qsarMover.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/qsar/qsarMover.cc
/// @author Sam DeLuca

#include <protocols/qsar/qsarMover.hh>
#include <protocols/qsar/qsarMoverCreator.hh>
#include <protocols/qsar/qsarMap.hh>
#include <protocols/qsar/scoring_grid/SingleGrid.hh>
#include <protocols/qsar/scoring_grid/GridManager.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>

#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>

#include <basic/Tracer.hh>

#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <utility/vector0.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>

namespace protocols {
namespace qsar {
static basic::Tracer TR("protocols.ligand_docking.qsar.qsarMover");


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

protocols::moves::MoverOP
qsarCreator::create_mover() const {
  return new qsarMover;
}

std::string
qsarCreator::mover_name()
{
  return "qsar";
}

qsarMover::qsarMover():
    qsar_map_(0),
    chain_(),
    initialize_(false)
{}

//@brief parse XML (specifically in the context of the parser/scripting scheme)
void
qsarMover::parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & /*datamap*/,
    protocols::filters::Filters_map const & /*filters*/,
    protocols::moves::Movers_map const & /*movers*/,
    core::pose::Pose const & /*pose*/
)
{
  if ( tag->getName() != "qsarMover" ) throw utility::excn::EXCN_RosettaScriptsOption("This should be impossible");

  if ( ! tag->hasOption("chain") ) throw utility::excn::EXCN_RosettaScriptsOption("'qsar' mover requires chain tag");
  chain_= tag->getOption<std::string>("chain");

  if ( ! tag->hasOption("grids") ) throw utility::excn::EXCN_RosettaScriptsOption("'qsarMover' requires grids tag");

  std::string grids_string= tag->getOption<std::string>("grids");
  utility::vector1<std::string> grid_strings(utility::string_split(grids_string, ','));
  grids_to_use_ = grid_strings;
}

void qsarMover::apply(core::pose::Pose & pose)
{
  scoring_grid::GridManager* grid_manager(scoring_grid::GridManager::get_instance());

  core::Size const chain_id(core::pose::get_chain_id_from_chain(chain_,pose));
  core::Size const begin(pose.conformation().chain_begin(chain_id));
  /// TODO The next line assumes the chain is one residue. fix this.
  core::conformation::ResidueOP residue = new core::conformation::Residue(pose.residue(begin));

  if(grids_to_use_.size()==0)
  {
    TR << "WARNING: no grids specified, QSAR scoring function will be empty!!" <<std::endl;
    return;
  }else if(!initialize_)
  {
    utility::vector1<std::string>::iterator grid_iterator(grids_to_use_.begin());
    for(; grid_iterator != grids_to_use_.end();++grid_iterator)
    {
      //grid_manager->make_new_grid(*grid_iterator);
      grid_manager->get_grid(*grid_iterator);
      TR.Debug << "getting grid: " << *grid_iterator << std::endl;
    }
    if(qsar_map_ == 0)
    {

      qsar_map_ = new qsarMap("default",residue);

      qsar_map_->fill_with_value(1,grids_to_use_);
    }

    grid_manager->set_qsar_map(qsar_map_);

  }

  if(!initialize_ || pose.conformation().structure_moved())
  {
    core::Size const jump_id(core::pose::get_jump_id_from_chain_id(chain_id,pose));
    core::Vector const center(geometry::downstream_centroid_by_jump(pose,jump_id));

    if(!initialize_)
    {
      TR.Debug <<"initializing grids" << std::endl;
      grid_manager->initialize_all_grids(center);
      TR.Debug <<"grids initialized" <<std::endl;
    }
    grid_manager->update_grids(pose,center);
    TR.Debug <<"grids updated, scoring.."<<std::endl;
    core::Real score(grid_manager->total_score(*residue));
    TR.Debug << "total score is " << score <<std::endl;
    std::map<std::string,core::Real> scores(grid_manager->get_cached_scores());


    jd2::JobOP job(jd2::JobDistributor::get_instance()->current_job());
    grid_manager->append_cached_scores(job);
    //grid_manager->write_grids("test_");
  }
  if(!initialize_)
    initialize_=true;
}

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

}
}