ResidueBurialFilter.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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// (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_filters/ResidueBurialFilter.cc
/// @brief
/// @author Sarel Fleishman (sarelf@u.washington.edu), Jacob Corn (jecorn@u.washington.edu)

#include <protocols/simple_filters/ResidueBurialFilter.hh>
#include <protocols/simple_filters/ResidueBurialFilterCreator.hh>

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <utility/tag/Tag.hh>
#include <protocols/moves/DataMap.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

#include <basic/Tracer.hh>
#include <core/pack/task/TaskFactory.hh>

namespace protocols{
namespace simple_filters {

static basic::Tracer residue_burial_filter_tracer( "protocols.simple_filters.ResidueBurialFilter" );

ResidueBurialFilter::ResidueBurialFilter() :
  Filter( "ResidueBurial" ),
  target_residue_( 0 ),
  neighbors_( 1 ),
  distance_threshold_( 8.0 ),
  task_factory_( NULL ) {}

ResidueBurialFilter::ResidueBurialFilter( core::Size const target_residue, core::Size const neighbors, core::Real const distance_threshold ) :
      Filter( "ResidueBurial" ),
      target_residue_( target_residue ),
      neighbors_( neighbors ),
      distance_threshold_( distance_threshold ),
      task_factory_( NULL ) {}

protocols::filters::FilterOP
ResidueBurialFilterCreator::create_filter() const { return new ResidueBurialFilter; }

std::string
ResidueBurialFilterCreator::keyname() const { return "ResidueBurial"; }

ResidueBurialFilter::~ResidueBurialFilter(){}

void
ResidueBurialFilter::task_factory( core::pack::task::TaskFactoryOP tf ){
  task_factory_ = tf;
}

core::pack::task::TaskFactoryOP
ResidueBurialFilter::task_factory() const{ return task_factory_; }

bool
ResidueBurialFilter::apply( core::pose::Pose const & pose ) const {
  if( task_factory() ){//taskfactory is on, iterate over all designable residues and check whether any one passes the filter
/// This looks like recursion but is really quite limited, b/c the call below to rbf.apply uses the functionality where task_factory() is off, so it goes by a different route, and could never go to a depth of more than 2
    utility::vector1< core::Size > const target_residues( protocols::rosetta_scripts::residue_packer_states( pose, task_factory(), true/*designable*/, false/*packable*/ ) );
    core::Size const total_designable( target_residues.size() );
    residue_burial_filter_tracer<<"total target residues: "<<total_designable<<". At least "<<(core::Real)total_designable * (core::Real)residue_fraction_buried()<<" should be buried to pass."<<std::endl;
    core::Size count_buried( 0 );
    foreach( core::Size const resi, target_residues ){
      ResidueBurialFilter const rbf( resi/*target_residue*/, neighbors_, distance_threshold_ );
      if( rbf.apply( pose ) ){
        count_buried++;
        if( (core::Real ) ( (core::Real) count_buried / (core::Real) total_designable ) >= residue_fraction_buried() )
          return true;
      }
    }
    return false;
  }

  core::Size const count_neighbors( compute( pose ) );

  residue_burial_filter_tracer<<"Number of interface neighbors of residue "<<pose.residue( target_residue_ ).name3()<<target_residue_<<" is "<<count_neighbors<<std::endl;
  return( count_neighbors >= neighbors_ );
}

void
ResidueBurialFilter::parse_my_tag( utility::tag::TagPtr const tag, moves::DataMap & data, filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const & pose )
{
  if( tag->hasOption( "res_num" ) || tag->hasOption( "pdb_num" ) )
    target_residue_ = core::pose::get_resnum( tag, pose );
  distance_threshold_ = tag->getOption<core::Real>( "distance", 8.0 );
  neighbors_ = tag->getOption<core::Size>( "neighbors", 1 );
  residue_fraction_buried( tag->getOption< core::Real >( "residue_fraction_buried", 0.0001 ) );
  if( tag->hasOption( "task_operations" ) )
    task_factory( protocols::rosetta_scripts::parse_task_operations( tag, data ) );

  residue_burial_filter_tracer<<"ResidueBurialFilter with distance threshold of "<<distance_threshold_<<" around residue "<<target_residue_<<" residue_fraction_buried "<<residue_fraction_buried()<<" with "<<neighbors_<<" neighbors."<<std::endl;
}

void
ResidueBurialFilter::report( std::ostream & out, core::pose::Pose const & pose ) const {
  if( !task_factory() ){
    core::Size const count_neighbors( compute( pose ) );

    out<<"Number of interface neighbors of residue "<<pose.residue( target_residue_ ).name3()<<target_residue_<<" is "<<count_neighbors<<'\n';
  }
}

core::Real
ResidueBurialFilter::report_sm( core::pose::Pose const & pose ) const {
  if( !task_factory() ){
    core::Size const count_neighbors( compute( pose ) );

    return( count_neighbors );
  }
  else return( 0 );
}

/// @details counts the number of residues to target_residue_ across all chains in the pose, other than the one containing target_residue_
core::Size
ResidueBurialFilter::compute( core::pose::Pose const & pose ) const {
  core::Size chain( 1 );
  for( ; chain <= pose.conformation().num_chains(); ++chain )
    if( pose.conformation().chain_begin( chain ) <= target_residue_ && pose.conformation().chain_end( chain ) >= target_residue_ ) break;

  core::Size const chain_begin( pose.conformation().chain_begin( chain ) );
  core::Size const chain_end( pose.conformation().chain_end( chain ) );

residue_burial_filter_tracer<<"chain span "<<chain_begin<< " "<<chain_end<<std::endl;
  core::Size count_neighbors( 0 );
  core::conformation::Residue const res_target( pose.conformation().residue( target_residue_ ) );
  for( core::Size i=1; i<=pose.total_residue(); ++i ){
    if( i>=chain_begin && i<=chain_end ) continue;
    core::conformation::Residue const resi( pose.residue( i ) );
    core::Real const distance( resi.xyz( resi.nbr_atom() ).distance( res_target.xyz( res_target.nbr_atom() ) ) );
    if( distance <= distance_threshold_ ) ++count_neighbors;
  }
  return( count_neighbors);
}

filters::FilterOP
ResidueBurialFilter::clone() const {
    return new ResidueBurialFilter( *this );
}

filters::FilterOP
ResidueBurialFilter::fresh_instance() const{
    return new ResidueBurialFilter();
}


}
}