match.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   apps/public/match.cc
/// @brief
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com), porting to mini


#include <devel/init.hh>

#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>

#include <core/id/AtomID.hh>

#include <basic/options/option.hh>

#include <basic/options/keys/match.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>

#include <core/pose/Pose.hh>
//#include <core/scoring/ScoreFunctionFactory.hh>

#include <basic/options/util.hh>

#include <protocols/match/Matcher.hh>
#include <protocols/match/MatcherMover.hh>
#include <protocols/match/MatcherTask.hh>

#include <protocols/match/output/ProcessorFactory.hh>
#include <protocols/match/output/MatchProcessor.hh>


#include <core/pack/rotamers/SingleLigandRotamerLibrary.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>

#include <basic/Tracer.hh>

#include <utility/string_util.hh>

#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>

#include <utility/excn/Exceptions.hh>

#if defined(WIN32) || defined(__CYGWIN__)
#include <ctime>
#endif


void
match_main();

/* moved to protocols/match/MatcherMover.cc as one step toward integrating match app with MatcherMover */
//void
//set_ligpose_rotamer( core::pose::Pose & ligpose );

int main( int argc, char * argv [] )
{
  try {
    using namespace basic::options;
    using namespace basic::options::OptionKeys;

    devel::init( argc, argv );

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

void
match_main()
{
  using namespace core;
  using namespace core::chemical;
  using namespace core::id;
  using namespace core::io;
  using namespace core::pose;
  using namespace protocols::match;
  using namespace protocols::match::downstream;
  using namespace protocols::match::output;
  using namespace protocols::match::upstream;

  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  basic::Tracer T( "apps.public.match.match" );

  //we need this for the output to be correct
  option[OptionKeys::run::preserve_header ].value(true);

  MatcherTaskOP mtask( new MatcherTask );

  utility::vector1< std::string > input_jobs = basic::options::start_files();
  if ( input_jobs.size() == 0 ) utility_exit_with_message("No input scaffold structures specified for matcher. Check for -s <pdbfile> in arguments.");


  pose::Pose scaffold;
  core::import_pose::pose_from_file( scaffold, input_jobs[ 1 ] , core::import_pose::PDB_file);
  scaffold.update_residue_neighbors();

  pose::Pose ligpose;
  core::conformation::ResidueOP ligres = core::conformation::ResidueFactory::create_residue(
    core::chemical::ChemicalManager::get_instance()->residue_type_set( FA_STANDARD )->name_map(
    option[ basic::options::OptionKeys::match::lig_name ] )
  );
  ligpose.append_residue_by_jump( *ligres, 1 );

  if ( option[ OptionKeys::match::ligand_rotamer_index ].user() ) {
    set_ligpose_rotamer( ligpose );
  }


  Size cent, nbr1, nbr2;
  ligres->select_orient_atoms( cent, nbr1, nbr2 );

  T << "Selecting orientation atoms:";
  T << " " << ligres->atom_name( cent );
  T << " " << ligres->atom_name( nbr1 );
  T << " " << ligres->atom_name( nbr2 ) << std::endl;

  mtask->set_upstream_pose( scaffold );

  utility::vector1< core::id::AtomID > oats( 3 );
  oats[ 1 ] = AtomID( nbr2, 1 ); oats[ 2 ] = AtomID( nbr1, 1 ); oats[ 3 ] = AtomID( cent, 1 );

  mtask->set_downstream_pose( ligpose,  oats );
  mtask->initialize_from_command_line();
  //task->consolidate_matches( false );

  time_t matcher_start_time = time(NULL), find_hits_end_time( time( NULL ) );
  long processing_time(0);
  MatcherOP matcher( new Matcher );
  matcher->initialize_from_task( *mtask );
  MatchProcessorOP processor = ProcessorFactory::create_processor( matcher, mtask );

  if ( matcher->find_hits() ) {
    find_hits_end_time = time(NULL);
    time_t process_start_time( time(NULL) );
    matcher->process_matches( *processor );
    processing_time = (long) (time(NULL) - process_start_time);

  } else {
    find_hits_end_time = time(NULL);
  }
  long find_hits_time = (long)(find_hits_end_time - matcher_start_time );
  time_t matcher_end_time = time(NULL);
  T << "Matcher ran for " << (long)(matcher_end_time - matcher_start_time) << " seconds, where finding hits took " << find_hits_time << " seconds and processing the matches took " << processing_time << " seconds."  << std::endl;

}