Source code for moldesign.molecules.coord_arrays

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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This module contains python "descriptors" (nothing to do with chemoinformatic "descriptors") that
help maintain the links between an atom's coordinates and its molecule's coordinates

[docs]class ProtectedArray(object): """ Descriptor for arrays that shouldn't be reassigned. Makes sure array attributes (specifically position and momentum) are modified in place Args: name (str): name of the instance attribute """ def __init__(self, name): = name def __get__(self, instance, cls=None): return getattr(instance, def __set__(self, instance, value): self.__get__(instance)[:] = value
[docs]class AtomArray(ProtectedArray): """ Descriptor for atom coordinates are stored in the parent molecule. Makes sure that the arrays and their references are maintained during both reassignment and copying/pickling Args: atomname (str): name of the attribute in the atom instance parentname (str): name of the corresponding attribute in the molecule instance """ def __init__(self, atomname, moleculename): = atomname self.moleculename = moleculename def __get__(self, instance, cls=None): if instance.molecule is None: return getattr(instance, else: return getattr(instance.molecule, self.moleculename)[instance.index]
[docs]class AtomCoordinate(object): """ Descriptor for use with the ``Atom`` class. Gives access to 3D coordinates as ``atom.x,atom.y,atom.z`` instead of ``atom.position[0],atom.position[1],atom.position[2]`` Args: quantity (str): name of the attribute that this accesses index (int): component of the attribute that this accesses """ def __init__(self, attrname, index): self.attrname = attrname self.index = index def __get__(self, instance, cls): array = getattr(instance, self.attrname) return array[self.index] def __set__(self, instance, value): array = getattr(instance, self.attrname) array[self.index] = value