SetupForSymmetryMover.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file MinMover.cc
/// @brief
/// @author ashworth

// Unit headers
#include <protocols/simple_moves/symmetry/SetupForSymmetryMoverCreator.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>
#include <protocols/simple_moves/symmetry/SymDockingInitialPerturbation.hh>
#include <core/conformation/symmetry/SymmData.hh>

// AUTO-REMOVED #include <protocols/moves/DataMap.hh>
// AUTO-REMOVED #include <protocols/rosetta_scripts/util.hh>
#include <utility/tag/Tag.hh>
#include <utility/excn/Exceptions.hh>

// Package headers
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/symmetry/util.hh>

#include <basic/resource_manager/ResourceManager.hh>
#include <basic/resource_manager/util.hh>

// AUTO-REMOVED #include <core/conformation/symmetry/util.hh>

#include <core/scoring/symmetry/SymmetricScoreFunction.hh>


// ObjexxFCL Headers

// C++ Headers
#include <string>

// Utility Headers
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>

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


namespace protocols {
namespace simple_moves{
namespace symmetry{

static basic::Tracer TR("protocols.simple_moves.symmetry.SetupForSymmetryMover");

// creators
std::string
SetupForSymmetryMoverCreator::keyname() const {
  return SetupForSymmetryMoverCreator::mover_name();
}

protocols::moves::MoverOP
SetupForSymmetryMoverCreator::create_mover() const {
  return new SetupForSymmetryMover;
}

std::string
SetupForSymmetryMoverCreator::mover_name() {
  return "SetupForSymmetry";
}

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

protocols::moves::MoverOP
ExtractAsymmetricUnitMoverCreator::create_mover() const {
  return new ExtractAsymmetricUnitMover;
}

std::string
ExtractAsymmetricUnitMoverCreator::mover_name() {
  return "ExtractAsymmetricUnit";
}

////////////////////

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

protocols::moves::MoverOP
ExtractAsymmetricPoseMoverCreator::create_mover() const {
  return new ExtractAsymmetricPoseMover;
}

std::string
ExtractAsymmetricPoseMoverCreator::mover_name() {
  return "ExtractAsymmetricPose";
}

////////////////////


SetupForSymmetryMover::SetupForSymmetryMover() :
  protocols::moves::Mover("SetupForSymmetryMover"),
  slide_(false),
  symmdef_()
{
}

SetupForSymmetryMover::SetupForSymmetryMover( std::string const & symmdef_file) :
  protocols::moves::Mover("SetupForSymmetryMover"),
  slide_(false),
  symmdef_()
{
  symmdef_ = new core::conformation::symmetry::SymmData();
  symmdef_->read_symmetry_data_from_file(symmdef_file);
}

SetupForSymmetryMover::~SetupForSymmetryMover(){}

void
SetupForSymmetryMover::apply( core::pose::Pose & pose )
{
  using namespace basic::options;

  // If we are alredy symmetric do nothing
  if ( core::pose::symmetry::is_symmetric( pose ) ) return;

  if(!symmdef_()){
    if(option[ OptionKeys::symmetry::symmetry_definition].user()){
      symmdef_ = new core::conformation::symmetry::SymmData();
      symmdef_->read_symmetry_data_from_file(
        option[OptionKeys::symmetry::symmetry_definition]);

    } else {
      throw utility::excn::EXCN_BadInput(
        "The -symmetry:symmetry_definition command line option "
        "was not specified.");
    }
  }


  core::pose::symmetry::make_symmetric_pose( pose, *symmdef_ );
  assert( core::pose::symmetry::is_symmetric( pose ) );

  //fpd  explicitly update disulfide lr energy container
  if ( pose.is_fullatom() ) {
    core::scoring::symmetry::SymmetricScoreFunction disulf_score;
    disulf_score.set_weight( core::scoring::dslf_ss_dst, 1.0 );
    disulf_score.setup_for_scoring( pose );
  }

