BinaryRNASilentStruct.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:
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//
// (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 core/io/silent/BinaryRNASilentStruct.hh
///
/// @brief
/// @author Frank DiMaio
/// @author Mike Tyka
/// @author Rhiju Das

#ifndef INCLUDED_core_io_silent_BinaryRNASilentStruct_hh
#define INCLUDED_core_io_silent_BinaryRNASilentStruct_hh

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

// AUTO-REMOVED #include <core/conformation/Residue.fwd.hh>

// AUTO-REMOVED #include <core/io/silent/RNA_SilentStruct.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>

#include <core/chemical/ResidueTypeSet.fwd.hh>

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

// C++ Headers
#include <string>

#include <core/io/silent/SilentStruct.hh>
#include <utility/vector1.hh>


namespace core {
namespace io {
namespace silent {

class BinaryRNASilentStruct : public SilentStruct {

public:

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

  BinaryRNASilentStruct();

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

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

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

  // destructor
  ~BinaryRNASilentStruct() {}

  /// @brief Test if this BinaryRNASilentStruct is equal to the given BinaryRNASilentStruct in terms of conformation.
  /// Doesn't check energies.
  /* BinaryRNASilentStruct & operator= (
    BinaryRNASilentStruct 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 BinaryRNASilentStruct.
  /// 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 BinaryRNASilentStruct. 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 BinaryRNASilentStruct to the given std::ostream.
  virtual void print_conformation( std::ostream & output ) const;

  /// @brief returns the positions of the CA atoms in this RNA_SilentStruct.
  /// Useful for RMS calculations.
  virtual ObjexxFCL::FArray2D< Real > get_CA_xyz() const;

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

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


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

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

  void set_fold_tree( kinematics::FoldTree const & f ) {
    fold_tree_ = f;
  }
  kinematics::FoldTree const& fold_tree( ) const {
    return fold_tree_;
  }

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

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

  bool fullatom_;

  utility::vector1< char > secstruct_;
  utility::vector1< utility::vector1< numeric::xyzVector<float> > > atm_coords_;
  utility::vector1< kinematics::RT > jumps_;
  bool bJumps_use_IntraResStub_;
  kinematics::FoldTree fold_tree_;

}; // class BinaryRNASilentStruct

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

#endif