extract_pdbs.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 extract_pdbs.cc
/// @brief simple application for extracting PDBs from a silent-file.
/// @author James Thompson

// libRosetta headers

#include <core/types.hh>

#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.hh>

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

#include <devel/init.hh>

#include <basic/options/option.hh>

#include <basic/Tracer.hh>

#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>

#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>

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

// C++ headers
#include <string>

#include <basic/options/option_macros.hh>

// option key includes

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>

#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <boost/algorithm/string/erase.hpp>

#include <utility/excn/Exceptions.hh>


int
main( int argc, char* argv [] ) {
  try {

    // define relevant options
    OPT(in::path::database);
    OPT(in::file::silent);
    OPT(in::file::tags);
    OPT(in::file::silent_struct_type);
    OPT(in::file::silent_renumber);
    OPT(out::file::residue_type_set);
    OPT(out::prefix);
    OPT(in::path::database);
    OPT(in::file::rescore);
    OPT(score::weights);
    OPT(score::patch);

    using namespace core::chemical;
    using namespace core::import_pose::pose_stream;
    using namespace basic::options;
    using namespace basic::options::OptionKeys;

    // options, random initialization
    devel::init( argc, argv );

    std::string usage("");
    usage += "\n\nusage:  extract_pdbs [options] -in::file::silent <silent_files>\n";
    usage += "\tTo see a list of other valid options, use the option -help.\n";

    if ( !option[ in::file::silent ].user() ) {
      std::cerr << usage << std::endl;
      std::exit(1);
    }

    basic::Tracer tr( "extract_pdbs" );

    core::chemical::ResidueTypeSetCOP rsd_set( NULL );
    if (  option[ out::file::residue_type_set ].user() ) {
      rsd_set = ChemicalManager::get_instance()->residue_type_set(
        option[ out::file::residue_type_set ]()
      );
    }
    PoseInputStreamOP input;
    if ( option[ in::file::silent ].user() ) {
      if ( option[ in::file::tags ].user() ) {
        input = PoseInputStreamOP( new SilentFilePoseInputStream(
          option[ in::file::silent ](),
          option[ in::file::tags ]()
          ) );
      } else if ( option[ in::file::tagfile ].user() ) {

        utility::vector1< std::string > input_tags;
        utility::io::izstream tag_file( option[ in::file::tagfile ]() );
        std::copy( std::istream_iterator< std::string >( tag_file ), std::istream_iterator< std::string >(),
          std::back_inserter( input_tags ) );
        input = PoseInputStreamOP( new SilentFilePoseInputStream( option[ in::file::silent ](), input_tags ) );

      } else {
        input = PoseInputStreamOP( new SilentFilePoseInputStream( option[ in::file::silent ]() ) );
      }
    }

    core::scoring::ScoreFunctionOP scorefxn;

    if ( option[ in::file::rescore ]() ) {
      scorefxn = core::scoring::get_score_function();
      tr.Debug << "scoring using ScoreFunction with weights: " << std::endl;
      scorefxn->show( tr.Debug );
      tr.flush();
    }

    core::pose::Pose pose;
    std::string out_prefix = option[ out::prefix ]();
    while ( input->has_another_pose() ) {
      //fpd  'fill_pose' assumes an asymmetric pose is input
      if ( core::pose::symmetry::is_symmetric( pose ) ) {
        core::pose::symmetry::make_asymmetric_pose( pose );
      }
      if ( rsd_set ) {
        input->fill_pose( pose, *rsd_set );
      } else {
        input->fill_pose( pose );
      }

      // make sure the parent/template name gets included in the REMARK line of the PDB
      using std::map;
      using std::string;
      map< string, string > score_line_strings( core::pose::get_all_score_line_strings( pose ) );
      for ( map< string, string >::const_iterator it = score_line_strings.begin(),
          end = score_line_strings.end();
          it != end; ++it ) {
        if ( it->first != "aln_id" ) continue;
        core::pose::add_comment( pose, "parents", it->second );
      }
      std::string tag( tag_from_pose( pose ) );
      // Many applications will put .pdb on the pose tag; remove it if it's there.
      if ( tag.find( ".pdb" ) != std::string::npos ) {
        tag.erase( tag.find( ".pdb" ) , tag.size() );
      }
      std::string fn( out_prefix + tag + ".pdb" );

      tr << "extracting Pose with tag " << tag << " into PDB file " << fn
        << std::endl;

      if ( option[ in::file::rescore ]() ) {
        tr.Debug << "rescoring Pose with tag " << tag << std::endl;
        scorefxn->show( tr.Debug );
        (*scorefxn)(pose);

        scorefxn->show( tr.Debug, pose );
        pose.dump_scored_pdb( fn, *scorefxn );
      } else {
        pose.dump_pdb( fn );
      }

      //fpd

      tr.flush();
    }

    exit( 0 );

  } catch ( utility::excn::EXCN_Base const & e ) {
    std::cout << "caught exception " << e.msg() << std::endl;
    return -1;
  }

  return 0;
} // main