MatcherMover.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
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/// @file   protocols/match/MatcherMover.cc
/// @brief  Implementation of mover wrapper for matcher
/// @author Florian Richter (floric@u.washington.edu), june 2010


// Unit headers
#include <protocols/match/MatcherMover.hh>
#include <protocols/match/MatcherMoverCreator.hh>

//package headers
#include <protocols/match/Matcher.hh>
#include <protocols/match/MatcherTask.hh>
#include <protocols/match/output/ProcessorFactory.hh>
#include <protocols/match/output/MatchProcessor.hh>
#include <protocols/match/output/PDBWriter.hh>

//project headers
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.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 <basic/Tracer.hh>
#include <utility/tag/Tag.hh>

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


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


namespace protocols {
namespace match {

static basic::Tracer tr( "protocols.match.MatcherMover" );


std::string
MatcherMoverCreator::keyname() const
{
  return MatcherMoverCreator::mover_name();
}

protocols::moves::MoverOP
MatcherMoverCreator::create_mover() const {
  return new MatcherMover;
}

std::string
MatcherMoverCreator::mover_name()
{
  return "MatcherMover";
}

MatcherMover::MatcherMover( bool incorporate_matches_into_pose ):
  Mover( "MatcherMover" ),
  incorporate_matches_into_pose_( incorporate_matches_into_pose ),
  ligres_(NULL)
{
  //we need this for the output to be correct
  basic::options::option[basic::options::OptionKeys::run::preserve_header ].value(true);
}

MatcherMover::~MatcherMover(){}

MatcherMover::MatcherMover( MatcherMover const & rval ) :
  //utility::pointer::ReferenceCount(),
  Mover( rval ),
  incorporate_matches_into_pose_( rval.incorporate_matches_into_pose_ ),
  ligres_( rval.ligres_ ),
  match_positions_( rval.match_positions_ )
{}

/// @brief clone this object
MatcherMover::MoverOP MatcherMover::clone() const
{
  return new MatcherMover( *this );
}

/// @brief create this type of object
MatcherMover::MoverOP MatcherMover::fresh_instance() const
{
  return new MatcherMover();
}

///
void
MatcherMover::apply( core::pose::Pose & pose )
{

  protocols::match::MatcherTaskOP mtask = new protocols::match::MatcherTask;

  core::pose::Pose ligpose;
  core::pose::Pose save_pose = pose;
  if( !ligres_ ) ligres_ = core::conformation::ResidueFactory::create_residue(
    core::chemical::ChemicalManager::get_instance()->residue_type_set( core::chemical::FA_STANDARD )->name_map(
      basic::options::option[ basic::options::OptionKeys::match::lig_name ] ) );

  if( !ligres_->type().is_ligand() ) std::cerr << "WARNING: downstream residue " << ligres_->type().name3() << " set in the matcher mover does not seem to be a ligand residue, matcher will likely not behave properly." << std::endl;

  ligpose.append_residue_by_jump( *ligres_, 1 );

  //we might have to remove the downstream pose from the input
  if( incorporate_matches_into_pose_ ){
    for( core::Size i = pose.total_residue(); i >  0; --i ){
      if( pose.residue_type( i ).name3() == ligres_->type().name3() ) pose.conformation().delete_residue_slow( i );
    }
  }

  //if ( option[ OptionKeys::match::ligand_rotamer_index ].user() ) {
  //  set_ligpose_rotamer( ligpose );
  //}
  Size cent, nbr1, nbr2;
  ligres_->select_orient_atoms( cent, nbr1, nbr2 );

  tr << "Selecting orientation atoms:";
  tr << " " << ligres_->atom_name( cent );
  tr << " " << ligres_->atom_name( nbr1 );
  tr << " " << ligres_->atom_name( nbr2 ) << std::endl;
  //pose.dump_pdb("pose_going_into_matcher.pdb");
  mtask->set_upstream_pose( pose );

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

  mtask->set_downstream_pose( ligpose,  oats );
  if( match_positions_.size() != 0 ){
    mtask->set_ignore_cmdline_for_build_points( true );
    mtask->set_original_scaffold_build_points( match_positions_ );
  }

  mtask->initialize_from_command_line();

  if( incorporate_matches_into_pose_ ) mtask->output_writer_name("PoseMatchOutputWriter");

  time_t matcher_start_time = time(NULL);
  protocols::match::MatcherOP matcher = new protocols::match::Matcher;
  matcher->initialize_from_task( *mtask );


  protocols::match::output::MatchProcessorOP processor = protocols::match::output::ProcessorFactory::create_processor( matcher, mtask );

  if( matcher->find_hits() ){
    matcher->process_matches( *processor );
  }

  time_t matcher_end_time = time(NULL);
  std::string success_str( processor->match_processing_successful() ? "successful." : "not sucessful." );
  tr << "Matcher ran for " << (long)(matcher_end_time - matcher_start_time) << " seconds and was " << success_str << std::endl;

  if( processor->match_processing_successful() ) this->set_last_move_status( protocols::moves::MS_SUCCESS );
  else{
    this->set_last_move_status( protocols::moves::FAIL_DO_NOT_RETRY );
    pose = save_pose;
    return;
  }

  if( incorporate_matches_into_pose_ ){
    protocols::match::output::PoseMatchOutputWriterOP outputter( static_cast< protocols::match::output::PoseMatchOutputWriter * >( processor->output_writer().get() ) );
    outputter->insert_match_into_pose( pose );
    // should make another mover to set these constraints  flo and nobu
    //protocols::enzdes::AddOrRemoveMatchCsts addcsts = protocols::enzdes::AddOrRemoveMatchCsts();
    //addcsts.set_cst_action(protocols::enzdes::ADD_NEW);
    //addcsts.apply(pose);
  }
  //pose.dump_pdb("pose_coming_from_matcher.pdb");

} //MatcherMover::apply function

std::string
MatcherMover::get_name() const
{
  return "MatcherMover";
}

void
MatcherMover::set_ligres(
  core::conformation::ResidueCOP ligres )
{
  ligres_ = new core::conformation::Residue(*ligres);
}

void
MatcherMover::set_match_positions(
  utility::vector1< core::Size > const & match_positions )
{
  match_positions_ = match_positions;
}

void
MatcherMover::parse_my_tag(
  TagPtr const tag,
  DataMap &,
  Filters_map const &,
  Movers_map const &,
  Pose const & )
{
  incorporate_matches_into_pose_ = tag->getOption<bool>( "incorporate_matches_into_pose", 1 );
}

}
}