not_universal_main.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/jobdist/not_universal_main.cc
/// @brief  Simple main method for applying a Mover to a set of
/// input Poses.
/// @author James Thompson

#include <core/types.hh>

#include <core/io/pdb/pose_io.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>

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

#include <core/chemical/ChemicalManager.hh>
#include <basic/Tracer.hh>

#include <protocols/moves/Mover.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/viewer/viewers.hh>

#include <string>

// option key includes
#include <basic/options/option.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

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



namespace protocols {
namespace jobdist {

static basic::Tracer tr("protocols.jobdist.not_universal_main");

bool pose_matches_user_tag(
  core::pose::Pose & pose,
  utility::vector1< std::string > const & user_tags
) {
  using std::string;
  using utility::vector1;

  bool valid_tag( false );
  std::string this_id( "" );
  get_comment( pose, "user_tag", this_id );
  if ( this_id == "" ) get_comment( pose, "user_ta", this_id );
  if ( this_id == "" ) {
    tr.Error << "can't find user_tag in pose!" << std::endl;
  }

  typedef vector1< string >::const_iterator iter;
  for ( iter it = user_tags.begin(), end = user_tags.end();
        it != end && !valid_tag && this_id != ""; ++it
  ) {
    if ( this_id.find( *it ) != std::string::npos ) {
      break;
      valid_tag = true;
      tr.Debug << "processing Pose with user_tag " << this_id << std::endl;
    }
  } // for user_tags

  if ( !valid_tag ) {
    tr.Warning << "skipping Pose with user_tag " << this_id << std::endl;
  }

  return valid_tag;
}

/////////////////////////////////////////////////////////////////////////////
/// @brief main function that applies a mover to a set of input poses and
/// only does silent-file output.  Similar in idea to universal_main, but
/// without all of the code duplication for silent-files/PDB files.
int not_universal_main(
  protocols::moves::Mover & mover
) {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::chemical;
  using namespace core::io::silent;
  using namespace core::import_pose::pose_stream;

  using core::Size;
  using core::Real;
  using std::string;
  using utility::vector1;

  core::chemical::ResidueTypeSetCAP rsd_set;
  rsd_set = core::chemical::ChemicalManager::get_instance()->residue_type_set(
    option[ in::file::residue_type_set ]()
  );

  core::pose::Pose native_pose, current_pose;
  if ( option[ in::file::native ].user() ) {
    core::import_pose::pose_from_pdb(
      native_pose, *rsd_set, option[ in::file::native ]()
    );
  }

  core::scoring::ScoreFunctionOP scorefxn = core::scoring::getScoreFunction();
  if ( option[ constraints::cst_weight ].user() ) {
    Real const weight( option[ constraints::cst_weight ]() );
    scorefxn->set_weight( core::scoring::angle_constraint,      weight );
    scorefxn->set_weight( core::scoring::dihedral_constraint,   weight );
    scorefxn->set_weight( core::scoring::atom_pair_constraint,  weight );
    scorefxn->set_weight( core::scoring::dunbrack_constraint,   weight );
    scorefxn->set_weight( core::scoring::coordinate_constraint, weight );
  }
  scorefxn->show( tr.Debug );
  tr.flush_all_channels();

  vector1< string > user_tags;
  if ( option[ in::file::user_tags ].user() ) {
    user_tags = option[ in::file::user_tags ]();
  }

  MetaPoseInputStream input = streams_from_cmd_line();

  Size const n_repeats( option[ run::repeat ]() );

  SilentFileData sfd_out;
  while( input.has_another_pose() ) {
    input.fill_pose( current_pose, *rsd_set );

    if ( option[ in::file::user_tags ].user() ) {
      if ( ! pose_matches_user_tag( current_pose, user_tags ) ) {
        continue;
      }
    }

    for ( Size ii = 1; ii <= n_repeats; ++ii ) {
      // only keep input scores if specified by the user.
      if ( !option[ in::file::keep_input_scores ]() ) {
        clearPoseExtraScores( current_pose );
      }

      protocols::viewer::add_conformation_viewer(
        current_pose.conformation(), "start_pose"
      );

      mover.apply( current_pose );

      // rescore the Pose if necessary, on by default.
      if ( option[ in::file::rescore ]() ) {
        (*scorefxn)(current_pose);
      }

      // output
      if ( !option[ out::nooutput ]() ) {
        core::io::silent::SilentStructOP ss
          = SilentStructFactory::get_instance()->get_silent_struct_out();
        ss->fill_struct( current_pose );

        // add model quality information if a native was given.
        if ( option[ in::file::native ].user() ) {
          core::Real CA_rmsd
            = core::scoring::CA_rmsd( native_pose, current_pose );
          core::Real CA_maxsub
            = core::scoring::CA_maxsub( native_pose, current_pose );
          core::Real CA_gdtmm
            = core::scoring::CA_gdtmm( native_pose, current_pose );
          ss->add_energy( "rmsd", CA_rmsd );
          ss->add_energy( "maxsub", CA_maxsub );
          ss->add_energy( "gdtmm", CA_gdtmm );
        }

        sfd_out.write_silent_struct( *ss, option[ out::file::silent ]() );
      } // if ( !option[ out::nooutput ]() )
    }
    tr.flush();
  } // while( input.has_another_pose() )
  tr.flush();

  return 0;
} // not_universal_main

} // jobdist
} // protocols