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.
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class
schrodinger.application.canvas.topo_descriptors.
Descriptor
(func, cast_type, label, key)¶ Bases:
tuple
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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cast_type
¶ Alias for field number 1
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count
(value) → integer -- return number of occurrences of value¶
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func
¶ Alias for field number 0
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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key
¶ Alias for field number 3
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label
¶ Alias for field number 2
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exception
schrodinger.application.canvas.topo_descriptors.
TopoError
¶ Bases:
Exception
Error raised when unable to calculate topological descriptor
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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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.
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class
schrodinger.application.canvas.topo_descriptors.
TopologicalDescriptors
(default_descriptor_value=None)¶ Bases:
object
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__init__
(default_descriptor_value=None)¶ Initializes valid topological descriptors, and creates an empty cached property dictionary.
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allDescriptorFullLabels
()¶ Returns all topological descriptor labels as label-key string
Returns: list of all descriptors as “Label (Key)” strings Return type: list of str
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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
- st (
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m2ioPropertyName
(descriptor)¶ Create descriptor m2io property name for a Descriptor.
Parameters: descriptor ( Descriptor
) – descriptor entryReturns: m2io formatted descriptor property name Return type: str
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schrodinger.application.canvas.topo_descriptors.
check_canvas_license
()¶ Check that a CANVAS_FULL license is available to use
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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.