util.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   core/scoring/util.cc
/// @brief  Nonmember functions for evaluating some or all energy methods on residues or residue pairs
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)

// Unit headers
#include <core/scoring/util.hh>

// Package headers
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/methods/ContextDependentTwoBodyEnergy.hh>

// Project headers
#include <core/types.hh>
#include <core/conformation/Residue.hh>

// Numeric headers
#include <numeric/xyzVector.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {

void
eval_scsc_sr2b_energies(
  conformation::Residue const & r1,
  conformation::Residue const & r2,
  Vector const & r1sc_centroid,
  Vector const & r2sc_centroid,
  Real const & r1sc_radius,
  Real const & r2sc_radius,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap & emap
)
{
  Real const scsc_d2 = r1sc_centroid.distance_squared( r2sc_centroid );
  Real const scsc_radsum = r1sc_radius + r2sc_radius;
  for ( ScoreFunction::CI_2B_Methods::const_iterator
      iter = sfxn.ci_2b_begin(), iter_end = sfxn.ci_2b_end();
      iter != iter_end; ++iter ) {
    Real cutoff = scsc_radsum + (*iter)->atomic_interaction_cutoff();
    if ( ! (*iter)->divides_backbone_and_sidechain_energetics() || scsc_d2 < cutoff * cutoff ) {
      (*iter)->sidechain_sidechain_energy( r1, r2, pose, sfxn, emap );
    }
  }
  for ( ScoreFunction::CD_2B_Methods::const_iterator
      iter = sfxn.cd_2b_begin(), iter_end = sfxn.cd_2b_end();
      iter != iter_end; ++iter ) {
    Real cutoff = scsc_radsum + (*iter)->atomic_interaction_cutoff();
    if ( ! (*iter)->divides_backbone_and_sidechain_energetics() || scsc_d2 < cutoff * cutoff ) {
      (*iter)->sidechain_sidechain_energy( r1, r2, pose, sfxn, emap );
    }
  }
}

void
eval_bbsc_sr2b_energies(
  conformation::Residue const & r1,
  conformation::Residue const & r2,
  Vector const & r1bb_centroid,
  Vector const & r2sc_centroid,
  Real const & r1bb_radius,
  Real const & r2sc_radius,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap & emap
)
{
  Real const bbsc_d2 = r1bb_centroid.distance_squared( r2sc_centroid );
  Real const bbsc_radsum = r1bb_radius + r2sc_radius;
  for ( ScoreFunction::CI_2B_Methods::const_iterator
      iter = sfxn.ci_2b_begin(), iter_end = sfxn.ci_2b_end();
      iter != iter_end; ++iter ) {
    if ( (*iter)->divides_backbone_and_sidechain_energetics() ) {
      Real cutoff = bbsc_radsum + (*iter)->atomic_interaction_cutoff();
      if ( bbsc_d2 < cutoff * cutoff ) {
        (*iter)->backbone_sidechain_energy( r1, r2, pose, sfxn, emap );
      }
    }
  }
  for ( ScoreFunction::CD_2B_Methods::const_iterator
      iter = sfxn.cd_2b_begin(), iter_end = sfxn.cd_2b_end();
      iter != iter_end; ++iter ) {
    if ( (*iter)->divides_backbone_and_sidechain_energetics() ) {
      Real cutoff = bbsc_radsum + (*iter)->atomic_interaction_cutoff();
      if ( bbsc_d2 < cutoff * cutoff ) {
        (*iter)->backbone_sidechain_energy( r1, r2, pose, sfxn, emap );
      }
    }
  }
}

void
eval_bbbb_sr2b_energies(
  conformation::Residue const & r1,
  conformation::Residue const & r2,
  Vector const & r1bb_centroid,
  Vector const & r2bb_centroid,
  Real const & r1bb_radius,
  Real const & r2bb_radius,
  pose::Pose const & pose,
  ScoreFunction const & sfxn,
  EnergyMap & emap
)
{
  Real const bbbb_d2 = r1bb_centroid.distance_squared( r2bb_centroid );
  Real const bbbb_radsum = r1bb_radius + r2bb_radius;
  for ( ScoreFunction::CI_2B_Methods::const_iterator
      iter = sfxn.ci_2b_begin(), iter_end = sfxn.ci_2b_end();
      iter != iter_end; ++iter ) {
    if ( (*iter)->divides_backbone_and_sidechain_energetics() ) {
      Real cutoff = bbbb_radsum + (*iter)->atomic_interaction_cutoff();
      if ( bbbb_d2 < cutoff * cutoff ) {
        (*iter)->backbone_backbone_energy( r1, r2, pose, sfxn, emap );
      }
    }
  }
  for ( ScoreFunction::CD_2B_Methods::const_iterator
      iter = sfxn.cd_2b_begin(), iter_end = sfxn.cd_2b_end();
      iter != iter_end; ++iter ) {
    if ( (*iter)->divides_backbone_and_sidechain_energetics() ) {
      Real cutoff = bbbb_radsum + (*iter)->atomic_interaction_cutoff();
      if ( bbbb_d2 < cutoff * cutoff ) {
        (*iter)->backbone_backbone_energy( r1, r2, pose, sfxn, emap );
      }
    }
  }
}

/// @details returns the origin if there are no backbone atoms
Vector
compute_bb_centroid(
  conformation::Residue const & res
)
{
  Vector bb_centroid( 0.0 );
  Size count_n_bb( 0 );
  for ( Size ii = 1; ii <= res.type().first_sidechain_atom() - 1; ++ii ) {
    ++count_n_bb;
    bb_centroid += res.xyz( ii );
  }
  if ( count_n_bb != 0 ) bb_centroid /= count_n_bb;
  return bb_centroid;
}

Real
compute_bb_radius(
  conformation::Residue const & res,
  Vector const & bb_centroid
)
{
  Real bb_radius = 0;
  for ( Size ii = 1; ii <= res.type().first_sidechain_atom() - 1; ++ii ) {
    Real d2 = res.xyz( ii ).distance_squared( bb_centroid );
    if ( bb_radius < d2 ) bb_radius = d2;
  }
  return bb_radius;
}

Vector
compute_sc_centroid(
  conformation::Residue const & res
)
{
  Vector centroid( 0.0 );
  Size count( 0 );
  for ( Size ii = res.type().first_sidechain_atom(); ii <= res.type().nheavyatoms(); ++ii ) {
    count += 1;
    centroid += res.xyz( ii );
  }
  if ( count == 0 ) {
    return compute_bb_centroid( res );
  } else {
    centroid /= count;
    return centroid;
  }
}

Real
compute_sc_radius(
  conformation::Residue const & res,
  Vector const & centroid
)
{
  Real max_d2 = 0;
  for ( Size ii = res.type().first_sidechain_atom(); ii <= res.type().nheavyatoms(); ++ii ) {
    Real d2 = res.xyz(ii).distance_squared( centroid );
    if ( d2 > max_d2 ) max_d2 = d2;
  }
  return std::sqrt( max_d2 );
}

}
}