ligand_dock_impl.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/ligand_docking/ligand_dock_impl.cc
///
/// @brief
/// @author Rocco Moretti (rmoretti@u.washington.edu); Ian Davis (ian.w.davis@gmail.com)

// Unit Headers

#include <protocols/ligand_docking/LigandDockProtocol.hh>
#include <protocols/moves/Mover.hh>

// Package Headers

#include <protocols/jd2/JobDistributor.hh>
// AUTO-REMOVED #include <protocols/jd2/util.hh>

#include <protocols/jd2/AtomTreeDiffJobOutputter.hh>

// Project Headers

#include <core/types.hh>
#include <core/import_pose/import_pose.hh>

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

#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh> //for addding constraints if demanded by user
#include <core/chemical/ChemicalManager.hh>
// AUTO-REMOVED #include <core/pose/datacache/CacheableDataType.hh>
// AUTO-REMOVED #include <basic/datacache/BasicDataCache.hh>
// AUTO-REMOVED #include <basic/datacache/CacheableString.hh>

// Utility Headers

#include <basic/options/option.hh>
#include <basic/Tracer.hh>

// option key includes

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

#include <protocols/jd2/Job.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace ligand_docking {

basic::Tracer TR("protocols.ligand_docking.main");

class LigandDockMain : public protocols::ligand_docking::LigandDockProtocol {
public:
  LigandDockMain():
    LigandDockProtocol()
  {
    if( basic::options::option[ basic::options::OptionKeys::in::file::native ].user() ) {
      native_ = new core::pose::Pose();
      core::import_pose::pose_from_pdb( *native_, basic::options::option[ basic::options::OptionKeys::in::file::native ]().name() );
    }

    if( basic::options::option[ basic::options::OptionKeys::enzdes::cstfile].user() ){
      //we need the residue type set, assuming FA standard is used
      core::chemical::ResidueTypeSetCAP restype_set = core::chemical::ChemicalManager::get_instance()->residue_type_set( core::chemical::FA_STANDARD );
      basic::options::option[ basic::options::OptionKeys::run::preserve_header ].value(true);
      constraints_ = new protocols::toolbox::match_enzdes_util::EnzConstraintIO( restype_set );
      constraints_->read_enzyme_cstfile( basic::options::option[ basic::options::OptionKeys::enzdes::cstfile ] );

      core::scoring::ScoreFunctionOP scorefunc = this->get_scorefxn();
      if (scorefunc->has_zero_weight( core::scoring::coordinate_constraint ) ) scorefunc->set_weight(core::scoring::coordinate_constraint, 1.0 ) ;
      if (scorefunc->has_zero_weight( core::scoring::atom_pair_constraint ) ) scorefunc->set_weight(core::scoring::atom_pair_constraint, 1.0 ) ;
      if (scorefunc->has_zero_weight( core::scoring::angle_constraint ) ) scorefunc->set_weight(core::scoring::angle_constraint, 1.0 ) ;
      if (scorefunc->has_zero_weight( core::scoring::dihedral_constraint ) ) scorefunc->set_weight(core::scoring::dihedral_constraint, 1.0 ) ;
    }

  }

  virtual
  ~LigandDockMain(){};

  virtual
  void
  apply( core::pose::Pose & pose ) {

    if( constraints_ ){
      constraints_->add_constraints_to_pose( pose, this->get_scorefxn(), false );
    }

    LigandDockProtocol::apply( pose );

    // Score new structure and add to silent file
    std::map< std::string, core::Real > scores;
    core::import_pose::atom_tree_diffs::map_of_weighted_scores(pose, *(this->get_scorefxn()), scores);
    if( native_ ) {
      this->append_ligand_docking_scores(*native_, pose, this->get_scorefxn(), scores, constraints_);
    } else { // input serves as native
      core::pose::PoseCOP input_pose(protocols::jd2::JobDistributor::get_instance()->current_job()->get_pose());
      this->append_ligand_docking_scores(*input_pose, pose, this->get_scorefxn(), scores, constraints_);
    }

    // Attach relevant scores to current job (Assumes use of JD2)
    {
    protocols::jd2::JobOP curr_job( protocols::jd2::JobDistributor::get_instance()->current_job() );
    std::map< std::string, core::Real >::const_iterator curr( scores.begin() );
    std::map< std::string, core::Real >::const_iterator end( scores.end() );
    for (; curr != end; ++curr) {
      curr_job->add_string_real_pair(curr->first, curr->second);
    }
    }

    /* TODO: From old jd1 code:
    // Want to recycle the reference poses from the input silent file, or else every entry becomes a new reference pose!
    if( use_silent_in ) {
      //std::cout << "Ref addr " << (atdiff->ref_pose_for( curr_job->input_tag() ))() << std::endl;
      jobdist.dump_pose( curr_job->output_tag(curr_nstruct), scores, *(atdiff->ref_pose_for( curr_job->input_tag() )), *the_pose );
    }
    else jobdist.dump_pose( curr_job->output_tag(curr_nstruct), scores, *input_pose, *the_pose );
    */


  }

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

  virtual
  protocols::moves::MoverOP
  fresh_instance() const {
    return new LigandDockMain;
  }

  virtual
  bool
  reinitialize_for_each_job() const { return false; }

  virtual
  bool
  reinitialize_for_new_input() const { return false; }

private:

  core::pose::PoseOP native_;
  protocols::toolbox::match_enzdes_util::EnzConstraintIOOP constraints_;
};

typedef utility::pointer::owning_ptr< LigandDockMain > LigandDockMainOP;

} //namespace ligand_docking
} //namespace protocols

//////////////////////////////////////////////////////////////////////////////
/// @details Assumes option system has already been initialized!
int
ligand_dock_main()
{
  protocols::ligand_docking::LigandDockMainOP ligand_dock( new protocols::ligand_docking::LigandDockMain );

  // Change precision of AtomTreeDiffJobOutputter, for backward compatability reasons
  // makes silent file much smaller, ~3x vs. default 6,4,2
  // but has too much atom positioning error (~0.1 Ang) to be reliable for rescoring
  if ( ! basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_bb].user() &&
      ! basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_sc].user() &&
      ! basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_bl].user()) {
    protocols::ligand_docking::TR << "Changing atom_tree_diff output precision to 6,3,1." << std::endl;
    basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_bb].value(6);
    basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_sc].value(3);
    basic::options::option[ basic::options::OptionKeys::out::file::atom_tree_diff_bl].value(1);
  }

  protocols::jd2::JobOutputterOP  job_outputter(protocols::jd2::JobDistributor::get_instance()->job_outputter());
  protocols::jd2::AtomTreeDiffJobOutputterOP atd_outputter( dynamic_cast< protocols::jd2::AtomTreeDiffJobOutputter * >( job_outputter() ) );
  if ( atd_outputter ) {
    atd_outputter->use_input_for_ref(true); // match original ligand_dock application
  }

  protocols::jd2::JobDistributor::get_instance()->go(ligand_dock);

  return 0;
}