def __init__(self, distance_matrix, labels):
"""Initialize a similarity descriptor
Arguments:
distance_matrix -- a matrix with interatomic distances, this can
also be distances in a graph
labels -- a list with integer labels used to identify atoms of
the same type
"""
self.table_distances = similarity_table_distances(distance_matrix)
self.table_labels = similarity_table_labels(labels.astype(numpy.int32))
order = numpy.lexsort([self.table_labels[:, 1], self.table_labels[:, 0]])
self.table_labels = self.table_labels[order]
self.table_distances = self.table_distances[order]
def __init__(self, mol_or_graph, labels=None):
if labels is None:
self.labels = mol_or_graph.numbers.astype(numpy.int32)
else:
self.labels = labels.astype(numpy.int32)
self.table_labels = similarity_table_labels(self.labels)
if isinstance(mol_or_graph, Molecule):
self.table_distances = similarity_table_distances(mol_or_graph.distance_matrix)
elif isinstance(mol_or_graph, MolecularGraph):
self.table_distances = similarity_table_distances(mol_or_graph.distances)
#order = self.table_labels.argsort(axis=0,kind='heapsort')
order = numpy.lexsort([self.table_labels[:,1], self.table_labels[:,0]])
self.table_labels = self.table_labels[order]
self.table_distances = self.table_distances[order]
def __init__(self, distance_matrix, labels):
"""Initialize a similarity descriptor
Arguments:
distance_matrix -- a matrix with interatomic distances, this can
also be distances in a graph
labels -- a list with integer labels used to identify atoms of
the same type
"""
self.table_distances = similarity_table_distances(distance_matrix)
self.table_labels = similarity_table_labels(labels.astype(numpy.int32))
order = numpy.lexsort(
[self.table_labels[:, 1], self.table_labels[:, 0]])
self.table_labels = self.table_labels[order]
self.table_distances = self.table_distances[order]
def __init__(self, mol_or_graph, labels=None):
if labels is None:
self.labels = mol_or_graph.numbers.astype(numpy.int32)
else:
self.labels = labels.astype(numpy.int32)
self.table_labels = similarity_table_labels(self.labels)
if isinstance(mol_or_graph, Molecule):
self.table_distances = similarity_table_distances(
mol_or_graph.distance_matrix)
elif isinstance(mol_or_graph, MolecularGraph):
self.table_distances = similarity_table_distances(
mol_or_graph.distances)
#order = self.table_labels.argsort(axis=0,kind='heapsort')
order = numpy.lexsort(
[self.table_labels[:, 1], self.table_labels[:, 0]])
self.table_labels = self.table_labels[order]
self.table_distances = self.table_distances[order]