  // (Optionally) set rigid-body dofs from file
  //    SymDockingInitialPerturbation's behavior is controlled by flags and does nothing by default
  protocols::moves::MoverOP symdock =
    new protocols::simple_moves::symmetry::SymDockingInitialPerturbation(slide_);
  symdock->apply( pose );
}

void SetupForSymmetryMover::parse_my_tag(
      utility::tag::TagPtr const tag,
      moves::DataMap & /*data*/,
      filters::Filters_map const & /*filters*/,
      moves::Movers_map const & /*movers*/,
      core::pose::Pose const & /*pose*/ ) {

  using namespace basic::options;
  using namespace basic::resource_manager;

  if(tag->hasOption("definition") && tag->hasOption("resource_description")){
    throw utility::excn::EXCN_BadInput(
      "SetupForSymmetry takes either a 'definition' OR "
      "a 'resource_description' tag but not both.");
  }

  if(tag->hasOption("definition")){
    symmdef_ = new core::conformation::symmetry::SymmData();
    symmdef_->read_symmetry_data_from_file(
      tag->getOption<std::string>("definition"));
    option[OptionKeys::symmetry::symmetry_definition].value( "dummy" );

  } else if(tag->hasOption("resource_description")){
    symmdef_ = get_resource< core::conformation::symmetry::SymmData >(
      tag->getOption<std::string>("resource_description"));
    option[OptionKeys::symmetry::symmetry_definition].value( "dummy" );

  } else if(option[ OptionKeys::symmetry::symmetry_definition].user()){
    symmdef_ = new core::conformation::symmetry::SymmData();
    symmdef_->read_symmetry_data_from_file(
      option[OptionKeys::symmetry::symmetry_definition]);

  } else {
    throw utility::excn::EXCN_BadInput(
      "To use SetupForSymmetryMover with rosetta scripts please supply either a 'definition' tag, a 'resource_decription' tag or specify -symmetry:symmetry_definition the command line.");
  }
}

std::string
SetupForSymmetryMover::get_name() const {
  return SetupForSymmetryMoverCreator::mover_name();
}

////////////////////

ExtractAsymmetricUnitMover::ExtractAsymmetricUnitMover()
  : protocols::moves::Mover("ExtractAsymmetricUnitMover") { }

ExtractAsymmetricUnitMover::~ExtractAsymmetricUnitMover(){}

void
ExtractAsymmetricUnitMover::apply( core::pose::Pose & pose )
{
  // If we are not symmetric do nothing
  if ( !core::pose::symmetry::is_symmetric( pose ) ) return;

  core::pose::Pose pose_asu;
  core::pose::symmetry::extract_asymmetric_unit(pose, pose_asu);
  pose = pose_asu;
}

void ExtractAsymmetricUnitMover::parse_my_tag(
  utility::tag::TagPtr const /*tag*/,
  moves::DataMap & /*data*/,
  filters::Filters_map const & /*filters*/,
  moves::Movers_map const & /*movers*/,
  core::pose::Pose const & /*pose*/ ) { }

std::string
ExtractAsymmetricUnitMover::get_name() const {
  return ExtractAsymmetricUnitMoverCreator::mover_name();
}

/////////////////

ExtractAsymmetricPoseMover::ExtractAsymmetricPoseMover()
  : protocols::moves::Mover("ExtractAsymmetricPoseMover") { }

ExtractAsymmetricPoseMover::~ExtractAsymmetricPoseMover(){}


void
ExtractAsymmetricPoseMover::apply( core::pose::Pose & pose )
{
  // If we are not symmetric do nothing
  if ( !core::pose::symmetry::is_symmetric( pose ) ) return;

  core::pose::symmetry::make_asymmetric_pose( pose );
}

void ExtractAsymmetricPoseMover::parse_my_tag(
  utility::tag::TagPtr const /*tag*/,
  moves::DataMap & /*data*/,
  filters::Filters_map const & /*filters*/,
  moves::Movers_map const & /*movers*/,
  core::pose::Pose const & /*pose*/ ) { }

std::string
ExtractAsymmetricPoseMover::get_name() const {
  return ExtractAsymmetricPoseMoverCreator::mover_name();
}


} //symmetry
} // simple_moves
} // protocols