LigandBaseProtocol.cc File Reference

#include <protocols/ligand_docking/LigandBaseProtocol.hh>
#include <utility/graph/Graph.hh>
#include <core/chemical/automorphism.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/id/AtomID.hh>
#include <basic/database/open.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/options/option.hh>
#include <core/pack/rotamer_set/UnboundRotamersOperation.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/pack/palette/CustomBaseTypePackerPalette.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <basic/Tracer.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <numeric/random/random.hh>
#include <algorithm>
#include <cmath>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <basic/options/keys/enzdes.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/pose/variant_util.hh>
#include <utility/vector1.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::ligand_docking

Functions
static basic::Tracer	protocols::ligand_docking::TR ("protocols.ligand_docking.LigandBaseProtocol")
void	protocols::ligand_docking::select_best_poses (core::import_pose::atom_tree_diffs::ScoresPairList const &scores_in, core::import_pose::atom_tree_diffs::ScoresPairList &scores_out, core::Real to_keep=0.05)
	Trims scores_in based on ligand_is_touching (if present) and then by total_score. More...
void	protocols::ligand_docking::select_best_poses (core::import_pose::atom_tree_diffs::AtomTreeDiff const &atdiff, core::import_pose::atom_tree_diffs::ScoresPairList &scores_out, core::Real to_keep=0.05)
	Selects the best ligand docking results from a silent file and appends their scores to the supplied list. More...
void	protocols::ligand_docking::select_best_poses (core::import_pose::atom_tree_diffs::AtomTreeDiff const &atdiff, std::set< std::string > &tags_out)
	Convenience wrapper: selects the best ligand docking results from a silent file and appends their tags to the supplied set. More...
void	protocols::ligand_docking::frac_atoms_within (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Real > const &cutoffs, utility::vector1< core::Real > &fractions_out)
	Without superimposing, automorphically computes the fraction of atoms in these residues that are within the given cutoff(s) of each other. More...

Detailed Description

Author

Ian W. Davis

Reworked a bit by Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org) during the 2019 PackerPalette mini-XRW to use PackerPalettes.