AbinitioBaseFilter.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 src/protocols/filters/Filters.hh
/// @brief header file for Filters.cc
/// @detailed
///   Contains currently: Filters
///
///
/// @author Robert Vernon

// Unit Headers

// Project Headers
#include <core/conformation/Residue.hh>

#include <core/pose/Pose.hh>
#include <core/pose/util.hh>

// AUTO-REMOVED #include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>


#include <protocols/simple_filters/AbinitioBaseFilter.hh>
// AUTO-REMOVED #include <protocols/simple_filters/RGFilter.hh>
// AUTO-REMOVED #include <protocols/simple_filters/COFilter.hh>
// AUTO-REMOVED #include <protocols/simple_filters/SheetFilter.hh>


// ObjexxFCL Headers
// AUTO-REMOVED #include <ObjexxFCL/FArray1D.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>


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

#include <utility/vector1.hh>

//Auto Headers
#include <core/conformation/Conformation.hh>


//// C++ headers

static basic::Tracer tr("protocols.simple_filters.AbinitioBaseFilter");

using namespace ObjexxFCL;
using namespace ObjexxFCL::fmt;

namespace protocols {
namespace simple_filters {

AbinitioBaseFilter::AbinitioBaseFilter() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  sstype_ = "";
}

bool
AbinitioBaseFilter::apply( core::pose::Pose const & pose ) const {
  if ( sstype_ == "" ) sstype_=get_protein_sstype( pose );
  tr.Info << "apply filter: " << name() << std::endl;
  return true;
}

std::string
AbinitioBaseFilter::get_protein_sstype( core::pose::Pose const & pose ) const {
  using core::Size;

  utility::vector1< char > secstructs = read_psipred_ss2_file( pose );

  if( secstructs.size() == 0 ) {
    tr.Error << "Warning: Needs psipred_ss2 to run filters" << std::endl;
    //    disable_all_filters_ = true;
    return "fail";
  }

  //  float beta_ratio;
  int alpha = 0;
  //  int
  beta_ = 0;
  int helix_length = 0;
  max_helix_length_ = 0;

  for ( Size i = 1; i <= pose.total_residue(); ++i ) {
    if ( ! pose.residue(i).is_protein() ) continue;
    if ( secstructs[i] == 'H' ) {
      ++alpha;
      ++helix_length;
      if ( helix_length > max_helix_length_ ) {
        max_helix_length_ = helix_length;
      }
    } else if ( secstructs[i] == 'E' ) {
      ++beta_;
      helix_length = 0;
    } else {
      helix_length = 0;
    }
  }
  max_helix_fraction_ = static_cast< core::Real >( max_helix_length_ ) / pose.total_residue();

//car protein_ss_type
  std::string protein_sstype;
  beta_ratio_ = static_cast< float >( beta_ ) / ( alpha + beta_ );
  if ( beta_ratio_ >= 0.8 ) {
    tr.Trace << "Protein type: all beta  Fraction beta: " <<
     F( 6, 3, beta_ratio_ ) << std::endl;
    protein_sstype = 'b';
  } else if ( beta_ratio_ > 0.2 && beta_ >= 10 ) {
    tr.Trace << "Protein type: alpha/beta  Fraction beta: " <<
     F( 6, 3, beta_ratio_ ) << std::endl;
    protein_sstype = "ab";
  } else {
    tr.Trace << "Protein type: all alpha  Fraction beta: " <<
     F( 6, 3, beta_ratio_ ) << "nbeta" << I( 6, beta_ ) << std::endl;
    protein_sstype = 'a';
  }

  return protein_sstype;

}

} // filters
} // protocols