Source code for moldesign.geom.monitor

# 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
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

import moldesign as mdt

from . import toplevel
from . import constraints, grads, coords, setcoord

[docs]class Monitor(object): def __init__(self, *atoms): if len(atoms) != self.NUM_ATOMS: raise ValueError('%s requires %d atoms, but %d passed' % (type(self), self.NUM_ATOMS, len(atoms))) self.atoms = atoms @property def value(self): return self.GETTER(*self.atoms) @value.setter def value(self, val): args = self.atoms + (val,) self.SETTER(*args)
[docs] def gradient(self): return grads._atom_grad_to_mol_grad(self.atoms, self.GRAD(*self.atoms))
[docs] def constrain(self, **kwargs): """ Constrain this coordinate. This will add a new item to the parent molecule's constraint list. Args: **kwargs (dict): kwargs for constraints.GeometryConstraint Returns: constraints.GeometryConstraint: the constraint object """ c = self.CONSTRAINT(*self.atoms, **kwargs) mol = self.atoms[0].molecule for atom in mol.atoms[1:]: if atom.molecule is not mol: raise ValueError("Can't create constraint; atoms are not part of the same Molecule") mol.constraints.append(c) mol._reset_methods() return c
def __call__(self, obj): """ Calculate this value for the given trajectory Args: obj (mdt.Molecule or mdt.Trajectory): molecule or trajectory to measure Returns: moldesign.units.Quantity: this coordinate's value (for a molecule), or a list of values (for a trajectory) Note: Atoms are identified by their index only; the atoms defined in the Monitor must have the same indices as those in the passed object """ return self.GETTER(*(obj.atoms[a.index] for a in self.atoms)) def __str__(self): return '%s: %s' % (type(self).__name__, self.value) def __repr__(self): return '<%s for atoms %s: %s>' % (type(self).__name__, ','.join(str(atom.index) for atom in self.atoms), self.value)
[docs]class DistanceMonitor(Monitor): NUM_ATOMS = 2 GETTER = staticmethod(coords.distance) SETTER = staticmethod(setcoord.set_distance) GRAD = staticmethod(grads.distance_gradient) CONSTRAINT = constraints.DistanceConstraint
[docs]class AngleMonitor(Monitor): NUM_ATOMS = 3 GETTER = staticmethod(coords.angle) SETTER = staticmethod(setcoord.set_angle) GRAD = staticmethod(grads.angle_gradient) CONSTRAINT = constraints.AngleConstraint
[docs]class DihedralMonitor(Monitor): def __init__(self, *atoms): if len(atoms) in (1, 2): atoms = coords._infer_dihedral(*atoms) super(DihedralMonitor, self).__init__(*atoms) NUM_ATOMS = 4 GETTER = staticmethod(coords.dihedral) SETTER = staticmethod(setcoord.set_dihedral) GRAD = staticmethod(grads.dihedral_gradient) CONSTRAINT = constraints.DihedralConstraint