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

// Project Headers
#include <core/types.hh>
#include <utility/exit.hh>

#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
//#include <protocols/moves/ResidueMover.hh>
#include <utility/tag/Tag.hh>
#include <protocols/moves/DataMap.hh>
#include <protocols/rosetta_scripts/util.hh>

// Utility Headers
#include <basic/Tracer.hh>

// Unit Headers

// C++ headers
#include <map>
#include <string>

#include <core/chemical/AA.hh>
#include <utility/vector0.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>

using namespace core;
using namespace core::scoring;

static basic::Tracer TR( "protocols.protein_interface_design.parse_filters" );

namespace protocols {
namespace protein_interface_design {
using namespace protocols::filters;

using namespace protocols::moves;

using namespace utility::tag;
using namespace std;

void
ResiduesInInterfaceFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  residues_in_interface_threshold_ = tag->getOption<core::Size>( "residues", 20 );
  rb_jump_ = tag->getOption<core::Size>( "jump_number", 1 );

  TR<<"residues in interface filter over jump number " << rb_jump_ << " with threshold "<<residues_in_interface_threshold_<<std::endl;
}

void
ScoreTypeFilter::parse_my_tag( TagPtr const tag, DataMap & data, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  using namespace core::scoring;

  std::string const scorefxn_name( tag->getOption<string>( "scorefxn", "score12" ) );
  scorefxn_ = new ScoreFunction( *(data.get< ScoreFunction * >( "scorefxns", scorefxn_name )) );
  score_type_ = core::scoring::score_type_from_name( tag->getOption<string>( "score_type", "total_score" ) );
  if( ! tag->hasOption( "threshold" ) ) throw utility::excn::EXCN_RosettaScriptsOption("Must specify 'threshold' for ScoreTypeFilter.");
  score_type_threshold_ = tag->getOption<core::Real>( "threshold" );

  TR<<"ScoreType filter for score_type "<<score_type_<<" with threshold "<<score_type_threshold_<<std::endl;
}

void
InterfaceSasaFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  lower_threshold_ = tag->getOption<core::Real>( "threshold", 800 );
  jump( tag->getOption< core::Size >( "jump", 1 ));
  hydrophobic_ = tag->getOption<bool>( "hydrophobic", false );
  polar_ = tag->getOption<bool>( "polar", false );
  runtime_assert( !hydrophobic_ || !polar_ );
  if( jump() != 1 && ( polar_ || hydrophobic_ ) )
    throw utility::excn::EXCN_RosettaScriptsOption( "ERROR: presently, only total sasa is supported across a jump other than 1. Remove polar and hydrophobic flags and try again." );

  TR<<"SasaFilter with lower threshold of "<<lower_threshold_<<" Ang^2 and jump "<<jump()<<'\n';
  if( hydrophobic_ )
    TR<<"Only reporting hydrophobic sasa\n";
  if( polar_ )
    TR<<"Only reporting polar sasa\n";
  TR.flush();
}

void
AlaScan::parse_my_tag( TagPtr const tag, DataMap & data, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  distance_threshold_ = tag->getOption<core::Real>( "interface_distance_cutoff", 8.0 );
  chain1_ = tag->getOption< bool >( "partner1", 0 );
  chain2_ = tag->getOption< bool >( "partner2", 1 );
  jump_ = tag->getOption< Size >( "jump", 1 );
  runtime_assert( chain1_ || chain2_ );
  std::string const scorefxn_name( tag->getOption< string >( "scorefxn", "score12" ));
  repeats_ = tag->getOption< core::Size >( "repeats", 1 );
  symmetry_ = tag->getOption< bool >( "symmetry", 0 );
  repack( tag->getOption< bool >( "repack", 1 ) );

  if ( symmetry_ ) {
    using namespace core::scoring::symmetry;
    scorefxn_ = new SymmetricScoreFunction( *data.get< ScoreFunction * >( "scorefxns", scorefxn_name ) );
    TR<<"Symmetric AlaScan with distance threshold of "<<distance_threshold_<<" Ang "<<". jump="<<jump_<<" partner1="<<chain1_<<", partner2="<<chain2_<<" using "<<repeats_<<" repeats."<<std::endl;
    return;
  }
  using namespace core::scoring;
  scorefxn_ = new ScoreFunction( *(data.get< ScoreFunction * >( "scorefxns", scorefxn_name )) );
  TR<<"AlaScan with distance threshold of "<<distance_threshold_<<" Ang "<<". jump="<<jump_<<" partner1="<<chain1_<<", partner2="<<chain2_<<" using "<<repeats_<<" repeats repack "<<repack()<<std::endl;
}

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

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

void
ResidueBurialFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & pose )
{
  target_residue_ = protocols::rosetta_scripts::get_resnum( tag, pose );
  distance_threshold_ = tag->getOption<core::Real>( "distance", 8.0 );
  neighbors_ = tag->getOption<core::Size>( "neighbors", 1 );

