text: #!/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.
  
  """
  Merge molecules by chain.
  """
  
  from ..molecule import Molecule
  from ..processors.processor import Processor
  
  
  def merge_chains(system, chains):
      """
      Merge molecules with the given chains as a single molecule.
  
      Molecules are merged into the resulting molecule if their chain is in the
      list of chains to merge. The resulting molecule is not connected.
  
      If a molecule comprises multiple chains, then it is merged only if all the
      chains it comprises are part of the selection.
  
      The meta variable are not conserved in the process.
  
      The input system is modified in-place.
  
      Parameters
      ----------
      system: vermouth.system.System
          The system to modify.
      chains: list[str]
          A container of chain identifier.
      """
      chains = set(chains)
      merged = Molecule()
      merged._force_field = system.force_field
      has_merged = False
      new_molecules = []
      for molecule in system.molecules:
          molecule_chains = set(node.get('chain') for node in molecule.nodes.values())
          if molecule_chains.issubset(chains):
              if not has_merged:
                  merged.nrexcl = molecule.nrexcl
                  new_molecules.append(merged)
              merged.merge_molecule(molecule)
              has_merged = True
          else:
              new_molecules.append(molecule)
  
      system.molecules = new_molecules
  
  
  class MergeChains(Processor):
      name = 'MergeChains'
  
      def __init__(self, chains):
          self.chains = chains
  
      def run_system(self, system):
          merge_chains(system, self.chains)
  