PackStatFilter.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/filters/PackStatFilter.cc
/// @brief filter structures by packstat score
/// @detailed
/// @author Nobuyasu Koga ( nobuyasu@uw.edu )

// Unit Headers
#include <protocols/simple_filters/PackStatFilter.hh>
#include <protocols/simple_filters/PackStatFilterCreator.hh>

// Project Headers
#include <core/types.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/util.hh>

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

// Parser headers
#include <protocols/filters/Filter.hh>
#include <utility/tag/Tag.hh>

#include <utility/vector0.hh>
#include <utility/vector1.hh>


//// C++ headers
static basic::Tracer tr("protocols.filters.PackStatFilter");

namespace protocols {
namespace simple_filters {

// @brief default constructor
PackStatFilter::PackStatFilter():
  Filter( "PackStat" ),
  chain_( 0 ),
  repeats_( 1 ),
  filtered_score_( 0.58 )  // ideally, ~0.65 is required for good packing
{}

//PackStatFilter::~PackStatFilter(){}

// @brief constructor with arguments
PackStatFilter::PackStatFilter( Real const & score ):
  Filter( "PackStat" ),
  chain_(0),
  repeats_(1),
  filtered_score_( score )
{}

// @brief copy constructor
PackStatFilter::PackStatFilter( PackStatFilter const & rval ):
  //utility::pointer::ReferenceCount(),
  Super( rval ),
  chain_(rval.chain_),
  repeats_(rval.repeats_),
  filtered_score_( rval.filtered_score_ )
{}

// @brief set filtered secondary structure
void PackStatFilter::filtered_score( Real const & score )
{
  filtered_score_ = score;
}

/// @brief
PackStatFilter::Real
PackStatFilter::compute( Pose const & pose ) const
{
  // calc packstat
  core::Real packscore;
  
  // repeats to average
  core::Real packscore_average( 0.0 );

    for( core::Size i = 1; i<=repeats_; i++ ){
      if( chain_ < 1 )
        packscore = core::scoring::packstat::compute_packing_score( pose );
      else{
        core::pose::Pose single_chain( pose.split_by_chain( chain_ ) );
        packscore = core::scoring::packstat::compute_packing_score( single_chain );   
      }
    packscore_average += packscore;
    tr << "repeat " << i << ": packscore: " << packscore << std::endl;
    }

    return packscore_average / (core::Real)repeats_;
}

/// @brief
PackStatFilter::Real
PackStatFilter::report_sm( Pose const & pose ) const
{
  return compute( pose );
}

// @brief returns true if the given pose passes the filter, false otherwise.
// In this case, the test is whether the give pose is the topology we want.
bool PackStatFilter::apply( Pose const & pose ) const
{
  Real score = compute( pose );
  if( score > filtered_score_ ){
    tr << "Successfully filtered: " << score << std::endl;
    return true;
  }else{
    tr << "Filter failed current/threshold=" << score << "/" << filtered_score_ << std::endl;
    return false;
  }
} // apply_filter

/// @brief parse xml
void
PackStatFilter::parse_my_tag(
  TagPtr const tag,
  DataMap &,
  filters::Filters_map const &,
  Movers_map const &,
  Pose const & )
{
  filtered_score_ = tag->getOption<Real>( "threshold", 0.58 ); // ideally, ~0.65 is required for good packing
  tr << "Structures with packstat score " << filtered_score_ << " will be filtred." << std::endl;
  chain_ = tag->getOption<core::Size>( "chain", 0 );
  repeats_ = tag->getOption<core::Size>( "repeats", 1 );
}

filters::FilterOP
PackStatFilterCreator::create_filter() const { return new PackStatFilter; }

std::string
PackStatFilterCreator::keyname() const { return "PackStat"; }


} // filters
} // protocols