# 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.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
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):
self.name = name
def __get__(self, instance, cls=None):
return getattr(instance, self.name)
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):
self.name = atomname
self.moleculename = moleculename
def __get__(self, instance, cls=None):
if instance.molecule is None:
return getattr(instance, self.name)
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