Source code for vermouth.processors.processor

#!/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
#
#    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.
"""
Provides an abstract base class for processors.
"""




class Processor:
    """
    An abstract base class for processors. Subclasses must implement a
    `run_molecule` method.
    """


    def run_system(self, system):
        """
        Process `system`.

        Parameters
        ----------
        system: vermouth.system.System
            The system to process. Is modified in-place.
        """
        mols = []
        for molecule in system.molecules:
            mols.append(self.run_molecule(molecule))
        system.molecules = mols




    def run_molecule(self, molecule):
        """
        Process a single molecule. Must be implemented by subclasses.

        Parameters
        ----------
        molecule: vermouth.molecule.Molecule
            The molecule to process.

        Returns
        -------
        vermouth.molecule.Molecule
            Either the provided molecule, or a brand new one.
        """
        raise NotImplementedError