SymmData.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:
//
// This file is made available under the Rosetta Commons license.
// See http://www.rosettacommons.org/license
// (C) 199x-2007 University of Washington
// (C) 199x-2007 University of California Santa Cruz
// (C) 199x-2007 University of California San Francisco
// (C) 199x-2007 Johns Hopkins University
// (C) 199x-2007 University of North Carolina, Chapel Hill
// (C) 199x-2007 Vanderbilt University

/// @brief  Symmetry data container
/// @file   core/conformation/symmetry/SymmData.hh
/// @author Ingemar Andre


#ifndef INCLUDED_core_conformation_symmetry_SymmData_hh
#define INCLUDED_core_conformation_symmetry_SymmData_hh


// Unit headers
#include <core/conformation/symmetry/SymmData.fwd.hh>
#include <core/conformation/symmetry/VirtualCoordinate.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymSlideInfo.hh>

// Utility headers
#include <utility/pointer/owning_ptr.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <core/types.hh>

// C++ headers
#include <map>

#include <utility/vector1_bool.hh>
#include <numeric/xyzMatrix.hh>


namespace core {
namespace conformation {
namespace symmetry {

class SymmData : public utility::pointer::ReferenceCount
{

//  typedef utility::vector1< Size > Clones;
  typedef utility::vector1< std::pair<Size,Real> > WtedClones;

  public:

  SymmData();
  SymmData( core::Size nres, core::Size njump );
  SymmData( SymmData const &);
  SymmDataOP
  clone() const;
  virtual ~SymmData();

  friend
  bool
  operator==(SymmData const & a, SymmData const & b);

  friend
  bool
  operator!=(SymmData const & a, SymmData const & b);

  //void test( SymmData tmp );

  private:

  std::string symmetry_name_;
  std::string symmetry_type_;
  core::Size subunits_;
  core::Size num_components_;
  core::Size interfaces_;
  core::Size score_subunit_;
  std::string anchor_residue_;
  bool recenter_;
  core::Size root_;
  SymSlideInfo slide_info_;
  std::vector< std::string > slide_order_string_;
  std::vector< std::vector< std::string > > symm_transforms_;
  std::vector< numeric::xyzMatrix< core::Real> > rotation_matrices_;
  std::vector< numeric::xyzMatrix< core::Real> > translation_matrices_;
  std::map< std::string, VirtualCoordinate > virtual_coordinates_;
  std::map< std::string, std::pair< std::string, std::string > > jump_string_to_virtual_pair_;
  std::map< std::string, Size > jump_string_to_jump_num_;
  std::map< std::string, Size > virt_id_to_virt_num_;
  std::map< std::string, Size > virt_id_to_subunit_num_;
  std::map< std::string, char > virt_id_to_subunit_chain_;
  std::map< std::string, std::string > virt_id_to_subunit_residue_;
  std::map< Size, std::string > virt_num_to_virt_id_;
  std::map< Size, std::string > subunit_num_to_virt_id_;
  std::map< Size, WtedClones > jump_clones_;
  std::map< Size, SymDof > dofs_;
  std::vector< Size > allow_virtual_;
  utility::vector1< Size > score_multiply_subunit_;
  utility::vector1< Size > include_subunit_;
  utility::vector1< Size > output_subunit_;

  core::Real cell_a_;
  core::Real cell_b_;
  core::Real cell_c_;
  core::Real cell_alfa_;
  core::Real cell_beta_;
  core::Real cell_gamma_;

  utility::vector1<char> components_;
  std::map<std::string,char> name2component_;
  std::map<std::string,utility::vector1<char> > jname2components_;
  std::map<std::string,utility::vector1<Size> > jname2subunits_;

  utility::vector1<std::string> leaves_of_jump(std::string const & jname) const;

  public:
  typedef numeric::xyzVector< core::Real > Vector;
  typedef numeric::xyzMatrix< core::Real > Matrix;

  public:
  void
  read_symmetry_info_from_pdb(
    std::string filename
  );
  void
  read_symmetry_data_from_file(
    std::string filename
  );
  void
  read_symmetry_data_from_stream(
    std::istream & infile
  );

  //void read_symmetry_name();

  // void read_symmetry_type();

