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

cast_type

Alias for field number 1

func

Alias for field number 0

key

Alias for field number 3

label

Alias for field number 2

exception schrodinger.application.canvas.topo_descriptors.TopoError

Bases: exceptions.Exception

Error raised when unable to calculate topological descriptor

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

Bases: object

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.cached_topo_descriptor(func)

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

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.

schrodinger.application.canvas.topo_descriptors.pairwise(iterable)

s -> (s0,s1), (s1,s2), (s2, s3), …