mol_parser.hh

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/// @file core/chemical/sdf/mol_parser.hh
///
/// @brief header file for molfile parser
/// @author Sam DeLuca



#ifndef INCLUDED_core_chemical_sdf_mol_parser_HH
#define INCLUDED_core_chemical_sdf_mol_parser_HH

// AUTO-REMOVED #include <core/chemical/ResidueType.hh>
#include <utility/vector1.hh>
#include <core/chemical/sdf/mol_parser.fwd.hh>
#include <core/chemical/sdf/MolData.hh>
//#include <protocols/ligand_docking/ColoredGraph.fwd.hh>


#include <string>

#include <core/chemical/AtomTypeSet.fwd.hh>
#include <core/chemical/ElementSet.fwd.hh>
#include <core/chemical/MMAtomTypeSet.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.fwd.hh>



namespace core {
namespace chemical {
namespace sdf {

class MolFileParser
{
public:

  MolFileParser(const utility::vector1<std::string> mol_file_lines);
  MolFileParser(const std::string file_name);
  void parse_mol_file(core::chemical::AtomTypeSetCAP atom_types, ElementSetCAP elements, core::chemical::MMAtomTypeSetCAP mm_atom_types, core::chemical::orbitals::OrbitalTypeSetCAP orbital_type_set);
  core::chemical::ResidueTypeOP GetResidueTypeOP();
  core::chemical::ResidueType GetResidueType();

  std::string GetMoleculeName();
  std::string GetMoleculeInfo();
  std::string GetMoleculeComments();

private:

  std::string FindNbrAtom();

  utility::vector1<std::string> mol_file_lines_;
  core::chemical::ResidueTypeOP molecule_container_;
  MolData mol_data_;
  //protocols::ligand_docking::ColoredGraphOP molecule_container_;
  std::string molecule_name_;
  std::string molecule_info_;
  std::string molecule_comments_;
};

} // sdf
} // io
} // core

#endif /* MOL_PARSER_HH_ */