protocols::ligand_docking Namespace Reference

Namespaces
	ligand_options
	rdf
	scoring_grid

Classes
class	AddHydrogen
class	AddHydrogens
class	AddHydrogensCreator
class	AtomCountFilter
class	AtomCountFilterCreator
class	ChainExistsFilter
class	ChainExistsFilterCreator
class	CompleteConnectionsFilter
class	CompleteConnectionsFilterCreator
class	CompoundTranslate
class	CompoundTranslateCreator
class	ComputeLigandRDF
class	ComputeLigandRDFCreator
class	DistributionMap
	A singleton class that returns a map of strings to enum types. More...
class	FinalMinimizer
class	FinalMinimizerCreator
class	GrowLigand
class	GrowLigandCreator
class	HBondAcceptorFilter
class	HBondAcceptorFilterCreator
class	HBondDonorFilter
class	HBondDonorFilterCreator
class	HeavyAtomFilter
class	HeavyAtomFilterCreator
class	HighResDocker
class	HighResDockerCreator
class	InterfaceBuilder
class	InterfaceBuilderLoader
	A class for loading InterfaceBuilders into the XML parser's basic::datacache::DataMap. More...
class	InterfaceBuilderLoaderCreator
class	InterfaceScoreCalculator
class	InterfaceScoreCalculatorCreator
struct	Ligand_info
class	LigandArea
class	LigandAreaLoader
class	LigandAreaLoaderCreator
class	LigandBaseProtocol
	Shared functionality for protocols that dock ligands. More...
class	LigandDesign
class	LigandDesignCreator
class	LigandDockMain
class	LigandDockProtocol
class	MinimizeBackbone
class	MinimizeBackboneCreator
class	MinimizeLigand
class	MolarMassFilter
class	MolarMassFilterCreator
class	MolecularMassFilter
class	MolecularMassFilterCreator
class	MoveMapBuilder
class	MoveMapBuilderLoader
	A class for loading MoveMapBuilders into the XML parser's basic::datacache::DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder. More...
class	MoveMapBuilderLoaderCreator
class	RandomConformerMover
	Replace the residue at the given position with a randomly selected conformer from its rotamer library. More...
class	RandomConformers
class	RandomConformersCreator
class	ResidueTorsionRestraints
	Manages harmonic restraints on torsions, so they can be turned off for packing. More...
class	RigidSearchMover
	An optimized mover for Monte Carlo trial of rigid body perturbations. More...
class	Rotate
struct	Rotate_info
class	RotateCreator
class	Rotates
class	RotatesCreator
class	SlideTogether
class	SlideTogetherCreator
class	StartFrom
class	StartFromCreator
class	TetherLigand
class	Transform
struct	Transform_info
class	TransformCreator
class	Translate
struct	Translate_info
class	TranslateCreator
class	UnconstrainedTorsionsMover
	Juggles torsional constraints with packing or rotamer trials. More...
class	WriteLigandMolFile
class	WriteLigandMolFileCreator

