xmltopologyreader.h

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/*
 * Copyright 2009-2020 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_XMLTOPOLOGYREADER_PRIVATE_H
#define VOTCA_CSG_XMLTOPOLOGYREADER_PRIVATE_H
 
// Standard includes
#include <stack>
#include <string>
 
// Third party includes
#include <boost/unordered_map.hpp>
 
// Local VOTCA includes
#include "votca/csg/topologyreader.h"
 
namespace votca {
namespace csg {
 
namespace TOOLS = votca::tools;
 
class BondBead {
 public:
  BondBead(std::string &line) {
    TOOLS::Tokenizer tok(line, ":");
    std::vector<std::string> tmp_vec = tok.ToVector();
    if (tmp_vec.size() != 2) {
      throw std::runtime_error("Wrong number of elements in bead: " + line);
    }
    molname = tmp_vec[0];
    atname = tmp_vec[1];
    molname.erase(molname.find_last_not_of(" \n\r\t") + 1);
    atname.erase(atname.find_last_not_of(" \n\r\t") + 1);
  }
 
  std::string molname;
  std::string atname;
};
 
class XMLBead {
 public:
  XMLBead(std::string name_, std::string type_, double mass_ = 1.0,
          double q_ = 0.0)
      : name(name_), type(type_), mass(mass_), q(q_) {};
  XMLBead() = default;
 
  Index pid;
  std::string name;
  std::string type;
  double mass;
  double q;
};
 
class XMLMolecule {
 public:
  XMLMolecule(std::string name_, Index nmols_) : name(name_), nmols(nmols_) {}
  std::string name;
  Index nmols;
  Index pid;
  std::vector<XMLBead *> beads;
  std::map<std::string, XMLBead *> name2beads;
  Molecule *mi;
};
 
class XMLTopologyReader : public TopologyReader {
 public:
  bool ReadTopology(std::string filename, Topology &top) override;
  ~XMLTopologyReader() override;
 
 private:
  typedef boost::unordered_multimap<std::string, XMLMolecule *> MoleculesMap;
 
  void ReadTopolFile(std::string file);
 
  void ParseRoot(tools::Property &property);
  void ParseMolecules(tools::Property &p);
  void ParseBeadTypes(tools::Property &el);
  void ParseBonded(tools::Property &el);
  void ParseBox(tools::Property &p);
  void ParseMolecule(tools::Property &p, std::string molname, Index nmols);
  void ParseBond(tools::Property &p);
  void ParseAngle(tools::Property &p);
  void ParseDihedral(tools::Property &p);
 
 private:
  Topology *top_;
  MoleculesMap molecules_;
  Index mol_index_;
  Index bead_index_;
 
  bool has_base_topology_;
};
 
}  // namespace csg
}  // namespace votca
 
#endif  // VOTCA_CSG_XMLTOPOLOGYREADER_PRIVATE_H