NeighborTypeFilter.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 protocols/simple_filters/NeighborTypeFilter.cc
/// @brief
/// @author Sarel Fleishman (sarelf@u.washington.edu), Jacob Corn (jecorn@u.washington.edu)

#include <protocols/simple_filters/NeighborTypeFilter.hh>
#include <protocols/simple_filters/NeighborTypeFilterCreator.hh>

#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>

namespace protocols {
namespace simple_filters {

static basic::Tracer neighbor_type_filter_tracer( "protocols.simple_filters.NeighborTypeFilter" );

protocols::filters::FilterOP
NeighborTypeFilterCreator::create_filter() const { return new NeighborTypeFilter; }

std::string
NeighborTypeFilterCreator::keyname() const { return "NeighborType"; }

NeighborTypeFilter::~NeighborTypeFilter() {}

void
NeighborTypeFilter::parse_my_tag( utility::tag::TagPtr const tag, moves::DataMap &, filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const & pose )
{
  residue_types_.assign( core::chemical::num_canonical_aas, false );
  utility::vector0< utility::tag::TagPtr > const neighbor_type_tags( tag->getTags() );
  for( utility::vector0< utility::tag::TagPtr >::const_iterator nt_it=neighbor_type_tags.begin(); nt_it!=neighbor_type_tags.end(); ++nt_it ) {
    utility::tag::TagPtr const nt_tag_ptr = *nt_it;
    if( nt_tag_ptr->getName() == "Neighbor" ) {
      std::string const type( nt_tag_ptr->getOption<std::string>( "type" ) );
      residue_types_[ core::chemical::aa_from_name( type ) ] = true;
    }
  }
  target_residue_ = core::pose::get_resnum( tag, pose );
  distance_threshold_ = tag->getOption<core::Real>( "distance", 8.0 );

  neighbor_type_filter_tracer<<"NeighborTypeFilter with distance threshold of "<<distance_threshold_<<" around residue "<<target_residue_<<std::endl;
}

bool
NeighborTypeFilter::apply( core::pose::Pose const & pose ) const
{
  std::vector< core::Size > neighbors = compute( pose );
  if( neighbors.size() == 0 ) return false;
  neighbor_type_filter_tracer<<"neighbours of residue "<<pose.residue( target_residue_ ).name3()<<target_residue_<<": ";
  for( std::vector< core::Size >::const_iterator n_it=neighbors.begin(); n_it!=neighbors.end(); ++n_it ) {
    neighbor_type_filter_tracer<<pose.residue( *n_it ).name3()<<*n_it<<" ";
  }
  neighbor_type_filter_tracer<<std::endl;
  return true;
}

void
NeighborTypeFilter::report( std::ostream & out, core::pose::Pose const & pose ) const
{
  std::vector< core::Size > neighbors = compute( pose );
  out<<"neighbours of residue "<<pose.residue( target_residue_ ).name3()<<target_residue_<<": ";
  for( std::vector< core::Size >::const_iterator n_it=neighbors.begin(); n_it!=neighbors.end(); ++n_it ) {
    out<<pose.residue( *n_it ).name3()<<*n_it<<" ";
  }
  out<<'\n';
}

core::Real
NeighborTypeFilter::report_sm( core::pose::Pose const & pose ) const
{
  std::vector< core::Size > neighbors = compute( pose );
  return( neighbors.size() != 0 );
}

std::vector< core::Size >
NeighborTypeFilter::compute( core::pose::Pose const & pose ) const
{
  std::vector< core::Size > neighbors;

  core::Size const chain2begin( pose.conformation().chain_begin( 2 ) );
  core::Size const residue_num( pose.total_residue() );

  core::Size const start( target_residue_ < chain2begin ? chain2begin : 1 );
  core::Size const end( target_residue_ < chain2begin ? residue_num : chain2begin-1 );
  core::conformation::Residue const res_target( pose.residue( target_residue_ ) );

  runtime_assert( target_residue_ <= residue_num );
  for( core::Size res=start; res<=end; ++res ) {
    core::conformation::Residue const resi( pose.residue( res ) );
    if( !residue_types_[ resi.aa() ] ) continue;

    core::Real const distance( res_target.xyz( res_target.nbr_atom() ).distance( resi.xyz( resi.nbr_atom() )) );
    if( distance <= distance_threshold_ )
      neighbors.push_back( res );
  }
  return neighbors;
}

}
}