Typedefs
typedef utility::pointer::shared_ptr < AddHydrogen >	AddHydrogenOP
typedef utility::pointer::shared_ptr < AddHydrogen const >	AddHydrogenCOP
typedef utility::pointer::shared_ptr < AddHydrogens >	AddHydrogensOP
typedef utility::pointer::shared_ptr < AddHydrogens const >	AddHydrogensCOP
typedef utility::pointer::shared_ptr < ComputeLigandRDF >	ComputeLigandRDFOP
typedef utility::pointer::shared_ptr < ComputeLigandRDF const >	ComputeLigandRDFCOP
typedef utility::pointer::shared_ptr < FinalMinimizer >	FinalMinimizerOP
typedef utility::pointer::shared_ptr < FinalMinimizer const >	FinalMinimizerCOP
typedef utility::vector1 < FinalMinimizerOP >	FinalMinimizerOPs
typedef utility::vector1 < FinalMinimizerCOP >	FinalMinimizerCOPs
typedef utility::pointer::shared_ptr < core::grid::CartGrid< int > >	CartGridIntOP
typedef utility::pointer::shared_ptr < GrowLigand >	GrowLigandOP
typedef utility::pointer::shared_ptr < GrowLigand const >	GrowLigandCOP
typedef utility::pointer::shared_ptr < HighResDocker >	HighResDockerOP
typedef utility::pointer::shared_ptr < HighResDocker const >	HighResDockerCOP
typedef utility::vector1 < HighResDockerOP >	HighResDockerOPs
typedef utility::vector1 < HighResDockerCOP >	HighResDockerCOPs
typedef utility::pointer::shared_ptr < InterfaceBuilder >	InterfaceBuilderOP
typedef utility::pointer::shared_ptr < InterfaceBuilder const >	InterfaceBuilderCOP
typedef utility::vector1 < InterfaceBuilderOP >	InterfaceBuilderOPs
typedef utility::vector1 < InterfaceBuilderCOP >	InterfaceBuilderCOPs
typedef utility::pointer::shared_ptr < InterfaceScoreCalculator >	InterfaceScoreCalculatorOP
typedef utility::pointer::shared_ptr < InterfaceScoreCalculator const >	InterfaceScoreCalculatorCOP
typedef utility::vector1 < InterfaceScoreCalculatorOP >	InterfaceScoreCalculatorOPs
typedef utility::vector1 < InterfaceScoreCalculatorCOP >	InterfaceScoreCalculatorCOPs
typedef utility::pointer::shared_ptr < LigandDockMain >	LigandDockMainOP
typedef utility::pointer::shared_ptr < LigandArea >	LigandAreaOP
typedef utility::pointer::shared_ptr < LigandArea const >	LigandAreaCOP
typedef utility::vector1 < LigandAreaOP >	LigandAreaOPs
typedef utility::vector1 < LigandAreaCOP >	LigandAreaCOPs
typedef std::map< char, LigandAreaOP >	LigandAreas
typedef utility::pointer::shared_ptr < LigandBaseProtocol >	LigandBaseProtocolOP
typedef utility::pointer::shared_ptr < LigandBaseProtocol const >	LigandBaseProtocolCOP
typedef utility::pointer::shared_ptr < LigandDesign >	LigandDesignOP
typedef utility::pointer::shared_ptr < LigandDesign const >	LigandDesignCOP
typedef utility::pointer::shared_ptr < LigandDockProtocol >	LigandDockProtocolOP
typedef utility::pointer::shared_ptr < LigandDockProtocol const >	LigandDockProtocolCOP
typedef utility::pointer::shared_ptr < MinimizeBackbone >	MinimizeBackboneOP
typedef utility::pointer::shared_ptr < MinimizeBackbone const >	MinimizeBackboneCOP
typedef utility::vector1 < MinimizeBackboneOP >	MinimizeBackboneOPs
typedef utility::vector1 < MinimizeBackboneCOP >	MinimizeBackboneCOPs
typedef utility::pointer::shared_ptr < MinimizeLigand >	MinimizeLigandOP
typedef utility::pointer::shared_ptr < MinimizeLigand const >	MinimizeLigandCOP
typedef utility::vector1 < MinimizeLigandOP >	MinimizeLigandOPs
typedef utility::vector1 < MinimizeLigandCOP >	MinimizeLigandCOPs
typedef utility::pointer::shared_ptr < MoveMapBuilder >	MoveMapBuilderOP
typedef utility::pointer::shared_ptr < MoveMapBuilder const >	MoveMapBuilderCOP
typedef utility::vector1 < MoveMapBuilderOP >	MoveMapBuilderOPs
typedef utility::vector1 < MoveMapBuilderCOP >	MoveMapBuilderCOPs
typedef utility::pointer::shared_ptr < RandomConformerMover >	RandomConformerMoverOP
typedef utility::pointer::shared_ptr < RandomConformerMover const >	RandomConformerMoverCOP
typedef utility::pointer::shared_ptr < ResidueTorsionRestraints >	ResidueTorsionRestraintsOP
typedef utility::pointer::shared_ptr < ResidueTorsionRestraints const >	ResidueTorsionRestraintsCOP
typedef utility::pointer::shared_ptr < RigidSearchMover >	RigidSearchMoverOP
typedef utility::pointer::shared_ptr < RigidSearchMover const >	RigidSearchMoverCOP
typedef utility::pointer::shared_ptr < Rotate >	RotateOP
typedef utility::pointer::shared_ptr < Rotate const >	RotateCOP
typedef utility::vector1 < RotateOP >	RotateOPs
typedef utility::vector1 < RotateCOP >	RotateCOPs
typedef utility::pointer::shared_ptr < Rotates >	RotatesOP
typedef utility::pointer::shared_ptr < Rotates const >	RotatesCOP
typedef utility::vector1 < RotatesOP >	RotatesOPs
typedef utility::vector1 < RotatesCOP >	RotatesCOPs
typedef utility::pointer::shared_ptr < StartFrom >	StartFromOP
typedef utility::pointer::shared_ptr < TetherLigand >	TetherLigandOP
typedef utility::pointer::shared_ptr < TetherLigand const >	TetherLigandCOP
typedef utility::vector1 < TetherLigandOP >	TetherLigandOPs
typedef utility::vector1 < TetherLigandCOP >	TetherLigandCOPs
typedef utility::pointer::shared_ptr < Translate >	TranslateOP
typedef utility::pointer::shared_ptr < Translate const >	TranslateCOP
typedef utility::vector1 < TranslateOP >	TranslateOPs
typedef utility::vector1 < TranslateCOP >	TranslateCOPs
typedef utility::pointer::shared_ptr < UnconstrainedTorsionsMover >	UnconstrainedTorsionsMoverOP
typedef utility::pointer::shared_ptr < UnconstrainedTorsionsMover const >	UnconstrainedTorsionsMoverCOP
typedef utility::pointer::shared_ptr < WriteLigandMolFile >	WriteLigandMolFileOP

