DecoyStruct.cc

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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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file core/io/raw_data/DecoyStruct.cc
///
/// @brief protein-specific "silent" file reader and writer for mini.
/// @author James Thompson, Monica Berrondo

// C++ Headers
#include <vector>
#include <string>
#include <map>

// mini headers
// AUTO-REMOVED #include <utility/io/izstream.hh>
// AUTO-REMOVED #include <utility/io/ozstream.hh>
// AUTO-REMOVED #include <utility/file/file_sys_util.hh>

// AUTO-REMOVED #include <basic/Tracer.hh>

#include <core/io/raw_data/DecoyStruct.hh>

// AUTO-REMOVED #include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/conformation/ResidueFactory.hh>

#include <numeric/model_quality/rms.hh>

#include <core/chemical/ChemicalManager.hh>
#include <core/pose/annotated_sequence.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>


namespace core {
namespace io {
namespace raw_data {

using namespace ObjexxFCL::fmt;

DecoyStruct::DecoyStruct(
  core::pose::Pose const & pose,
  std::string tag, // = "empty_tag",
  bool fa // = false
) : fullatom_( fa ) {
  // tag information
  decoy_tag_ = tag;

  // conformation information
  sequence_ = pose.sequence();
  resize( pose.total_residue() );
  static const std::string important_atom = "CA";
  for ( unsigned int i = 1; i <= pose.total_residue(); ++i ) {
    core::conformation::Residue resi = pose.residue(i);
    phi_  [i]     = resi.mainchain_torsion( 1 );
    psi_  [i]     = resi.mainchain_torsion( 2 );
    omega_[i]     = resi.mainchain_torsion( 3 );
    coords_[i]    = resi.xyz( important_atom );
    secstruct_[i] = pose.secstruct(i);
    if ( fullatom() ) {
      chi_[i] = resi.chi();
    } // if ( fullatom )
  } // for ( unsigned int i = 1; i <= pose.total_residue(); ++i )
} // DecoyStruct


/// @brief Resize this silent-struct to the appropriate number of residues.
void
DecoyStruct::resize(
  Size const nres_in
)
{
  nres_ = nres_in;
  secstruct_.resize( nres_ );
  phi_      .resize( nres_ );
  psi_      .resize( nres_ );
  omega_    .resize( nres_ );
  coords_   .resize( nres_ );
  chi_      .resize( nres_ );
}

// @brief Fill a Pose with the data in this DecoyStruct.
void DecoyStruct::fill_pose(
  core::pose::Pose & pose
) {
  using namespace core::chemical;
  ResidueTypeSetCAP residue_set;
  if ( fullatom() ) {
    residue_set = ChemicalManager::get_instance()->residue_type_set( FA_STANDARD );
  } else {
    residue_set = ChemicalManager::get_instance()->residue_type_set( CENTROID );
  }
  fill_pose( pose, *residue_set );
} // fill_pose

void DecoyStruct::fill_pose(
  core::pose::Pose & pose,
  core::chemical::ResidueTypeSet const& residue_set
) {

  // make_pose_match_sequence_( pose, sequence_, residue_set );
  core::pose::make_pose_from_sequence( pose, sequence_, residue_set );

  for ( Size seqpos = 1; seqpos <= pose.total_residue(); ++seqpos ) {
    pose.set_phi   ( seqpos, phi_   [seqpos] );
    pose.set_psi   ( seqpos, psi_   [seqpos] );
    pose.set_omega ( seqpos, omega_ [seqpos] );
    if ( fullatom_ ) {
      for ( Size j = 1; j <= pose.residue(seqpos).nchi(); ++j ){
        pose.set_chi( j, seqpos, chi_[seqpos][j] );
      }
    }
    pose.set_secstruct( seqpos, secstruct_[seqpos] );
  }

} // fill_pose

/// @brief Print the conformation information contained in this object to the given ozstream.
void DecoyStruct::print_conformation( std::ostream& output ) const {
  using namespace ObjexxFCL;

  for ( Size i = 1; i <= nres_; ++i ) {
    output << I( 4, i ) << ' '
        << secstruct_[i] << ' '
        << F( 9, 3, phi_[i] )
        << F( 9, 3, psi_[i] )
        << F( 9, 3, omega_[i] )
        << F( 9, 3, coords_[i].x() )
        << F( 9, 3, coords_[i].y() )
        << F( 9, 3, coords_[i].z() );
    if ( fullatom_ ) {
      for ( unsigned int chino = 1; chino <= 4; ++chino ) {
        Real chi_to_print = 0.0f;
        if ( chino <= chi_[i].size() ) {
          chi_to_print = chi_[i][chino];
        }
        output << F( 9, 3, chi_to_print );
      }
    }

    output << ' ' << decoy_tag_;
    output << std::endl;
  } // for ( Size i = 1; i <= nres; ++i )
} // print_conformation

Real DecoyStruct::get_debug_rmsd() {
  using namespace ObjexxFCL;

  pose::Pose temp_pose;
  FArray2D< Real > rebuilt_coords (3, coords_.size() ), original_coords( 3, coords_.size() );
  static std::string atom_name = "CA";

  // build temp_pose from coordinates
  fill_pose( temp_pose );

  for ( Size i = 1; i <= temp_pose.total_residue(); ++i ) {
    for ( Size k = 1; k <= 3; ++k ) { // k = X, Y and Z
      rebuilt_coords (k,i) = temp_pose.residue(i).xyz( atom_name )[k-1];
      original_coords(k,i) = coords_[i][k-1];
    }
  }

  Real rmsd = numeric::model_quality::rms_wrapper( temp_pose.total_residue(), rebuilt_coords, original_coords );
  return rmsd;
}

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