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

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.