Enumerations
enum	Distribution { Uniform, Gaussian }

Functions
std::string	generate_unique_name (std::string)
static thread_local basic::Tracer	add_hydrogen_tracer ("protocols.ligand_docking.AddHydrogen", basic::t_debug)
static thread_local basic::Tracer	add_hydrogens_tracer ("protocols.ligand_docking.LigandDesign", basic::t_debug)
static thread_local basic::Tracer	atom_tracer ("protocols.ligand_docking.AtOOomCountFilter")
static thread_local basic::Tracer	atom_tracer ("protocols.ligand_docking.ChainExistsFilter")
static thread_local basic::Tracer	complete_connections_tracer ("protocols.ligand_docking.CompleteConnectionsFilter")
static thread_local basic::Tracer	translate_tracer ("protocols.ligand_docking.CompoundTranslate", basic::t_debug)
static thread_local basic::Tracer	compute_rdf_tracer ("protocols.ligand_docking.ComputeLigandRDF")
Distribution	get_distribution (std::string distribution_str)
static thread_local basic::Tracer	FinalMinimizer_tracer ("protocols.ligand_docking.ligand_options.FinalMinimizer", basic::t_debug)
static thread_local basic::Tracer	TR ("protocols.ligand_docking.grid_functions", basic::t_debug)
int	grid_score (core::grid::CartGrid< int > const &grid, core::conformation::Residue const &rsd, int max_score=9999)
	Sum the grid values for all heavy atoms in the residue. More...
void	grid_score_atr_rep (core::grid::CartGrid< int > const &grid, core::conformation::Residue const &rsd, int &atr_out,int &rep_out,int max_rep=9999)
	Sum the grid values for all heavy atoms in the residue. More...
void	rb_grid_score_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose const &pose, core::Size begin, core::Size const end, int &atr_out, int &rep_out, int max_rep)
	Sum the grid values for all heavy atoms in the residue. More...
std::pair< int, int >	get_rb_atr_and_rep_scores (core::grid::CartGrid< int > const &grid, core::pose::Pose const &pose, core::Size begin, core::Size end)
	a cleaner implementation of rb_grid_score_atr_rep More...
void	grid_rotamer_trials (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no, int const min_score=0)
	Try all rotamers for the specified residue and install the first one that minimizes the grid score. Only tested with ligand residues w/ a conformer library. More...
void	grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no)
	Try all rotamers for the specified residue and install the first one that minimizes the repulsive score, breaking ties by the attractive score. Only tested with ligand residues w/ a conformer library. More...
void	rb_grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size begin, core::Size end)
void	rotamers_for_trials (core::pose::Pose &pose, core::Size rsd_no, utility::vector1< core::conformation::ResidueOP > &conformers_out)
	Internal helper function for rotamer trials; fills conformers_out. More...
void	set_sphere (core::grid::CartGrid< int > &grid, core::Vector const &center, core::Real radius, int value)
void	set_repulsive_bb_cores (utility::pointer::shared_ptr< core::grid::CartGrid< int > >grid, core::pose::Pose const &pose, core::Real const rep_rad)
utility::pointer::shared_ptr < core::grid::CartGrid< int > >	make_atr_rep_grid (core::pose::Pose const &pose, core::Vector const &center)
	Set the value for all grid boxes whose centers fall inside the sphere. More...
utility::pointer::shared_ptr < core::grid::CartGrid< int > >	make_atr_rep_grid_without_ligand (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
	Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude. More...
utility::pointer::shared_ptr < core::grid::CartGrid< int > >	make_atr_rep_grid_without_ligands (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
	Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude. More...
template<typename T >
void	grid_to_kin (std::ostream &out, core::grid::CartGrid< T > const &grid, T min_val, T max_val, int stride)
static thread_local basic::Tracer	grow_ligand_tracer ("protocols.ligand_docking.GrowLigand", basic::t_debug)
static thread_local basic::Tracer	hbond_acceptor_tracer ("protocols.ligand_docking.HBondAcceptorFilter")
static thread_local basic::Tracer	hbond_donor_tracer ("protocols.ligand_docking.HBondDonorFilter")
