ligand_transform_with_pcs.cc File Reference

find a ligand position that minimizes experimental PCS data through a grid search and that can be used as starting position for ligand docking More...

#include <protocols/nmr/pcs/PCSLigandTransformMover.hh>
#include <core/scoring/nmr/pcs/PCSData.hh>
#include <devel/init.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/chains_util.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.fwd.hh>
#include <core/pack/rotamers/SingleLigandRotamerLibrary.hh>
#include <protocols/ligand_docking/LigandArea.hh>
#include <protocols/ligand_docking/InterfaceBuilder.hh>
#include <protocols/ligand_docking/MoveMapBuilder.hh>
#include <protocols/ligand_docking/HighResDocker.hh>
#include <protocols/ligand_docking/FinalMinimizer.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/string_util.hh>
#include <utility/graph/Graph.fwd.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/nmr.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <fstream>
#include <string>

Functions
core::Vector	ligand_centroid (core::conformation::Residue const &residue)
	Calculate the unweighted center-of-mass of this residue. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.nmr.ligand_transform_with_pcs")

Detailed Description

find a ligand position that minimizes experimental PCS data through a grid search and that can be used as starting position for ligand docking

last Modified: 06/02/17

Author

Georg Kuenze (georg.nosp@m..kue.nosp@m.nze@v.nosp@m.ande.nosp@m.rbilt.nosp@m..edu)

Function Documentation

ligand_centroid()

core::Vector ligand_centroid

(

core::conformation::Residue const &

residue

)

Calculate the unweighted center-of-mass of this residue.

References numeric::center_of_mass(), create_a3b_hbs::i, and residue.

Referenced by main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, basic::options::OptionKeys::in::file::centroid, test.T009_Exceptions::e, basic::options::OptionKeys::in::file::extra_res_fa, ObjexxFCL::format::F(), pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::nmr::pcs::input_file, ligand_centroid(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, NEW_OPT, local::nstruct, basic::options::OptionKeys::out::nstruct, OPT, basic::options::option, erraser_single_res_analysis::out, basic::options::OptionKeys::nmr::pcs::pcs, clean_pdb_keep_ligand::pdbfile, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), numeric::random::random_range(), ObjexxFCL::format::RJ(), docking::s, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, vancomycin::task, utility::to_string(), basic::options::TR, utility_exit_with_message, and basic::Tracer::Warning.

Variable Documentation

TR

basic::Tracer TR("apps.public.nmr.ligand_transform_with_pcs") ( "apps.public.nmr.ligand_transform_with_pcs"  )

static