AddCavitiesMover.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
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/// @file   protocols/simple_moves/AddCavitiesMover.cc
///
/// @brief
/// @author

#include <protocols/simple_moves/AddCavitiesMover.hh>

#include <core/scoring/packstat/types.hh>
#include <core/scoring/packstat/compute_sasa.hh>

#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>

#include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/chemical/AtomTypeSet.hh>
// AUTO-REMOVED #include <core/chemical/MMAtomTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
// AUTO-REMOVED #include <core/chemical/ResidueSelector.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/ResidueFactory.hh>
// AUTO-REMOVED #include <core/chemical/residue_io.hh>
// AUTO-REMOVED #include <core/chemical/VariantType.hh>

#include <core/scoring/constraints/CoordinateConstraint.hh>
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/Func.hh>
#include <core/scoring/constraints/HarmonicFunc.hh>

#include <basic/datacache/BasicDataCache.hh>
#include <core/pose/datacache/CacheablePoseRawPtr.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace simple_moves {

  using namespace core;
  using namespace core::scoring::packstat;
  using core::id::AtomID;


  AddCavitiesMover::AddCavitiesMover(
    core::Size max_cav ,
    core::Real min_size,
    core::Size min_nb  ,
    core::Real min_sep
  ) : max_cav_(max_cav), min_size_(min_size), min_nb_(min_nb), min_sep_(min_sep) {}

  core::id::AtomID
  AddCavitiesMover::get_closest_heavy_atom( Pose & pose, numeric::xyzVector<Real> xyz ) {
    id::AtomID closest;
    Real closest_dist = 9e9;
    for( size_t ir = 1; ir <= pose.total_residue(); ++ir ) {
      for( size_t ia = 1; ia <= pose.residue(ir).natoms(); ++ia ) {
        id::AtomID id( ia, ir );
        if( 22 <= pose.residue(id.rsd()).atom(id.atomno()).type() ) continue;
        if( pose.xyz(id).distance_squared( xyz ) < closest_dist ) {
          closest_dist = pose.xyz(id).distance_squared( xyz );
          closest = id;
        }
      }
    }
    return closest;
  }

  core::conformation::ResidueOP
  AddCavitiesMover::get_suck_res() {
    using namespace core;
    using namespace chemical;
    using namespace conformation;
    ResidueTypeSetCAP residue_set( ChemicalManager::get_instance()->residue_type_set( FA_STANDARD ) );
    return ResidueFactory::create_residue( residue_set->name_map("SUCK") );
  }

  CavBalls
  AddCavitiesMover::get_cavities( Pose & pose, Real nbdis, int nbcount, Real minsep ) {
    Spheres spheres = core::scoring::packstat::pose_to_pack_data(pose).spheres;

    SasaOptions opts;
    opts.prune_max_iters = 5;
    opts.prune_max_delta = 0;
    opts.num_cav_ball_layers = 2;
    opts.frac_cav_ball_required_exposed = 0.0;
    opts.area_cav_ball_required_exposed = 0.0;
    opts.surrounding_sasa_smoothing_window = 1;
    for( PackstatReal pr = 3.0; pr >= 0.9; pr -= 0.1 )
      opts.probe_radii.push_back(pr);
    opts.prune_cavity_burial_probe_radii.push_back( 1.6 );

    CavBalls cball = compute_sasa( spheres, opts )->cavballs;
    CavBalls cbph  = prune_hidden_cavity_balls( cball, opts );
    CavBalls cbpr  = prune_cavity_balls( spheres, cbph, opts );
    compute_cav_ball_neighbor_count( spheres, cbpr, nbdis );
    CavBalls cbbur;
    for( CavBallIter i = cbpr.begin(); i != cbpr.end(); ++i ) if( i->anb > nbcount ) cbbur.push_back( *i );
    CavBalls selcb = select_cav_balls(cbbur,minsep);

    CavBalls cb;

    return selcb;
  }

  void
  AddCavitiesMover::clear_suckers( Pose & pose ) {
    //using namespace core::pose::datacache::CacheableDataType;
    using namespace basic::datacache;
    using namespace core::pose::datacache;
    if( !pose.data().has(core::pose::datacache::CacheableDataType::POSE_BEFORE_CAVITIES_ADDED) ) {
      return;
    }
    CacheableDataOP cd = pose.data().get_ptr( core::pose::datacache::CacheableDataType::POSE_BEFORE_CAVITIES_ADDED );
    core::pose::PoseOP cache_pose = dynamic_cast< core::pose::datacache::CacheablePoseRawPtr*>(cd())->pose();
    pose.data().set( core::pose::datacache::CacheableDataType::POSE_BEFORE_CAVITIES_ADDED, NULL );
    Pose orig_pose = *cache_pose;
    orig_pose.copy_segment( orig_pose.total_residue(), pose, 1, 1 );
    pose = orig_pose;
  }

  void
  AddCavitiesMover::add_suckers( Pose & pose ) {
    using namespace core::scoring;
    using namespace constraints;
    //using namespace core::pose::datacache::CacheableDataType;
    using namespace basic::datacache;
    using namespace core::pose::datacache;

    clear_suckers(pose);

    using namespace basic;
    pose.data().set( core::pose::datacache::CacheableDataType::POSE_BEFORE_CAVITIES_ADDED, new CacheablePoseRawPtr( new Pose(pose)) );

    CavBalls cbs = get_cavities(pose, 10.0, min_nb_, 3.0 );
    int Ncb = max_cav_;

    // add VRT res for coord constraints
    pose.append_residue_by_jump
        ( *conformation::ResidueFactory::create_residue( pose.residue(1).residue_type_set().name_map( "VRT" ) ),
          pose.total_residue()/2 );
    int virt_resno = pose.total_residue();
    FuncOP func( new HarmonicFunc( 0.0, 1.0 ) );

    // std::cerr << "add sucker atoms" << std::endl;
    int count = 0;
    for( int i = 1; i <= std::min(Ncb,(int)cbs.size()); ++i ) {
      if( cbs[i].radius() < min_size_ ) {
        Ncb = i-1;
        break;
      }
      // std::cerr << "adding cb" << cbs[i].str() << std::endl;
      conformation::ResidueOP sucker = get_suck_res();
      sucker->set_xyz( 1, cbs[i].xyz() );
      AtomID closest = get_closest_heavy_atom( pose, cbs[i].xyz() );
      // std::cerr << "closest " << closest << " score before " << (*sf)(pose) << std::endl;
      pose.append_residue_by_jump( *sucker, closest.rsd() );
      int suck_resno = pose.total_residue();

      pose.add_constraint( new CoordinateConstraint( AtomID(1,suck_resno),
                                                         AtomID(1,virt_resno),
                                                         sucker->xyz(1),
                                                         func ) );
      ++count;
    }
    //std::cerr << "added " << count << " suckers" << std::endl;

  }
  // strip off the suckers and virt res

  void
  AddCavitiesMover::apply( core::pose::Pose & pose ) {
    clear_suckers( pose );
    if( 0 < max_cav_ ) {
      add_suckers( pose );
    }
  }

  std::string
  AddCavitiesMover::get_name() const {
    return "AddCavitiesMover";
  }



} // end namespace simple_moves
} // end namespace protocols