ResidueDatabaseIO.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   src/core/chemical/ResidueDatabaseIO.hh
/// @author Sam DeLuca
/// @author Matthew O'Meara

#ifndef INCLUDED_core_chemical_ResidueDatabaseIO_hh
#define INCLUDED_core_chemical_ResidueDatabaseIO_hh

#include <utility/pointer/ReferenceCount.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/ResidueDatabaseIO.fwd.hh>
#include <utility/sql_database/DatabaseSessionManager.fwd.hh>
#include <core/chemical/AtomTypeSet.fwd.hh>
#include <core/chemical/MMAtomTypeSet.fwd.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.fwd.hh>
#include <core/chemical/ElementSet.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>

#include <map>

namespace core {
namespace chemical {


class ResidueDatabaseIO : public utility::pointer::ReferenceCount {
public:

  ResidueDatabaseIO();

  virtual ~ResidueDatabaseIO();

  ///@brief generate the table schemas and write them to the database
  void
  write_schema_to_db(
    utility::sql_database::sessionOP db_session) const;

private:
  ///@brief generate the residue_type table schema
  void
  write_residue_type_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_atom table schema
  void
  write_residue_type_atom_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_bond table schema
  void
  write_residue_type_bond_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_cut_bond table schema
  void
  write_residue_type_cut_bond_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_chi table schema
  void
  write_residue_type_chi_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_chi_rotamer table schema
  void
  write_residue_type_chi_rotamer_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_proton_chi table schema
  void
  write_residue_type_proton_chi_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_property table schema
  void
  write_residue_type_property_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_variant_type table schema
  void
  write_residue_type_variant_type_table_schema(
    utility::sql_database::sessionOP db_session) const;

  ///@brief generate the residue_type_icoor table schema
  void
  write_residue_type_icoor_table_schema(
    utility::sql_database::sessionOP db_session) const;

public:
  ///@brief write the schema
  void initialize(utility::sql_database::sessionOP db_session);

  core::Real get_version();

  void write_residuetype_to_database(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  core::chemical::ResidueTypeOP read_residuetype_from_database(
    chemical::AtomTypeSetCAP atom_types,
    chemical::ElementSetCAP elements,
    chemical::MMAtomTypeSetCAP mm_atom_types,
    chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types,
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    utility::sql_database::sessionOP db_session) ;

  utility::vector1<std::string> get_all_residues_in_database(utility::sql_database::sessionOP db_session) ;

private:

  std::string
  get_atom_name_from_database_atom_index(
    std::string residue_name,
    core::Size atom_index,
    utility::sql_database::sessionOP db_session) ;


  void
  report_residue_type(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_atom(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_atom(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_bond(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_bond(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;
  void
  report_residue_type_cut_bond(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_cut_bond(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_chi(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_chi(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_chi_rotamer(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_chi_rotamer(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_proton_chi(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_proton_chi(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_properties(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_properties(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;


  void
  report_residue_type_variant(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_variant(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  report_residue_type_icoor(
    std::string const & residue_type_set_name,
    core::chemical::ResidueType const & res_type,
    utility::sql_database::sessionOP db_session) ;

  void
  read_residue_type_icoor(
    std::string const & residue_type_set_name,
    std::string const & residue_type_name,
    core::chemical::ResidueType & res_type,
    utility::sql_database::sessionOP db_session) ;


private:
  core::Real version_;

  std::map<std::pair<std::string,core::Size>, std::string > atom_name_id_cache_;

};



}
}


#endif /* RESIDUE_DBIO_HH_ */