ctab_parser.hh

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/// @file   core/chemical/sdf/ctab_parsher.hh
///
/// @brief parse the CTAB table into a residue object
/// @author Sam DeLuca


#ifndef INCLUDED_CORE_chemical_sdf_ctab_parser_HH
#define INCLUDED_CORE_chemical_sdf_ctab_parser_HH

#include <string>
#include <map>
#include <vector>
#include <core/chemical/sdf/ctab_parser.fwd.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <utility/vector1.hh>
#include <core/chemical/sdf/ctab_typer.hh>
#include <core/chemical/sdf/ctab_base.hh>
#include <core/chemical/sdf/MolData.hh>


namespace core {
namespace chemical {
namespace sdf {

static std::string const DEFAULT_ATOM_TYPE_="CH3";
static std::string const DEFAULT_MM_ATOM_TYPE_="X";

/*
struct addedH {
public:
  core::Size atom_number;
  std::string bonded_atom_name;
  std::string atom_type;
};


class elementToType {
public:
  elementToType();
  std::string get(std::string key);
private:
  std::map<std::string, std::string> e_to_t;
};
*/
static elementToType element_to_default_type;

class ctabV2000Parser {

public:
  ctabV2000Parser(const utility::vector1<std::string> connection_table_lines, core::chemical::ResidueTypeOP molecule_container,MolData mol_data);
  void ParseTable();

  core::chemical::ResidueTypeOP GetResidueType();
  //protocols::ligand_docking::ColoredGraphOP GetResidueGraph();


private:
  void set_atom_type(core::Size atomno, std::string atomname);
  void ParseAtom(const std::string atom_line, core::Size atom_number);
  void ParseBond(const std::string bond_line);
  std::map<core::Size,std::string> ParseAtomTypeData();

private:
  utility::vector1<std::string> connection_table_lines_;
  MolData mol_data_;
  std::map<core::Size, std::string> index_to_names_map_;
  core::chemical::ResidueTypeOP molecule_container_;
  utility::vector1<addedH> added_H_;
  core::Size current_atom_;

};

class ctabV3000Parser {
public:
  ctabV3000Parser(const utility::vector1<std::string> connection_table_lines, core::chemical::ResidueTypeOP molecule_container, MolData mol_data );

  void ParseTable();

  core::chemical::ResidueTypeOP GetResidueType();
  //protocols::ligand_docking::ColoredGraphOP GetResidueGraph();


private:
  void set_atom_type(core::Size atomno, std::string atomname);
  void ParseAtom(const std::string atom_line);
  void ParseBond(const std::string bond_line );
  core::Real FindExtraParameter( std::vector<std::string> extra_parameters, const std::string query);
  std::map<core::Size,std::string> ParseAtomTypeData();

private:
  utility::vector1<std::string> connection_table_lines_;
  MolData mol_data_;
  std::map<core::Size, std::string> index_to_names_map_;
  core::chemical::ResidueTypeOP molecule_container_;
  utility::vector1<addedH> added_H_;
  core::Size current_atom_;

};



}
}
}


#endif /* CTAB_PARSER_HH_ */