [
sf.PartialRadialDistributionFunction(),
sf.BondFractions(),
sf.BagofBonds(),
sf.OrbitalFieldMatrix(flatten=True)
]