NonSequentialNeighborsFilter.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_filters/NonSequentialNeighborsFilter.cc
/// @brief
/// @author Gabi Pszolla & Sarel Fleishman


//Unit Headers
#include <protocols/simple_filters/NonSequentialNeighborsFilter.hh>
#include <protocols/simple_filters/NonSequentialNeighborsFilterCreator.hh>
#include <utility/tag/Tag.hh>
#include <core/conformation/Conformation.hh>
#include <numeric/xyzVector.hh>
//Project Headers
#include <basic/Tracer.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/pose/Pose.hh>
namespace protocols{
namespace simple_filters {

static basic::Tracer TR( "protocols.simple_filters.NonSequentialNeighborsFilter" );

protocols::filters::FilterOP
NonSequentialNeighborsFilterCreator::create_filter() const { return new NonSequentialNeighborsFilter; }

std::string
NonSequentialNeighborsFilterCreator::keyname() const { return "NonSequentialNeighbors"; }

//default ctor
NonSequentialNeighborsFilter::NonSequentialNeighborsFilter() :
protocols::filters::Filter( "NonSequentialNeighbors" ),
distance_threshold_( 8.0 ),
neighbor_cutoff_( 10 ),
bound_( false ),
resnum_( 0 ),
jump_( 1 )
{
}

NonSequentialNeighborsFilter::~NonSequentialNeighborsFilter() {}

void
NonSequentialNeighborsFilter::parse_my_tag( utility::tag::TagPtr const tag, moves::DataMap &, filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const & )
{
  distance_threshold( tag->getOption< core::Real >( "distance_threshold", 8.0 ) );
  neighbor_cutoff( tag->getOption< core::Size >( "neighbor_cutoff", 10 ));
  bound( tag->getOption< bool >( "bound", false ) );
  resnum( tag->getOption< core::Size >( "resnum", 0 ) );
  jump( tag->getOption< core::Size >( "jump", 1 ) );

  TR<<"jump: "<<jump()<<" distance_threshold: "<<distance_threshold()<<" neighbor_cutoff: "<<neighbor_cutoff()<<" bound: "<<bound()<<" resnum: "<<resnum()<<std::endl;
}

bool
NonSequentialNeighborsFilter::apply( core::pose::Pose const & pose ) const {
  compute( pose );
  return( true );
}

void
NonSequentialNeighborsFilter::report( std::ostream &, core::pose::Pose const & pose ) const {
  compute( pose );
}

core::Real
NonSequentialNeighborsFilter::report_sm( core::pose::Pose const & pose ) const {
  return( compute( pose ) );
}

core::Size
NonSequentialNeighborsFilter::residue_neighbors( core::pose::Pose const & pose, core::Size const resi ) const{
  core::Size count_neighbors = 0;
  core::Size const target_chain( pose.chain( resi ) );
  for( core::Size resj = pose.conformation().chain_begin( target_chain ); resj <= pose.conformation().chain_end( target_chain ); ++resj ){
    if( resj >= resi - neighbor_cutoff() && resj <= resi + neighbor_cutoff() )
      continue;
    core::Real const distance( pose.residue( resi ).xyz( pose.residue( resi ).nbr_atom() ).distance( pose.residue( resj ).xyz( pose.residue( resj ).nbr_atom() ) ) );
    if( distance <= distance_threshold() )
      count_neighbors++;
  }
  return( count_neighbors );
}

core::Real
NonSequentialNeighborsFilter::compute(
  core::pose::Pose const & pose
) const {
  core::pose::Pose copy_pose( pose );

  if( !bound() ){
    protocols::rigid::RigidBodyTransMover rbtm( copy_pose, jump() );
    rbtm.step_size( 10000.0 );
    rbtm.apply( copy_pose );
    TR.Debug<<"Unbound complex"<<std::endl;
  }
  if( resnum() == 0 ){// working on entire protein
    for( core::Size resi = 1; resi <= pose.total_residue(); ++resi ){
      core::Size const count_neighbors( residue_neighbors( copy_pose, resi ) );
      TR.Debug<<"neighbors of residue "<<resi<<": "<<count_neighbors<<std::endl;
    }// for resi
    return 1.0; // dummy return
  }// fi resnum==0
  core::Size const count_neighbors( residue_neighbors( copy_pose, resnum() ) );
  TR.Debug<<"neighbors of residue "<<resnum()<<": "<<count_neighbors<<std::endl;
  return( count_neighbors );
}

}
}