BinaryProteinSilentStruct.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:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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
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/// @file core/io/silent/BinaryProteinSilentStruct.hh
///
/// @brief
/// @author Frank DiMaio
/// @author Mike Tyka

#ifndef INCLUDED_core_io_silent_BinaryProteinSilentStruct_hh
#define INCLUDED_core_io_silent_BinaryProteinSilentStruct_hh

// mini headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

// AUTO-REMOVED #include <core/conformation/Residue.fwd.hh>
#include <core/io/silent/SilentStruct.hh>
// AUTO-REMOVED #include <core/io/silent/ProteinSilentStruct.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>

// AUTO-REMOVED #include <utility/vector1.hh>

// C++ Headers
#include <iostream>
#include <string>

#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <utility/vector1.hh>


namespace core {
namespace io {
namespace silent {

/// why this inheritance pathway? this makes no sense!
//class BinaryProteinSilentStruct : public ProteinSilentStruct {
class BinaryProteinSilentStruct : public SilentStruct {

public:

  /// @brief Constructors.
  BinaryProteinSilentStruct( Size const nres_in );

  BinaryProteinSilentStruct();

  BinaryProteinSilentStruct(
    core::pose::Pose const & pose,
    std::string tag = "empty_tag"
  );

  virtual SilentStructOP clone() const {
    return new BinaryProteinSilentStruct( *this );
  }

  /// @brief Re-dimension the storage capacity of this BinaryProteinSilentStruct to the given number of residues.
  void resize(
    Size const nres_in
  );

  // destructor
  ~BinaryProteinSilentStruct() {}

  /// @brief Test if this BinaryProteinSilentStruct is equal to the given
  /// BinaryProteinSilentStruct in terms of conformation.  Doesn't check
  /// energies.
  BinaryProteinSilentStruct & operator= (
    BinaryProteinSilentStruct const & src
  );

  /// @brief Initialize object from a set of lines
  virtual bool init_from_lines(
    utility::vector1< std::string > const & lines,
    SilentFileData & container
  );

  /// @brief Configure the conformation of the given Pose with the
  /// conformational data within this BinaryProteinSilentStruct. Calls
  /// pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue
  /// types.
  virtual void fill_pose(
    core::pose::Pose & pose
  ) const ;

  /// @brief Configure the conformation of the given Pose with the
  /// conformational data within this BinaryProteinSilentStruct. Calls
  /// pose.clear() and rebuilds Pose from scratch using the user-specified
  /// residue types.
  virtual void fill_pose(
    core::pose::Pose & pose,
    core::chemical::ResidueTypeSet const & residue_set
  ) const;

  /// @brief opposite of fill_pose
  virtual void fill_struct( core::pose::Pose const & pose, std::string tag );

  /// @brief print header information
  virtual void print_header( std::ostream & out ) const;

  /// @brief Prints the conformation information within this
  /// BinaryProteinSilentStruct to the given std::ostream.
  virtual void print_conformation( std::ostream & output ) const;

  /// @brief returns the positions of the CA atoms
  virtual ObjexxFCL::FArray2D< Real > get_CA_xyz() const;

  // model quality-related methods.
  virtual Real CA_rmsd( BinaryProteinSilentStruct other_pss );

  /// @brief calculates the RMSD between the C-alpha atoms of a Pose built from
  /// the torsions in this ProteinSilentStruct and the C-alpha atoms from this
  /// ProteinSilentStruct.
  virtual Real get_debug_rmsd();


  void add_jump( kinematics::Jump jump ) {
    jumps_.push_back( jump.rt() );
  }

  kinematics::RT const & jump( Size jump_num ) const {
    return jumps_[ jump_num ];
  }

  void fold_tree( kinematics::FoldTree f ) {
    fold_tree_ = f;
  }

  kinematics::FoldTree const& fold_tree( ) const {
    return fold_tree_;
  }

  bool fullatom() const {
    return fullatom_;
  }

  virtual void fullatom( bool fullatom ) {
    fullatom_ = fullatom;
  }

  char secstruct( unsigned int seqpos ) const {
    return secstruct_[seqpos];
  }

  void secstruct( unsigned int seqpos, char ss ) {
    secstruct_[seqpos] = ss;
  }

  void symmetry_info( core::conformation::symmetry::SymmetryInfo & s ) {
    symminfo_ = new core::conformation::symmetry::SymmetryInfo( s );
  }

  core::conformation::symmetry::SymmetryInfoCOP symmetry_info( ) const {
    return symminfo_;
  }

  bool is_symmetric() const {
    return symminfo_->get_use_symmetry();
  }

  void parse_chain_endings( std::istream & stream );
  void chain_endings( utility::vector1< Size > const & endings );
  std::string chain_endings_str() const;
  utility::vector1< Size > const & chain_endings() const {
    return chain_endings_;
  }
  void add_chain_ending( Size const seqpos );

private:
  bool fullatom_;

  utility::vector1< char > secstruct_;

  utility::vector1< kinematics::RT > jumps_;
  bool bJumps_use_IntraResStub_;
  kinematics::FoldTree fold_tree_;
  core::conformation::symmetry::SymmetryInfoOP symminfo_;
  utility::vector1< Size > chain_endings_;
  utility::vector1< utility::vector1< numeric::xyzVector<float> > > atm_coords_;
}; // class BinaryProteinSilentStruct

} // namespace silent
} // namespace io
} // namespace core

#endif