cgmoleculedef.h

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/*
 * 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.
 *
 */
 
#ifndef VOTCA_CSG_CGMOLECULEDEF_H
#define VOTCA_CSG_CGMOLECULEDEF_H
 
// Standard includes
#include <list>
#include <map>
#include <memory>
#include <string>
#include <vector>
 
// VOTCA includes
#include <votca/tools/property.h>
#include <votca/tools/types.h>
 
// Local VOTCA includes
#include "exclusionlist.h"
#include "map.h"
#include "molecule.h"
 
namespace votca {
namespace csg {
 
class CGMoleculeDef {
 public:
  CGMoleculeDef() = default;
  ~CGMoleculeDef();
 
  Molecule *CreateMolecule(Topology &top);
  Map CreateMap(const Molecule &in, Molecule &out);
 
  void Load(std::string filename);
 
  const std::string &getName() { return name_; }
  const std::string &getIdent() { return ident_; }
 
 private:
  tools::Property options_;
 
  struct beaddef_t {
    std::string name_;
    std::string type_;
    Bead::Symmetry symmetry_;
    std::string mapping_;
    std::vector<std::string> subbeads_;
    tools::Property *options_;
  };
 
  // name of the coarse grained molecule
  std::string name_;
  // name of the molecule to coarse grain
  std::string ident_;
 
  // beads of the cg molecule
  std::vector<beaddef_t *> beads_;
  std::map<std::string, beaddef_t *> beads_by_name_;
 
  // mapping schemes
  std::map<std::string, tools::Property *> maps_;
 
  std::vector<tools::Property *> bonded_;
 
  void ParseTopology(tools::Property &options);
  void ParseBeads(tools::Property &options);
  void ParseBonded(tools::Property &options);
  void ParseMapping(tools::Property &options);
 
  beaddef_t *getBeadByName(const std::string &name);
  tools::Property *getMapByName(const std::string &name);
};
 
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_CGMOLECULEDEF_H