chainbreak_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.
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/// @file   core/scoring/methods/chainbreak_util.cc
/// @brief  Utility functions for scoring chainbreaks.
/// @author James Thompson

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/VariantType.hh>
// AUTO-REMOVED #include <core/id/AtomID.hh>
#include <boost/unordered/unordered_set.hpp>

#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace methods {

bool is_lower_cutpoint(
  core::Size residue,
  core::pose::Pose const & pose
) {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  const bool is_cutpoint_in_tree_lower  = pose.fold_tree().is_cutpoint(residue);
  //const bool is_cutpoint_in_tree_upper  = pose.fold_tree().is_cutpoint(residue - 1);
  const bool use_pose_cutpoint_variants = option[OptionKeys::score::score_pose_cutpoint_variants]();
  const bool has_lower_variant_type     = pose.residue(residue).has_variant_type(chemical::CUTPOINT_LOWER);
  return (has_lower_variant_type && (is_cutpoint_in_tree_lower || use_pose_cutpoint_variants));
}

bool is_upper_cutpoint(
  core::Size residue,
  core::pose::Pose const & pose
) {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  const bool is_cutpoint_in_tree_upper  = pose.fold_tree().is_cutpoint(residue - 1);
  const bool use_pose_cutpoint_variants = option[OptionKeys::score::score_pose_cutpoint_variants]();
  const bool has_upper_variant_type     = pose.residue(residue).has_variant_type(chemical::CUTPOINT_UPPER);
  if (residue <= 1) return false;
  return (has_upper_variant_type && (is_cutpoint_in_tree_upper || use_pose_cutpoint_variants));
}

void find_cutpoint_variants(
  const core::pose::Pose& pose,
  const core::kinematics::FoldTree&,
  utility::vector1<int>* cutpoints
) {
  using core::Size;
  using boost::unordered_set;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  assert(cutpoints);
  unordered_set<int> unique_cutpoints;

  for ( Size ii = 1; ii <= pose.total_residue(); ++ii ) {
    if ( is_lower_cutpoint(ii,pose) ) unique_cutpoints.insert(ii);
  }

  // Update output parameter
  std::copy(unique_cutpoints.begin(),
            unique_cutpoints.end(),
            std::back_inserter(*cutpoints));

  std::sort(cutpoints->begin(), cutpoints->end());
}

} // namespace methods
} // namespace scoring
} // namespace core