schrodinger.application.canvas.topo_descriptors module

Module which computes constitutional and topological descriptors, walk and path counts, and connectivity indices.

Details of the descriptors implemented here are taken from: “Handbook of Molecular Descriptors” by Mannhols, Kubinyi and Timmerman “Molecular Descriptors for Chemoinformatics, Vol. I”, by Todeschini and Consonni

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.canvas.topo_descriptors.Descriptor(func, cast_type, label, key)

Bases: tuple

__contains__(key, /)

Return key in self.

__len__()

Return len(self).

cast_type

Alias for field number 1

count(value, /)

Return number of occurrences of value.

func

Alias for field number 0

index(value, start=0, stop=9223372036854775807, /)

Return first index of value.

Raises ValueError if the value is not present.

key

Alias for field number 3

label

Alias for field number 2

exception schrodinger.application.canvas.topo_descriptors.TopoError

Bases: Exception

Error raised when unable to calculate topological descriptor

__init__(*args, **kwargs)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.canvas.topo_descriptors.cached_topo_descriptor(func, self, *args, **kwargs)

Decorator to extract previously calculated descriptor value from cached descriptors dictionary. If not available, the descriptor is calculated and stored for future reference.

class schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors(default_descriptor_value=None)

Bases: object

__init__(default_descriptor_value=None)

Initializes valid topological descriptors, and creates an empty cached property dictionary.

allDescriptorFullLabels()

Returns all topological descriptor labels as label-key string

Returns

list of all descriptors as “Label (Key)” strings

Return type

list of str

calculateTopologicalDescriptors(st, descriptor_strings)

Calculates a set of topological descriptors for a given structure.

Parameters

• st (structure.Structure) – structure to consider

• descriptor_strings (list of str) – list of descriptors to calculate

Returns

Structure copy appended with successful descriptor properties

Return type

structure.Structure

m2ioPropertyName(descriptor)

Create descriptor m2io property name for a Descriptor.

Parameters

descriptor (Descriptor) – descriptor entry

Returns

m2io formatted descriptor property name

Return type

str

schrodinger.application.canvas.topo_descriptors.check_canvas_license()

Check that a CANVAS_FULL license is available to use

schrodinger.application.canvas.topo_descriptors.matrix_reciprocal(matrix)

Returns a matrix whose elements are the reciprocal of each of the elements of the original matrix. The diagonal of the matrix must be zeros, and the routine assumes that no other zeros exist in the matrix.