OutputWriter.cc

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//
// (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/match/output/OutputWriter.cc
/// @brief  Implementation for the class to write output matches that have (presumably) passed the output filters.
/// @author Alex Zanghellini (zanghell@u.washington.edu)
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), Florian Richter (floric@u.washington.edu) porting to mini

// Unit headers
#include <protocols/match/output/OutputWriter.hh>

#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>
#include <protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.hh>
#include <protocols/match/MatcherTask.hh>
#include <protocols/match/Hit.hh>

//utility headers
#include <utility/string_util.hh>

#include <utility/vector1.hh>




namespace protocols {
namespace match {
namespace output {

OutputWriter::OutputWriter()
  : cst_io_(NULL)
{}

OutputWriter::~OutputWriter() {}

protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP
OutputWriter::cst_io() const
 {
    return cst_io_;
 }


void
OutputWriter::initialize_from_matcher_task(
  MatcherTaskCOP mtask
){
  cst_io_ = mtask->enz_input_data();
}


void
OutputWriter::determine_redundant_upstream_matchres(
  match_dspos1 const & m,
  std::map< core::Size, core::Size > & redundant_upstream_res
) const
{
  using namespace core;
  using namespace toolbox::match_enzdes_util;

  redundant_upstream_res.clear();
  std::map< Size, Size > seen_scafpos_to_geom_cst;
  std::map< Size, Size > bb_scafpos_to_geom_cst;

  for ( core::Size i = 1; i <= m.upstream_hits.size(); ++i ) {
    core::Size this_scafpos = m.upstream_hits[i].scaffold_build_id();
    MatchConstraintFileInfoCOP cur_mcfi =
      cst_io_->mcfi_list( i )->mcfi( m.upstream_hits[i].external_geom_id() );
    bool bb_interaction( cur_mcfi->is_backbone( cur_mcfi->upstream_res() ) );

    std::map< Size, Size >::iterator seen_it = seen_scafpos_to_geom_cst.find( this_scafpos );
    std::map< Size, Size >::iterator bb_seen_it = bb_scafpos_to_geom_cst.find( this_scafpos );

    //first case: this residue position has already been seen,
    //so either this or the previously seen constraint are redundant
    if ( seen_it != seen_scafpos_to_geom_cst.end() ) {
      if ( bb_interaction ) {
        redundant_upstream_res[ i ] = seen_it->second;
        continue;
      } else {
        if ( bb_seen_it != bb_scafpos_to_geom_cst.end() ) {
          redundant_upstream_res[ bb_seen_it->second ] = i;
        } else {
          utility_exit_with_message("Error in matcher: two sidechains (for geomcsts "+utility::to_string( i )+" and " +utility::to_string( seen_it->second )+") placed at the same scaffold location ("+utility::to_string( this_scafpos)+") considered a match. Hint: if one of these geomcsts is supposed to be a backbone only interaction, this needs to be specified in the cstfile through the \"TEMPLATE::   ATOM_MAP: <residue num> is_backbone \" tag.");
        }
      }
    } else {
      //otherwise this position has not been encountered before
      seen_scafpos_to_geom_cst[ this_scafpos] = i;
      if ( bb_interaction ) {
        bb_scafpos_to_geom_cst[ this_scafpos ] = i;
      }
    }
  } //loop over all matchres
}

}
}
}