TorsionFilter.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 sw=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.

/// @author Sarel Fleishman (sarelf@uw.edu)
#include <protocols/protein_interface_design/filters/TorsionFilter.hh>
#include <protocols/protein_interface_design/filters/TorsionFilterCreator.hh>
#include <sstream>
#include <core/conformation/Residue.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <utility/tag/Tag.hh>
#include <protocols/filters/Filter.hh>
// AUTO-REMOVED #include <protocols/moves/DataMap.hh>
#include <basic/Tracer.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH
//Auto Headers
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <core/pack/task/TaskFactory.hh>


namespace protocols {
namespace protein_interface_design{
namespace filters {

static basic::Tracer TR( "protocols.protein_interface_design.filters.Torsion" );
static basic::Tracer TR_database( "protocols.protein_interface_design.filters.Torsion_database" );

///@brief default ctor
Torsion::Torsion() :
  parent( "Torsion" ),
  lower_( false ),
  upper_( true ),
  resnum_( 0 ),
  torsion_( "" ),
  task_factory_( NULL ),
  task_factory_set_( false )
{}

bool
Torsion::apply(core::pose::Pose const & pose ) const
{
  if( task_factory_set() ){
    utility::vector1< core::Size > designable( protocols::rosetta_scripts::residue_packer_states( pose, task_factory(), true/*designable*/, false/*packable*/ ) );
    std::sort( designable.begin(), designable.end() );
    core::Size const start( designable[ 1 ] );
    core::Size const stop( designable[ designable.size() ] );
    for( core::Size i = start; i<=stop; ++i )
      TR_database<<pose.phi( i )<<" "<<pose.psi( i )<<" "<<pose.omega( i )<<" "<<pose.residue( i ).name3()<<" ";
    TR_database<<std::endl;
    return true;
  }
  else if( resnum() == 0 ){ // just print all torsions
    std::stringstream s("");
    for( core::Size i = 1; i <= pose.total_residue(); ++i ){
      if( i % 5 == 0 ) s << pose.residue( i ).name1()<<pose.pdb_info()->number( i )<<pose.pdb_info()->chain( i )<<'\t';
      TR<<"Residue "<<pose.residue( i ).name1()<<pose.pdb_info()->number( i )<<pose.pdb_info()->chain( i )<<'\t';
      if( torsion() == "phi" || torsion() == "" ){
        TR<<" phi "<<pose.phi( i )<<'\t';
        s<<pose.phi( i )<<' ';
      }
      if( torsion() == "psi" || torsion() == "" ){
        TR<<" psi "<<pose.psi( i )<<'\t';
        s<<pose.psi( i )<<' ';
      }
      if( torsion() == "omega" || torsion() == "" ){
        TR<<" omega "<<pose.omega( i )<<std::endl;
        s<<pose.omega( i )<<' ';
      }
    }
    TR<<s.str()<<std::endl;
    return true;
  }
  else{
    TR<<"Residue "<<pose.residue( resnum() ).name1()<<pose.pdb_info()->number( resnum() )<<pose.pdb_info()->chain( resnum() )<<'\t';
    if( torsion() == "phi" || torsion() == "" ){
      core::Real const phi( pose.phi( resnum() ) );
      TR<<" phi "<<phi<<std::endl;
      if( torsion() == "phi" )
        return( phi>=lower() && phi<=upper() );
    }
    if( torsion() == "psi" || torsion() == "" ){
      core::Real const psi( pose.psi( resnum() ) );
      TR<<" psi "<<pose.psi( resnum() )<<std::endl;
      if( torsion() == "psi" )
        return( psi>=lower() && psi<=upper() );
    }
  }

  return false;
}

core::Real
Torsion::compute( core::pose::Pose const & p ) const{
  if( resnum() > 0 ){
    if( torsion() == "phi" ) return p.phi( resnum() );
    if( torsion() == "psi" ) return p.psi( resnum() );
    if( torsion() == "omega" ) return p.omega( resnum() );
  }
  return 0.; // You gotta return something!
}

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

void
Torsion::report( std::ostream & out, core::pose::Pose const & pose ) const
{
  out<<"Torsion returns "<<compute( pose )<<std::endl;
}

void
Torsion::parse_my_tag( utility::tag::TagPtr const tag,
    protocols::moves::DataMap & data,
  protocols::filters::Filters_map const &,
  protocols::moves::Movers_map const &,
    core::pose::Pose const & pose )
{
  task_factory_set( false );
  if( tag->hasOption( "task_operations" ) )
    task_factory_set( true );
  runtime_assert( task_factory_set_ != tag->hasOption( "resnum" ) );
  lower( tag->getOption< core::Real >( "lower", 0 ) );
  task_factory( protocols::rosetta_scripts::parse_task_operations( tag, data ) );
  upper( tag->getOption< core::Real >( "upper", 0 ) );
  torsion( tag->getOption< std::string >( "torsion", "" ) );
  if( tag->hasOption( "resnum" ))
    resnum( core::pose::parse_resnum( tag->getOption< std::string >( "resnum" ), pose ) );
  else resnum( 0 );
  TR<<"resnum: "<<resnum()<<" lower "<<lower()<<" upper: "<<upper()<<std::endl;
}

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

Torsion::~Torsion(){}

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

protocols::filters::FilterOP
TorsionCreator::create_filter() const { return new Torsion; }

std::string
TorsionCreator::keyname() const { return "Torsion"; }

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

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

} // filters
} // protein_interface_design
} // protocols