  TR<<"ResidueBurialFilter with distance threshold of "<<distance_threshold_<<" around residue "<<target_residue_<<" with "<<neighbors_<<" neighbors."<<std::endl;
}

void
ResidueDistanceFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & pose )
{
  res1_ = protocols::rosetta_scripts::get_resnum( tag, pose, "res1_" );
  res2_ = protocols::rosetta_scripts::get_resnum( tag, pose, "res2_" );
  distance_threshold_ = tag->getOption<core::Real>( "distance", 8.0 );

  TR<<"ResidueDistanceFilter with distance threshold of "<<distance_threshold_<<" between residues "<<res1_<<" and "<<res2_<<std::endl;
}

void
DdgFilter::parse_my_tag( TagPtr const tag, DataMap & data, Filters_map const & , Movers_map const & , core::pose::Pose const & )
{
  using namespace core::scoring;

  std::string const scorefxn_name( tag->getOption<string>( "scorefxn", "score12" ) );
  scorefxn_ = new ScoreFunction( *(data.get< ScoreFunction * >( "scorefxns", scorefxn_name )) );
  ddg_threshold_ = tag->getOption<core::Real>( "threshold", -15 );
  rb_jump_ = tag->getOption< core::Size >( "jump", 1 );
  repeats( tag->getOption< core::Size >( "repeats", 1 ) );
  repack( tag->getOption< bool >( "repack", 1 ) );
  symmetry_ = tag->getOption<bool>( "symmetry", 0 );

  if( repeats() > 1 && !repack() )
    throw utility::excn::EXCN_RosettaScriptsOption( "ERROR: it doesn't make sense to have repeats if repack is false, since the values converge very well." );

  if ( symmetry_ )
    TR<<"ddg filter with threshold "<< ddg_threshold_<<" repeats="<<repeats()<<" and scorefxn "<<scorefxn_name<<" with symmetry " <<std::endl;
  else
    TR<<"ddg filter with threshold "<< ddg_threshold_<<" repeats="<<repeats()<<" and scorefxn "<<scorefxn_name<<" over jump "<<rb_jump_<<" and repack "<<repack()<<std::endl;
}

void
HbondsToResidueFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & pose )
{
  partners_ = tag->getOption<core::Size>( "partners" );
  energy_cutoff_ = tag->getOption<core::Real>( "energy_cutoff", -0.5 );
  backbone_ = tag->getOption<bool>( "backbone", 0 );
  sidechain_ = tag->getOption<bool>( "sidechain", 1 );
  resnum_ = protocols::rosetta_scripts::get_resnum( tag, pose );

  TR<<"Hbonds to residue filter for resnum "<<resnum_<<" with "<<partners_<<" hbonding partners"<<std::endl;
}

void
EnergyPerResidueFilter::parse_my_tag( TagPtr const tag, DataMap & data, Filters_map const &, Movers_map const &, core::pose::Pose const & pose )
{
  using namespace core::scoring;

  std::string const scorefxn_name( tag->getOption<string>( "scorefxn", "score12" ) );
  scorefxn_ = new ScoreFunction( *(data.get< ScoreFunction * >( "scorefxns", scorefxn_name ) ));
  score_type_ = core::scoring::score_type_from_name( tag->getOption<string>( "score_type", "total_score" ) );
  threshold_ = tag->getOption<core::Real>( "energy_cutoff", 0.0 );
  whole_interface_ = tag->getOption<bool>( "whole_interface" , 0 );
  rb_jump_ = tag->getOption<core::Size>( "jump_number", 1 );
  interface_distance_cutoff_ = tag->getOption<core::Real>( "interface_distance_cutoff" , 8.0 );

  if (whole_interface_==1 ) {
    resnum_ = 1;
    TR<<"energies for all interface residues with a distance cutoff of "
    << interface_distance_cutoff_ << " A will be calculated \n"
    << "jump_number is set to "<< rb_jump_
    << "\n and scorefxn " <<scorefxn_name <<" will be used" <<std::endl;
  }
  else {
    resnum_ = protocols::rosetta_scripts::get_resnum( tag, pose );
    TR<<"EnergyPerResidueFilter for residue "<<resnum_<<" of score_type "<<score_type_<<" with cutoff "<<threshold_<<std::endl;
    }
}

void
BuriedUnsatHbondFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  jump_num_ = tag->getOption<core::Size>( "jump_number", 1 );
  upper_threshold_ = tag->getOption<core::Size>( "cutoff", 20 );

  TR<<"Buried Unsatisfied Hbond filter over jump number " << jump_num_ << " with cutoff " << upper_threshold_ << std::endl;
}

void
TerminusDistanceFilter::parse_my_tag( TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, core::pose::Pose const & )
{
  jump_num_ = tag->getOption<core::Size>( "jump_number", 1 );
  distance_ = tag->getOption<core::Size>( "distance", 5 );

  TR<<"Distance From Terminus filter over jump number " << jump_num_ << " with cutoff " << distance_ << std::endl;
}


} // protein_interface_design
} // devel