static thread_local basic::Tracer	heavy_atom_tracer ("protocols.ligand_docking.HeavyAtomFilter")
static thread_local basic::Tracer	high_res_docker_tracer ("protocols.ligand_docking.ligand_options.Protocol", basic::t_debug)
static thread_local basic::Tracer	interface_builder_tracer ("protocols.ligand_docking.ligand_options.InterfaceBuilder", basic::t_debug)
static thread_local basic::Tracer	InterfaceScoreCalculator_tracer ("protocols.ligand_docking.ligand_options.InterfaceScoreCalculator", basic::t_debug)
static thread_local basic::Tracer	TR ("protocols.ligand_docking.main")
static thread_local basic::Tracer	TR ("protocols.ligand_docking.ligand_functions")
core::scoring::constraints::ConstraintOP	torsion_constraints_from_mean_sd (core::Size rsd_no, core::Size chino, core::chemical::ResidueType const &rsd_type, utility::vector1< std::pair< core::Real, core::Real > > const &mean_sd_degrees)
	Helper function. More...
core::scoring::constraints::ConstraintOP	torsion_constraints_from_rotamers (core::Size rsd_no, core::Size chino, utility::vector1< core::conformation::ResidueCOP > const &rsds, core::Real stddev_degrees)
	Produce an ambiguous dihedral restraint for the specified chi angle, assuming that the provided conformations represent (all) energetic minima. More...
core::scoring::constraints::ConstraintOP	torsion_constraints_from_chi_rotamers (core::Size rsd_no, core::Size chino, core::chemical::ResidueType const &rsdtype)
	Produce an ambiguous dihedral restraint for the specified chi angle, assuming that ResidueType.chi_rotamers() lists (all) energetic minima. More...
void	get_ligand_torsion_constraints (core::pose::Pose &pose, core::Size rsd_no, core::Real stddev_degrees, utility::vector1< core::scoring::constraints::ConstraintOP > &csts_out, bool const constrain_all_torsions_equally)
	Produce dihedral restraints for all chi angles in the specified residue, from chi_rotamers() if available, and from the rotamer library otherwise. More...
void	constrain_ligand_torsions (core::pose::Pose &pose, core::Real stddev_degrees, bool constrain_all_torsions_equally=true)
	Call get_ligand_torsion_constraints() for all non-polymer residues and add the resulting constraints to the Pose. More...
utility::vector1< core::Size >	get_ligand_seqpos (core::pose::Pose const &pose)
	simple function to scan the pose for all ligand residues More...
void	append_interface_deltas (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, const core::scoring::ScoreFunctionOP scorefxn, std::string const &prefix)
	append interface_delta scores More...
void	append_interface_deltas (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, const core::scoring::ScoreFunctionOP scorefxn, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
void	append_ligand_travel (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
	Another interesting metric – how far does the ligand centroid move? More...
void	append_ligand_grid_scores (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, std::string const &prefix)
void	append_ligand_grid_scores (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
void	append_radius_of_gyration (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, std::string const &prefix)
	Calculate radius of gyration for downstream non-H atoms. More...
void	append_ligand_RMSD (core::Size const jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
void	append_multi_residue_ligand_RMSD (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
void	append_automorphic_rmsd (core::Size ligand_residue_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
static thread_local basic::Tracer	ligand_scores_tracer ("protocols.ligand_docking.ligand_scores", basic::t_debug)
static thread_local basic::Tracer	ligand_area_tracer ("protocols.ligand_docking.ligand_options.LigandArea", basic::t_debug)
static thread_local basic::Tracer	TR ("protocols.ligand_docking.LigandBaseProtocol")
void	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	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	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	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...
static thread_local basic::Tracer	ligand_design_tracer ("protocols.ligand_docking.LigandDesign", basic::t_debug)
