Source code for vermouth.system

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2018 University of Groningen
# 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.
Provides a class to describe a system.
from collections import defaultdict

[docs] class System: """ A system of molecules. Attributes ---------- molecules: list[:class:`~vermouth.molecule.Molecule`] The molecules in the system. """ def __init__(self, force_field=None): self.molecules = [] self._force_field = None self.force_field = force_field self.gmx_topology_params = defaultdict(list) @property def force_field(self): """ The forcefield used to describe the molecules in this system. """ return self._force_field @force_field.setter def force_field(self, value): """ Set the forcefield for all the molecules in the system. Parameters ---------- value: :class:`~vermouth.forcefield.ForceField` """ self._force_field = value for molecule in self.molecules: molecule._force_field = value # pylint: disable=protected-access
[docs] def add_molecule(self, molecule): """ Add a molecule to the system. Parameters ---------- molecule: :class:`~vermouth.molecule.Molecule` """ self.molecules.append(molecule)
@property def num_particles(self): """ The total number of particles in all the molecules in this system. """ return sum(len(mol) for mol in self.molecules)
[docs] def copy(self): """ Creates a copy of this system and it's molecules. Returns ------- System A deep copy of this system. """ new_system = self.__class__() new_system.molecules = [mol.copy() for mol in self.molecules] new_system.force_field = self.force_field return new_system