PlaceSurfaceProbe.cc

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/// @file protocols/hotspot_hashing/movers/PlaceSurfaceProbe.cc
/// @brief
/// @author Alex Ford fordas@uw.edu
//

#include <basic/Tracer.hh>

#include <utility/tag/Tag.hh>
#include <utility/exit.hh>

#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pack/task/TaskFactory.hh>

#include <protocols/moves/Mover.hh>
#include <protocols/moves/DataMap.fwd.hh>

#include <protocols/jd2/JobOutputter.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>

#include <protocols/rosetta_scripts/util.hh>

#include <protocols/hotspot_hashing/SearchPattern.hh>
#include <protocols/hotspot_hashing/SurfaceSearchPattern.hh>
#include <protocols/hotspot_hashing/SICSearchPattern.hh>

#include <protocols/hotspot_hashing/StubGenerator.hh>

#include <protocols/hotspot_hashing/movers/PlaceSurfaceProbe.hh>
#include <protocols/hotspot_hashing/movers/PlaceSurfaceProbeCreator.hh>


namespace protocols
{
namespace hotspot_hashing
{
namespace movers
{

static basic::Tracer TR( "protocols.hotspot_hashing.movers.PlaceSurfaceProbe" );

PlaceSurfaceProbe::PlaceSurfaceProbe() :
    protocols::moves::Mover("PlaceSurfaceProbe"),
    protocols::hotspot_hashing::movers::PlaceProbeMover(),
    surface_selection_(NULL),
    search_density_(0),
    coarse_angle_sampling_(0),
    coarse_sampling_(0),
    refinement_distance_(0),
    refinement_angle_sampling_(0),
    refinement_sampling_(0),
    refinement_pattern_(NULL)
{

}


PlaceSurfaceProbe::PlaceSurfaceProbe(
    std::string residue_name,
    core::Real search_density,
    core::Real coarse_angle_sampling,
    core::Real coarse_sampling,
    core::Real refinement_distance,
    core::Real refinement_angle_sampling,
    core::Real refinement_sampling,
    core::conformation::ResidueCOP target_residue,
    core::pack::task::TaskFactoryOP /*surface_selection*/,
    core::Size search_partition,
    core::Size total_search_partition) :
    protocols::moves::Mover( "PlaceSurfaceProbe" ),
    protocols::hotspot_hashing::movers::PlaceProbeMover(
      residue_name,
      target_residue,
      search_partition,
      total_search_partition),
    search_density_(search_density),
    coarse_angle_sampling_(coarse_angle_sampling),
    coarse_sampling_(coarse_sampling),
    refinement_distance_(refinement_distance),
    refinement_angle_sampling_(refinement_angle_sampling),
    refinement_sampling_(refinement_sampling),
    refinement_pattern_(initialize_refinement_pattern())
{
}

protocols::moves::MoverOP PlaceSurfaceProbe::clone() const
{
  return new PlaceSurfaceProbe(*this);
}

SearchPatternOP PlaceSurfaceProbe::create_search_pattern(core::pose::Pose const & target_pose)
{
  using core::conformation::ResidueOP;

  SearchPatternOP surface_pattern(
      new SurfaceSearchPattern(
              target_pose,
              surface_selection_,
              search_density_));

  core::Real expected_course_search_bound = std::sqrt(search_density_);
  SearchPatternOP residue_sampling_pattern(
      new ComposeSearchPatterns(
        new SphericalRotationSearchPattern(
          coarse_angle_sampling_,
          coarse_angle_sampling_,
          coarse_angle_sampling_,
          0, 360,
          0, 90,
          0, 360),
        new CartesianSearchPattern(
          0,
          coarse_sampling_,
          coarse_sampling_,
          0, 0,
          -(expected_course_search_bound / 2),
          expected_course_search_bound / 2,
          -(expected_course_search_bound / 2),
          expected_course_search_bound / 2)));

  core::pose::Pose residue_pose;

  ResidueOP virtual_bb_residue = core::pose::add_variant_type_to_residue(*target_residue_, "VIRTUAL_BB", target_pose);
  StubGenerator::placeResidueOnPose(residue_pose, virtual_bb_residue);