bool	grow (core::pose::Pose pose, core::Size start, core::Size end)
bool	has_incomplete_connections (core::pose::Pose pose, core::Size start, core::Size const end)
bool	passes_filters (core::pose::Pose const &pose, core::Size start, core::Size const end)
core::Size	random_connection (core::conformation::ResidueCOP residue)
utility::vector1< core::Size >	get_incomplete_connections (core::conformation::ResidueCOP residue)
utility::vector1< core::Size >	find_unconnected_residues (core::pose::Pose const &pose, core::Size start, core::Size const end)
static thread_local basic::Tracer	TR ("protocols.ligand_docking.LigandDockingLoaders")
static thread_local basic::Tracer	TR ("protocols.ligand_docking.LigandDockProtocol")
core::Size	count_buried_unsat_Hbonds (core::pose::Pose const &pose)
	Helper function to tame the PoseMetricCalculator madness. More...
void	print_buried_unsat_Hbonds (core::pose::Pose const &bound, core::pose::Pose const &unbound)
	Because inquiring minds want to know: what Hbonds are precluded by this docking? More...
static thread_local basic::Tracer	minimize_backbone_tracer ("protocols.ligand_docking.ligand_options.MinimizeBackbone", basic::t_debug)
void	reorder_with_first_non_mobile_as_root (core::kinematics::FoldTreeOP f, ligand_options::Interface const &interface, core::pose::Pose &pose)
core::Size	find_peptide_attach_pt (int const &start, int const &stop, std::map< core::Size, core::Size > const jump_to_attach)
core::Size	find_attach_pt (core::Size const jump_id, ligand_options::Interface const interface, core::pose::Pose const &pose)
void	restrict_to_protein_residues (ligand_options::Interface &interface, core::pose::Pose const &pose)
static thread_local basic::Tracer	MinimizeLigand_tracer ("protocols.ligand_docking.MinimizeLigand", basic::t_debug)
static thread_local basic::Tracer	atom_tracer ("protocols.ligand_docking.MolarMassFilter")
static thread_local basic::Tracer	mass_tracer ("protocols.ligand_docking.MolecularMassFilter")
static thread_local basic::Tracer	MoveMapBuilder_tracer ("protocols.ligand_docking.ligand_options.MoveMapBuilder", basic::t_debug)
void	set_jumps (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap, LigandAreas ligand_areas)
static thread_local basic::Tracer	random_conformer_tracer ("protocols.ligand_docking.ligand_options.RandomConformers", basic::t_debug)
static thread_local basic::Tracer	TR ("protocols.ligand_dock.ResidueTorsionRestraints", basic::t_debug)
static thread_local basic::Tracer	rotate_tracer ("protocols.ligand_docking.ligand_options.rotate", basic::t_debug)
void	add_ligand_conditionally (Ligand_info const &ligand_info, utility::vector1< Ligand_info > &ligands, core::Size const heavy_atom_number)
void	apply_rotate (protocols::rigid::RigidBodyMoverOP mover, core::pose::Pose &pose, core::Vector const &center, core::Size jump_id, utility::vector1< core::Size > const tag_along_jumps)
bool	check_score (Ligand_info const ligand, core::Size const heavy_atom_number)
	Convenience Functions for use with Rotate. More...
bool	check_RMSD (Ligand_info const ligand, core::Size const heavy_atom_number, utility::vector1< Ligand_info > const &ligands)
static thread_local basic::Tracer	rotates_tracer ("protocols.ligand_docking.ligand_options.rotates", basic::t_debug)
static thread_local basic::Tracer	slide_together_tracer ("protocols.ligand_docking.ligand_options.slide_together")
static thread_local basic::Tracer	start_from_tracer ("protocols.ligand_docking.ligand_options.Start_from", basic::t_debug)
void	move_ligand_to_desired_centroid (core::Size const jump_id, core::Vector const desired_centroid, core::pose::Pose &pose)
static thread_local basic::Tracer	tether_ligand_tracer ("protocols.ligand_docking.ligand_options.Tether_ligand", basic::t_debug)
core::scoring::constraints::ConstraintCOP	restrain_ligand_nbr_atom (core::Size const lig_id, core::Real const stddev_Angstroms, core::pose::Pose &pose)
static thread_local basic::Tracer	transform_tracer ("protocols.ligand_docking.Transform")
static thread_local basic::Tracer	translate_tracer ("protocols.ligand_docking.ligand_options.translate", basic::t_debug)
static thread_local basic::Tracer	write_ligand_tracer ("protocols.ligand_docking.WriteLigandMolFile")

