molecule.h

Go to the documentation of this file.

/*
 * Copyright 2009-2021 The VOTCA Development Team (http://www.votca.org)
 *
 * 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.
 *
 */
 
#pragma once
#ifndef VOTCA_CSG_MOLECULE_H
#define VOTCA_CSG_MOLECULE_H
 
// Standard includes
#include <cassert>
#include <map>
#include <string>
#include <vector>
 
// Local VOTCA includes
#include "bead.h"
 
namespace votca {
namespace csg {
 
class Interaction;
 
class Molecule {
 public:
  Index getId() const { return id_; }
 
  const std::string &getName() const { return name_; }
 
  void setName(const std::string &name) { name_ = name; }
 
  void AddBead(Bead *bead, const std::string &name);
  Bead *getBead(Index bead) { return beads_[bead]; }
  const Bead *getBead(Index bead) const { return beads_[bead]; }
  Index getBeadId(Index bead) const { return beads_[bead]->getId(); }
  Index getBeadIdByName(const std::string &name) const;
 
  Index BeadCount() const { return beads_.size(); }
 
  const std::vector<Bead *> &Beads() const { return beads_; }
  std::vector<Bead *> &Beads() { return beads_; }
  Index getBeadByName(const std::string &name) const;
  std::string getBeadName(const Index bead) { return bead_names_[bead]; }
  const std::string &getBeadName(const Index bead) const {
    return bead_names_[bead];
  }
 
  void AddInteraction(Interaction *ic) { interactions_.push_back(ic); }
 
  std::vector<Interaction *> Interactions() { return interactions_; }
  const std::vector<Interaction *> &Interactions() const {
    return interactions_;
  }
 
 private:
  // maps a name to a bead id
  std::map<std::string, Index> beadmap_;
  std::vector<Interaction *> interactions_;
 
  // id of the molecules
  Index id_;
 
  // name of the molecule
  std::string name_;
  // the beads in the molecule
  std::vector<Bead *> beads_;
  std::vector<std::string> bead_names_;
 
  Molecule(Index id, std::string name) : id_(id), name_(name) {}
 
  friend class Topology;
};
 
inline Index Molecule::getBeadIdByName(const std::string &name) const {
  Index i = getBeadByName(name);
  if (i < 0) {
    return i;
  }
  return beads_[i]->getId();
}
 
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_MOLECULE_H