Align_RmsdEvaluator.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:
//
// (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 Align_RmsdEvaluator
/// @author James Thompson

// Unit Headers
#include <protocols/comparative_modeling/Align_RmsdEvaluator.hh>

// Package Headers
#include <protocols/comparative_modeling/coord_util.hh>

// Project Headers
#include <core/id/SequenceMapping.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>

// Utility headers
#include <basic/Tracer.hh>
#include <numeric/xyzVector.hh>
#include <numeric/model_quality/maxsub.hh>
#include <numeric/model_quality/rms.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <utility/vector1.hh>

// C++ headers
#include <map>
#include <string>

static basic::Tracer tr("protocols.comparative_modeling.Align_RmsdEvaluator");

namespace protocols {
namespace comparative_modeling {

Align_RmsdEvaluator::~Align_RmsdEvaluator() {}

Align_RmsdEvaluator::Align_RmsdEvaluator(
  core::pose::PoseCOP native_pose,
  std::string tag,
  bool calc_gdt,
  core::sequence::SequenceAlignmentOP aln
) :
  AlignEvaluator( native_pose, tag, true, aln ),
  calc_gdt_ (calc_gdt),
  report_gdt_components_(false)
{}

void
Align_RmsdEvaluator::apply(
  core::pose::Pose & pose,
  std::string /*tag*/,
  core::io::silent::SilentStruct & ss
) const {
  using core::Real;
  using ObjexxFCL::FArray2D;
  using core::scoring::xyz_gdtmm;

  int n_atoms;
  FArray2D< Real > p1a, p2a;
  tr.Debug << "gathering xyz coordinates ... ";
  protocols::comparative_modeling::gather_coords(
    pose, *native_pose(),
    *get_alignment(pose),
    n_atoms, p1a, p2a
  );
  tr.Debug << "gathered " << n_atoms << "coordinates" << std::endl;
  tr.flush_all_channels();

  Real rmsd( numeric::model_quality::rms_wrapper( n_atoms, p1a, p2a ) );
  ss.add_energy( "rms_" + tag(), rmsd );

  Real const coverage(
    (Real) (n_atoms) / (Real) (native_pose()->total_residue())
  );

  if ( report_aln_components() ) {
    ss.add_energy( "nres_ali_" + tag(), n_atoms );
    ss.add_energy( "coverage_" + tag(), coverage );
  }

  if ( calc_gdt() ) {
    tr.Debug << "computing gdtmm for " << tag() << std::endl;
    Real m_1_1, m_2_2, m_3_3, m_4_3, m_7_4;
    Real gdtmm = xyz_gdtmm( p1a, p2a, m_1_1, m_2_2, m_3_3, m_4_3, m_7_4 );
    ss.add_energy ( "gdtmm_" + tag(), coverage * gdtmm );
    if ( report_gdt_components() ) {
      ss.add_energy( "m11", m_1_1 );
      ss.add_energy( "m22", m_2_2 );
      ss.add_energy( "m33", m_3_3 );
      ss.add_energy( "m43", m_4_3 );
      ss.add_energy( "m74", m_7_4 );
    }

    // high-accuracy statistics
    core::id::SequenceMapping mapping = get_alignment(pose)->sequence_mapping(1, 2);
    std::map<Size, Size> residues;
    for (Size idx_mod = 1; idx_mod <= mapping.size1(); ++idx_mod) {
      Size idx_ref = mapping[idx_mod];
      if (idx_ref > 0) {
        residues[idx_ref] = idx_mod;
      }
    }

    tr.Debug << "computing high-accuracy statistics for " << tag() << std::endl;
    ss.add_energy("gdtha_" + tag(), core::scoring::gdtha(*native_pose(), pose, residues));
    ss.add_energy("gdtsc_" + tag(), core::scoring::gdtsc(*native_pose(), pose, residues));

    tr.Debug << "computing maxsub for " << tag() << std::endl;
    ss.add_energy( "maxsub_" + tag(), core::scoring::xyz_maxsub( p1a, p2a, n_atoms ) );
  }
}

} // comparative_modeling
} // protocols