Typedef Documentation

typedef utility::pointer::shared_ptr< AddHydrogen const > protocols::ligand_docking::AddHydrogenCOP

typedef utility::pointer::shared_ptr< AddHydrogen > protocols::ligand_docking::AddHydrogenOP

typedef utility::pointer::shared_ptr< AddHydrogens const > protocols::ligand_docking::AddHydrogensCOP

typedef utility::pointer::shared_ptr< AddHydrogens > protocols::ligand_docking::AddHydrogensOP

typedef utility::pointer::shared_ptr<core::grid::CartGrid<int> > protocols::ligand_docking::CartGridIntOP

typedef utility::pointer::shared_ptr< ComputeLigandRDF const > protocols::ligand_docking::ComputeLigandRDFCOP

typedef utility::pointer::shared_ptr< ComputeLigandRDF > protocols::ligand_docking::ComputeLigandRDFOP

typedef utility::pointer::shared_ptr< FinalMinimizer const > protocols::ligand_docking::FinalMinimizerCOP

typedef utility::vector1<FinalMinimizerCOP> protocols::ligand_docking::FinalMinimizerCOPs

typedef utility::pointer::shared_ptr< FinalMinimizer > protocols::ligand_docking::FinalMinimizerOP

typedef utility::vector1<FinalMinimizerOP> protocols::ligand_docking::FinalMinimizerOPs

typedef utility::pointer::shared_ptr< GrowLigand const > protocols::ligand_docking::GrowLigandCOP

typedef utility::pointer::shared_ptr< GrowLigand > protocols::ligand_docking::GrowLigandOP

typedef utility::pointer::shared_ptr< HighResDocker const > protocols::ligand_docking::HighResDockerCOP

typedef utility::vector1<HighResDockerCOP> protocols::ligand_docking::HighResDockerCOPs

typedef utility::pointer::shared_ptr< HighResDocker > protocols::ligand_docking::HighResDockerOP

typedef utility::vector1<HighResDockerOP> protocols::ligand_docking::HighResDockerOPs

typedef utility::pointer::shared_ptr< InterfaceBuilder const > protocols::ligand_docking::InterfaceBuilderCOP

typedef utility::vector1< InterfaceBuilderCOP > protocols::ligand_docking::InterfaceBuilderCOPs

typedef utility::pointer::shared_ptr< InterfaceBuilder > protocols::ligand_docking::InterfaceBuilderOP

typedef utility::vector1< InterfaceBuilderOP > protocols::ligand_docking::InterfaceBuilderOPs

typedef utility::pointer::shared_ptr< InterfaceScoreCalculator const > protocols::ligand_docking::InterfaceScoreCalculatorCOP

typedef utility::vector1<InterfaceScoreCalculatorCOP> protocols::ligand_docking::InterfaceScoreCalculatorCOPs

typedef utility::pointer::shared_ptr< InterfaceScoreCalculator > protocols::ligand_docking::InterfaceScoreCalculatorOP

typedef utility::vector1<InterfaceScoreCalculatorOP> protocols::ligand_docking::InterfaceScoreCalculatorOPs

