LigandDiscoverySearch.cc File Reference

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#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <basic/options/option.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/dna/setup.hh>
#include <protocols/dna/RestrictDesignToProteinDNAInterface.hh>
#include <protocols/motifs/LigandMotifSearch.hh>
#include <protocols/motifs/LigandMotifSearch.fwd.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/motifs/Motif.hh>
#include <core/chemical/residue_io.hh>
#include <protocols/motifs/MotifHit.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <protocols/motifs/BuildPosition.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/chemical/GlobalResidueTypeSet.hh>
#include <protocols/dna/PDBOutput.hh>
#include <protocols/dna/util.hh>
#include <protocols/motifs/motif_utils.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/atom_tree_diffs/atom_tree_diff.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <map>
#include <queue>
#include <functional>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <basic/options/keys/protein_grid.OptionKeys.gen.hh>
#include <core/pose/xyzStripeHashPose.hh>
#include <numeric/geometry/hashing/xyzStripeHash.hh>
#include <numeric/geometry/hashing/xyzStripeHash.fwd.hh>
#include <numeric/xyzVector.hh>
#include <protocols/ligand_docking/InterfaceScoreCalculator.hh>
#include <protocols/ligand_docking/ligand_scores.hh>
#include <protocols/qsar/scoring_grid/AtrGrid.hh>
#include <protocols/qsar/scoring_grid/RepGrid.hh>
#include <protocols/qsar/scoring_grid/VdwGrid.hh>
#include <protocols/qsar/scoring_grid/HbaGrid.hh>
#include <protocols/qsar/scoring_grid/HbdGrid.hh>
#include <protocols/qsar/scoring_grid/GridSet.hh>
#include <protocols/ligand_docking/MoveMapBuilder.hh>
#include <protocols/ligand_docking/LigandArea.hh>
#include <protocols/ligand_docking/InterfaceBuilder.hh>
#include <protocols/ligand_docking/MoveMapBuilder.fwd.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <protocols/ligand_docking/LigandBaseProtocol.hh>
#include <protocols/ligand_docking/HighResDocker.hh>
#include <protocols/ligand_docking/ligand_dock_impl.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/chemical/PoseResidueTypeSet.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <protocols/motifs/LigandDiscoverySearch.hh>
#include <protocols/motifs/IdentifyLigandMotifs.hh>
#include <utility/Binary_Util.hh>
#include <protocols/protein_grid/ProteinGrid.hh>
#include <time.h>
#include <typeinfo>

Classes
struct	comparator

Functions
static basic::Tracer	ms_tr ("protocols.motifs.LigandDiscoverySearch")
std::vector< std::tuple< core::Real, core::pose::Pose, std::string > >	merge (std::vector< std::tuple< core::Real, core::pose::Pose, std::string >> left, std::vector< std::tuple< core::Real, core::pose::Pose, std::string >> right)
std::vector< std::tuple< core::Real, core::pose::Pose, std::string > >	mergeSort (std::vector< std::tuple< core::Real, core::pose::Pose, std::string >> m)

Detailed Description

aginsparg, ipatel, sthyme

Function Documentation

merge()

std::vector<std::tuple<core::Real, core::pose::Pose, std::string> > merge	(	std::vector< std::tuple< core::Real, core::pose::Pose, std::string >>	left,
		std::vector< std::tuple< core::Real, core::pose::Pose, std::string >>	right
	)

References core::sequence::left.

Referenced by protocols::tcr::initialize_template_ignore_list(), mergeSort(), protocols::forge::build::ConnectRight::modify_impl(), and protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_merge_chains().

mergeSort()

std::vector<std::tuple<core::Real, core::pose::Pose, std::string> > mergeSort

(

std::vector< std::tuple< core::Real, core::pose::Pose, std::string >>

m

)

References core::sequence::left, and merge().

Referenced by LigandDiscoverySearch::discover().

ms_tr()

static basic::Tracer ms_tr ( "protocols.motifs.LigandDiscoverySearch"  )

static

Referenced by LigandDiscoverySearch::discover(), IdentifyLigandMotifs::evaluate_motifs_of_pose(), LigandDiscoverySearch::get_motif_sublibrary_by_aa(), LigandDiscoverySearch::make_minipose(), LigandDiscoverySearch::score_minipose(), and LigandDiscoverySearch::seed_cutoff_values().