LigandBaseProtocol.cc File Reference

#include <protocols/ligand_docking/LigandBaseProtocol.hh>
#include <core/graph/Graph.hh>
#include <core/chemical/automorphism.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.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/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/constraints/HarmonicFunc.hh>
#include <core/pack/dunbrack/RotamerLibrary.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/chemical/AtomType.hh>
#include <core/pose/util.hh>
#include <utility/vector1.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/scoring/EnergyGraph.hh>

Go to the source code of this file.

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

Constant Groups
	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")
static numeric::random::RandomGenerator	protocols::ligand_docking::my_RG (810323)
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

Definition in file LigandBaseProtocol.cc.