RandomConformerMover.cc

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// vi: set ts=2 noet:
//
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/// @file   protocols/ligand_docking/RandomConformerMover.cc
///
/// @brief
/// @author Ian W. Davis


#include <protocols/ligand_docking/RandomConformerMover.hh>

#include <core/graph/Graph.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <numeric/random/random.hh>

// option key includes

#include <utility/vector1.hh>

static numeric::random::RandomGenerator my_RG(810106); // <- Magic number, do not change it!!! That's Ian Davis's thing- not sure why

namespace protocols {
namespace ligand_docking {


RandomConformerMover::RandomConformerMover(core::Size resid):
  Mover(),
  resid_(resid)
{
  Mover::type( "RandomConformerMover" );
}


RandomConformerMover::~RandomConformerMover()
{
}


void RandomConformerMover::apply( core::pose::Pose & pose )
{
  using core::conformation::ResidueOP;
  using namespace core::pack::task;
  utility::vector1< ResidueOP > conformers;
  // Dummy parameters that the ligand rotamer library doesn't use:
  core::scoring::ScoreFunction dummy_scorefxn;
  PackerTaskOP dummy_pack_task = TaskFactory::create_packer_task(pose);
  dummy_pack_task->initialize_from_command_line(); // -ex1 -ex2  etc.
  utility::vector1< utility::vector1< core::Real > > dummy_extra_chi_steps;
  core::graph::GraphCOP dummy_graph = new core::graph::Graph();
  // Retrieve conformers
  core::pack::dunbrack::SingleResidueRotamerLibraryCAP reslib = core::pack::dunbrack::RotamerLibrary::get_instance().get_rsd_library( pose.residue_type(resid_) );
  if( reslib.get() == NULL ) return;
  reslib->fill_rotamer_vector(
    pose,
    dummy_scorefxn,
    *dummy_pack_task,
    dummy_graph,
    &pose.residue_type(resid_), //ResidueTypeCOP
    pose.residue(resid_),
    dummy_extra_chi_steps,
    true /* sure, let's pretend it's buried */,
    conformers // output appended here
  );
  // If -include_current push back current conformer
  // This is rarely necessary...
  //if( option[ OptionKeys::packing::use_input_sc ] ) {
  //  ResidueOP curr_copy = new Residue( pose.residue(resid_) );
  //  conformers.push_back(curr_copy);
  //}
  // Choose one at random
  ResidueOP selected_res = conformers[ my_RG.random_range(1, conformers.size()) ];
  // Residue library has already superimpose residues appropriately, so don't orient again
  pose.replace_residue(resid_, *selected_res, false /*orient backbone*/);
}

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


} // namespace ligand_docking
} // namespace protocols