ConservedPosMutationFilter.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/ConservedPosMutationFilter.cc
/// @author Florian Richter (floric@u.washington.edu), may 2011

// Unit Headers
#include <protocols/simple_filters/ConservedPosMutationFilter.hh>
#include <protocols/simple_filters/ConservedPosMutationFilterCreator.hh>

// Package Headers
#include <protocols/toolbox/task_operations/SeqprofConsensusOperation.hh>

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

#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/pose/Pose.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/types.hh>

// AUTO-REMOVED #include <protocols/moves/DataMap.hh>

// Utility headers
#include <utility/string_util.hh>
#include <utility/tag/Tag.hh>

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


//// C++ headers
static basic::Tracer tr("protocols.simple_filters.ConservedPosMutationFilter");

namespace protocols {
namespace simple_filters {


ConservedPosMutationFilter::ConservedPosMutationFilter() :
  parent("ConservedPosMutationFilter"),
  conserved_pos_taskop_(new toolbox::task_operations::RestrictConservedLowDdgOperation()),
  max_allowed_conserved_pos_mutations_(0)
{
}

ConservedPosMutationFilter::~ConservedPosMutationFilter(){}

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

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


bool
ConservedPosMutationFilter::apply( core::pose::Pose const & pose ) const {

  core::Size conserved_pos_mutations(0);
  bool verbose( conserved_pos_taskop_->verbose() );
  std::string mutstring;

  for( core::Size i(1); i <= pose.total_residue(); ++i){
    if( !pose.residue_type(i).is_protein() ) continue;

    core::chemical::AA wt_aa( conserved_pos_taskop_->seqprof_wt_aa(i) );
    if( conserved_pos_taskop_->position_untouchable(i, wt_aa) && (wt_aa != pose.residue_type(i).aa() ) ){
      conserved_pos_mutations++;
      if( !verbose && (conserved_pos_mutations > max_allowed_conserved_pos_mutations_)){
        tr << "Pose has at least " << conserved_pos_mutations << " mutations at conserved positions, but only " << max_allowed_conserved_pos_mutations_ << " are allowed, returnig false..." << std::endl;
        return false;
      }
      else if (verbose ){
        using namespace core::chemical;
        mutstring = mutstring + oneletter_code_from_aa( wt_aa ) + utility::to_string( i ) + oneletter_code_from_aa( pose.residue_type(i).aa() ) + ", ";
      }
    }
    //if the user is interested, we'll write out the conservation and ddg info for every mutation
    if( verbose && (wt_aa != pose.residue_type(i).aa() ) ){
      tr << "Mutation at pos " << i << " with ala_ddg of " << conserved_pos_taskop_->position_ala_ddG( i ) << " and wt conservation " << conserved_pos_taskop_->seqprof()->profile()[ i ][ conserved_pos_taskop_->seqprof_wt_aa(i) ]  << std::endl;
    }
  }
  if( verbose ) tr << "Forbidden mutations detected: " << mutstring << std::endl;
  if( conserved_pos_mutations > max_allowed_conserved_pos_mutations_){
    tr << "Pose has " << conserved_pos_mutations << " mutations at conserved positions, but only " << max_allowed_conserved_pos_mutations_ << " are allowed, returnig false..." << std::endl;
    return false;
  }

  tr << "Pose has " << conserved_pos_mutations << " mutations at conserved positions, <= than the allowed value of " << max_allowed_conserved_pos_mutations_ << ", returnig true..." << std::endl;
  return true;
} // apply


void
ConservedPosMutationFilter::parse_my_tag( utility::tag::TagPtr const tag, protocols::moves::DataMap & , protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &  )
{
  conserved_pos_taskop_->parse_tag( tag );

  if (tag->hasOption("max_conserved_pos_mutations")) {
    max_allowed_conserved_pos_mutations_ = tag->getOption<core::Size>("max_conserved_pos_mutations");
  }
}


filters::FilterOP
ConservedPosMutationFilterCreator::create_filter() const { return new ConservedPosMutationFilter; }

std::string
ConservedPosMutationFilterCreator::keyname() const { return "ConservedPosMutationFilter"; }



} // filters
} // protocols