  //void read_transformation_matrixes();

  void
  sanity_check();
  void
  show();

  public:
  // Accessor functions

  std::string const &
  get_symmetry_name() const;

  std::string const &
  get_symmetry_type() const;

  core::Size
  get_subunits() const;

  core::Size get_num_components() const;

  core::Size
  get_interfaces() const;

  core::Size
  get_score_subunit() const;

  std::string const &
  get_anchor_residue() const;

  bool
  get_recenter() const;

  core::Size
  get_root() const;

  utility::vector1< Size > const &
  get_score_multiply_subunit() const;

  utility::vector1< Size > const &
  get_include_subunit() const;

  utility::vector1< Size > const &
  get_output_subunit() const;

  std::vector< numeric::xyzMatrix< core::Real > > const &
  get_rotation_matrix() const;

  std::vector< numeric::xyzMatrix< core::Real > > const &
  get_translation_matrix() const;

  //std::vector< std::vector< std::string> > get_symm_transforms() const;

  std::map< std::string, VirtualCoordinate > const &
  get_virtual_coordinates() const;

  core::Size
  get_num_virtual() const;

  std::map< Size, SymDof > const &
  get_dofs() const;

  std::map< Size, WtedClones > const &
  get_jump_clones() const;

  std::map< std::string, Size > const &
  get_jump_string_to_jump_num() const;

  std::map< std::string, Size > const &
  get_virtual_id_to_num() const;

  std::map< std::string, Size > const &
  get_virt_id_to_subunit_num() const;

  std::map< std::string, char > const &
  get_virt_id_to_subunit_chain() const;

  std::map< std::string, std::string > const &
  get_virt_id_to_subunit_residue() const;

  std::map< Size, std::string > const &
  get_subunit_num_to_virt_id() const;

  std::map< Size, std::string > const &
  get_virtual_num_to_id() const;

  std::map< std::string, std::pair< std::string, std::string > > const &
  get_virtual_connects() const;

  SymSlideInfo const &
  get_slide_info() const;

  core::Real
  get_cell_a() const;

  core::Real
  get_cell_b() const;

  core::Real
  get_cell_c() const;

  core::Real
  get_cell_alfa() const;

  core::Real
  get_cell_beta() const;

  core::Real
  get_cell_gamma() const;

  // Set functions
  //void
  //set_nres_subunit(
    //Size nres_subunit );

  //void
  //set_njump_subunit(
    //Size njump_subunit );

  void
  set_symmetry_name(
    std::string symm_name );

  void
  set_symmetry_type(
    std::string symm_type );

  void
  set_subunits(
    core::Size num_subunits );

  void
  set_interfaces(
    core::Size interfaces );

  void
  set_anchor_residue(
    std::string anchor
  );

  void
  set_score_multiply_subunit( utility::vector1< Size > & score_multiply_vector );

  void
  set_slide_info( SymSlideInfo slide_info );

  void
  set_rotation_matrix(
    std::vector< numeric::xyzMatrix< core::Real > > rotation_matrices );

  void
  set_translation_matrix(
    std::vector< numeric::xyzMatrix< core::Real > > translation_matrices );

  void
  set_symm_transforms(
    std::vector< std::vector< std::string> > symm_transforms );

  void
  set_cell_a(
    core::Real cell_a );

  void
  set_cell_b(
    core::Real cell_b );

  void
  set_cell_c(
    core::Real cell_c );

  void
  set_cell_alfa(
    core::Real cell_alfa );

  void
  set_cell_beta(
  core::Real cell_beta );

  void
  get_cell_gamma( core::Real cell_gamma );

  utility::vector1<char> const & get_components() const;
  std::map<std::string,char> const & get_subunit_name_to_component() const;
  std::map<std::string,utility::vector1<char> > const & get_jump_name_to_components() const;
  std::map<std::string,utility::vector1<Size> > const & get_jump_name_to_subunits() const;

  std::string const & get_parent_jump(std::string const & jname) const;
  std::string const & get_parent_virtual(std::string const & vname) const;
  bool is_ancestor_virtual(std::string const & ancestor, std::string const & child) const;
  std::string const & get_least_common_ancertor_jump(std::string const & jname1, std::string const & jname2) const;
  std::string const & get_least_common_ancertor_virtual(std::string const & vname1, std::string const & vname2) const;

  utility::vector1<char> components_moved_by_jump(std::string const & jname) const;
  utility::vector1<Size> subunits_moved_by_jump(std::string const & jname) const;

};

} // symmetry
} // conformation
} // core
#endif