InvrotTreeRCG.cc

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file   protocols/forge/constraints/InvrotTreeRCG.cc
///
/// @brief
/// @author Florian Richter, floric@u.washington.edu, may 2012
/// @modified Tom Linsky, tlinsky@uw.edu, nov 2012

// unit headers
#include <protocols/forge/constraints/InvrotTreeRCG.hh>
#include <protocols/forge/constraints/InvrotTreeCstGeneratorCreator.hh>

// project headers
#include <core/pose/Pose.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <protocols/forge/components/VarLengthBuild.hh>
#include <protocols/toolbox/match_enzdes_util/AlignPoseToInvrotTreeMover.hh>
#include <protocols/toolbox/match_enzdes_util/AllowedSeqposForGeomCst.hh>
#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>
#include <protocols/toolbox/match_enzdes_util/InvrotTree.hh>

// utility headers
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>


static basic::Tracer tr( "protocols.forge.constraints.InvrotTreeRCG" );

namespace protocols{
namespace forge{
namespace constraints{

protocols::moves::MoverOP
InvrotTreeCstGeneratorCreator::create_mover() const
{
  return new InvrotTreeRCG();
}

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

std::string
InvrotTreeCstGeneratorCreator::mover_name()
{
  return "InvrotTreeCstGenerator";
}

InvrotTreeRCG::InvrotTreeRCG()
  : RemodelConstraintGenerator(),
    add_ligand_to_pose_( false ),
    invrot_tree_( NULL ),
    enzcst_io_( NULL ),
    geomcst_seqpos_( NULL ),
    setup_align_pose_( NULL )
{}

InvrotTreeRCG::InvrotTreeRCG( InvrotTreeRCG const & rval )
  : RemodelConstraintGenerator( rval ),
    add_ligand_to_pose_( rval.add_ligand_to_pose_ ),
    invrot_tree_( rval.invrot_tree_ ),
    enzcst_io_( rval.enzcst_io_ ),
    geomcst_seqpos_( rval.geomcst_seqpos_ ),
    setup_align_pose_( rval.setup_align_pose_ )
{}

InvrotTreeRCG::InvrotTreeRCG(
                             toolbox::match_enzdes_util::InvrotTreeOP invrot_tree,
                             toolbox::match_enzdes_util::AllowedSeqposForGeomCstOP geomcst_seqpos
                             )
  : invrot_tree_(invrot_tree),
    geomcst_seqpos_(geomcst_seqpos)
{}

InvrotTreeRCG::~InvrotTreeRCG(){}

void
InvrotTreeRCG::parse_my_tag( TagPtr const tag,
                             protocols::moves::DataMap & data,
                             protocols::filters::Filters_map const & filters,
                             protocols::moves::Movers_map const & movers,
                             core::pose::Pose const & pose )
{
  RemodelConstraintGenerator::parse_my_tag( tag, data, filters, movers, pose );
  //in case we'ref folding up around a ligand
  std::string cstfilename = tag->getOption<std::string>( "cstfile", "" );
  if ( cstfilename == "" ) {
    throw utility::excn::EXCN_RosettaScriptsOption( "XML tag for invrot tree does not contain a cstfile option... this will probably fail when the InvrotTreeCstGenerator mover runs." );
  }
  set_cstfile( cstfilename );

  // should we add in the ligand, or is it already there
  set_add_ligand_to_pose( tag->getOption<bool>( "add_ligand_to_pose", add_ligand_to_pose_ ) );
}

std::string
InvrotTreeRCG::get_name() const
{
  return InvrotTreeCstGeneratorCreator::mover_name();
}

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

protocols::moves::MoverOP
InvrotTreeRCG::clone() const
{
  return new InvrotTreeRCG( *this );
}

void
InvrotTreeRCG::apply( core::pose::Pose & pose )
{
  //tr << "IN apply, id=" << id() << std::endl;
  init( pose );
  setup_align_pose_->apply( pose );

  runtime_assert( invrot_tree_ );
  runtime_assert( geomcst_seqpos_ );
  runtime_assert( setup_align_pose_ );

  //tr << "now id=" << id() << std::endl;
  // generate and add constraints
  this->add_remodel_constraints_to_pose( pose );
}

void
InvrotTreeRCG::generate_remodel_constraints(
    core::pose::Pose const & pose )
{
  tr << "in invrottreercg" << std::endl;

  //for now
  runtime_assert( invrot_tree_->num_target_states() == 1 );
  Size target_state = 1;

  tr << "generating inverse_rotamer_constraints" << std::endl;
  invrot_tree_->generate_inverse_rotamer_constraints( pose, geomcst_seqpos_ );
  tr << "done generating inverse_rotamer_constraints" << std::endl;
  core::scoring::constraints::ConstraintCOP cst_to_add( invrot_tree_->get_constraint_for_target_state( target_state ) );

  if( !cst_to_add ) utility_exit_with_message("InvrotTree failed to generate anything but NULL pointer csts. Something is wrong somewhere. Check your starting structure for whether it already has every interaction in the cstfile." );
  this->add_constraint( cst_to_add  );
}

/// @brief tells the mover whether it should add the ligand to the pose
void
InvrotTreeRCG::set_add_ligand_to_pose( bool const add_lig )
{
  add_ligand_to_pose_ = add_lig;
}

/// @brief sets up the invrot_tree_ and enzcst_io_ from an enzdes constraint filename.
void
InvrotTreeRCG::set_cstfile( std::string const & cstfilename )
{
  toolbox::match_enzdes_util::EnzConstraintIOOP enzcst_io( new toolbox::match_enzdes_util::EnzConstraintIO( core::chemical::ChemicalManager::get_instance()->residue_type_set( core::chemical::FA_STANDARD ) ) );
  enzcst_io->read_enzyme_cstfile( cstfilename );
  invrot_tree_ = new protocols::toolbox::match_enzdes_util::TheozymeInvrotTree( enzcst_io );
  invrot_tree_->generate_targets_and_inverse_rotamers();
  enzcst_io_ = enzcst_io;
} //set_cstfile()

/// @brief initializes the rcg object
void
InvrotTreeRCG::init( core::pose::Pose const & pose )
{
  // this function is invoked from BluePrintBDR after the VLB object is attached, but before we enter centroid mode
  // it is also invoked when the mover is applied, if it is called from somewhere else
  geomcst_seqpos_ = new protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst();
  //stupid: apparently we have to make a copy of the pose on the heap for
  //the initialization of allowed_seqpos to work
  core::pose::PoseOP posecopy( new core::pose::Pose( pose ) );
  geomcst_seqpos_->initialize_from_command_line( posecopy );

  // setup the align_pose movers
  // this one is called once before adding constraints
  setup_align_pose_ = new toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover( invrot_tree_, geomcst_seqpos_ );
  setup_align_pose_->set_add_target_to_pose( add_ligand_to_pose_ );
  setup_align_pose_->set_geomcst_for_superposition_from_enz_io( enzcst_io_ );

  // if a VLB is going on, this one can be called as a user-provided mover
  run_align_pose_ = new toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover( invrot_tree_, geomcst_seqpos_ );
  run_align_pose_->set_geomcst_for_superposition_from_enz_io( enzcst_io_ );
  if ( vlb() ) {
    vlb()->loop_mover_fold_tree_constant( true ); //we're taking care of the fold tree through the above align movers
    vlb()->add_setup_mover( setup_align_pose_ );
    vlb()->add_user_provided_mover( run_align_pose_ );
  }
}

} //namespace remodel
} //namespace forge
} //namespace protocols