  SearchPatternOP sampled_surface_pattern(
      new SICPatternAtTransform(
        target_pose,
        residue_pose,
        surface_pattern,
        residue_sampling_pattern));

  return sampled_surface_pattern;
}

SearchPatternOP PlaceSurfaceProbe::create_partitioned_search_pattern(core::pose::Pose const & target_pose)
{
  using core::conformation::ResidueOP;

  SearchPatternOP surface_pattern(
      new SurfaceSearchPattern(
              target_pose,
              surface_selection_,
              search_density_));

  SearchPatternOP partitioned_surface_pattern(
      new PartitionedSearchPattern(surface_pattern, search_partition_, total_search_partition_));

  SearchPatternOP residue_sampling_pattern(
      new SphericalRotationSearchPattern(
        coarse_angle_sampling_,
        coarse_angle_sampling_,
        coarse_angle_sampling_,
        0, 360,
        0, 180,
        0, 360));

  core::pose::Pose residue_pose;

  ResidueOP virtual_bb_residue = core::pose::add_variant_type_to_residue(*target_residue_, "VIRTUAL_BB", target_pose);
  StubGenerator::placeResidueOnPose(residue_pose, virtual_bb_residue);

  SearchPatternOP sampled_surface_pattern(
      new SICPatternAtTransform(
        target_pose,
        residue_pose,
        partitioned_surface_pattern,
        residue_sampling_pattern));

  return sampled_surface_pattern;
}

SearchPatternOP PlaceSurfaceProbe::create_refinement_pattern(core::pose::Pose const & /*target_pose*/, core::Size /*target_residue*/)
{
  return refinement_pattern_;
}

SearchPatternOP PlaceSurfaceProbe::initialize_refinement_pattern()
{
  return new ComposeSearchPatterns(
        new SphericalRotationSearchPattern(
          refinement_angle_sampling_,
          refinement_angle_sampling_,
          refinement_angle_sampling_,
          0, coarse_angle_sampling_,
          0, coarse_angle_sampling_,
          0, coarse_angle_sampling_),
        new CartesianSearchPattern(
          refinement_sampling_,
          refinement_sampling_,
          refinement_sampling_,
          -refinement_distance_, refinement_distance_,
          -(coarse_sampling_ / 2),
          coarse_sampling_ / 2,
          -(coarse_sampling_ / 2),
          coarse_sampling_ / 2));
}

void
PlaceSurfaceProbe::parse_my_tag( utility::tag::TagPtr const tag,
                                protocols::moves::DataMap & data,
                                protocols::filters::Filters_map const & filters_map,
                                protocols::moves::Movers_map const & movers_map,
                                core::pose::Pose const & target_pose)
{
  parse_place_probe_tag(
    tag,
    data,
    filters_map,
    movers_map,
    target_pose
  );

  // Surface Spec
  search_density_ = tag->getOption< core::Real >( "search_density", 1);
  surface_selection_ = protocols::rosetta_scripts::parse_task_operations( tag, data );

  // Coarse grid spec
  coarse_angle_sampling_ = tag->getOption< core::Real >( "coarse_angle_sampling");
  coarse_sampling_ = tag->getOption< core::Real >( "coarse_sampling");

  refinement_angle_sampling_ = tag->getOption< core::Real >( "refinement_angle_sampling");
  refinement_sampling_ = tag->getOption< core::Real >( "refinement_sampling");
  refinement_distance_ = tag->getOption< core::Real >( "refinement_distance");

  refinement_pattern_ = initialize_refinement_pattern();
}

protocols::moves::MoverOP
PlaceSurfaceProbeCreator::create_mover() const
{
  return new PlaceSurfaceProbe;
}

std::string
PlaceSurfaceProbeCreator::keyname() const
{
  return "PlaceSurfaceProbe";
}

std::string PlaceSurfaceProbeCreator::mover_name()
{
  return "PlaceSurfaceProbeMover";
}

}
}
}