typedef utility::pointer::shared_ptr< LigandArea const > protocols::ligand_docking::LigandAreaCOP

typedef utility::vector1< LigandAreaCOP > protocols::ligand_docking::LigandAreaCOPs

typedef utility::pointer::shared_ptr< LigandArea > protocols::ligand_docking::LigandAreaOP

typedef utility::vector1< LigandAreaOP > protocols::ligand_docking::LigandAreaOPs

typedef std::map<char, LigandAreaOP> protocols::ligand_docking::LigandAreas

typedef utility::pointer::shared_ptr< LigandBaseProtocol const > protocols::ligand_docking::LigandBaseProtocolCOP

typedef utility::pointer::shared_ptr< LigandBaseProtocol > protocols::ligand_docking::LigandBaseProtocolOP

typedef utility::pointer::shared_ptr< LigandDesign const > protocols::ligand_docking::LigandDesignCOP

typedef utility::pointer::shared_ptr< LigandDesign > protocols::ligand_docking::LigandDesignOP

typedef utility::pointer::shared_ptr< LigandDockMain > protocols::ligand_docking::LigandDockMainOP

typedef utility::pointer::shared_ptr< LigandDockProtocol const > protocols::ligand_docking::LigandDockProtocolCOP

typedef utility::pointer::shared_ptr< LigandDockProtocol > protocols::ligand_docking::LigandDockProtocolOP

typedef utility::pointer::shared_ptr< MinimizeBackbone const > protocols::ligand_docking::MinimizeBackboneCOP

typedef utility::vector1<MinimizeBackboneCOP> protocols::ligand_docking::MinimizeBackboneCOPs

typedef utility::pointer::shared_ptr< MinimizeBackbone > protocols::ligand_docking::MinimizeBackboneOP

typedef utility::vector1<MinimizeBackboneOP> protocols::ligand_docking::MinimizeBackboneOPs

typedef utility::pointer::shared_ptr< MinimizeLigand const > protocols::ligand_docking::MinimizeLigandCOP

typedef utility::vector1<MinimizeLigandCOP> protocols::ligand_docking::MinimizeLigandCOPs

typedef utility::pointer::shared_ptr< MinimizeLigand > protocols::ligand_docking::MinimizeLigandOP

typedef utility::vector1<MinimizeLigandOP> protocols::ligand_docking::MinimizeLigandOPs

typedef utility::pointer::shared_ptr< MoveMapBuilder const > protocols::ligand_docking::MoveMapBuilderCOP

typedef utility::vector1<MoveMapBuilderCOP> protocols::ligand_docking::MoveMapBuilderCOPs

typedef utility::pointer::shared_ptr< MoveMapBuilder > protocols::ligand_docking::MoveMapBuilderOP

typedef utility::vector1<MoveMapBuilderOP> protocols::ligand_docking::MoveMapBuilderOPs

typedef utility::pointer::shared_ptr< RandomConformerMover const > protocols::ligand_docking::RandomConformerMoverCOP

typedef utility::pointer::shared_ptr< RandomConformerMover > protocols::ligand_docking::RandomConformerMoverOP

typedef utility::pointer::shared_ptr< ResidueTorsionRestraints const > protocols::ligand_docking::ResidueTorsionRestraintsCOP

typedef utility::pointer::shared_ptr< ResidueTorsionRestraints > protocols::ligand_docking::ResidueTorsionRestraintsOP

typedef utility::pointer::shared_ptr< RigidSearchMover const > protocols::ligand_docking::RigidSearchMoverCOP

typedef utility::pointer::shared_ptr< RigidSearchMover > protocols::ligand_docking::RigidSearchMoverOP

typedef utility::pointer::shared_ptr< Rotate const > protocols::ligand_docking::RotateCOP

typedef utility::vector1<RotateCOP> protocols::ligand_docking::RotateCOPs

typedef utility::pointer::shared_ptr< Rotate > protocols::ligand_docking::RotateOP

typedef utility::vector1<RotateOP> protocols::ligand_docking::RotateOPs

typedef utility::pointer::shared_ptr< Rotates const > protocols::ligand_docking::RotatesCOP

typedef utility::vector1<RotatesCOP> protocols::ligand_docking::RotatesCOPs

typedef utility::pointer::shared_ptr< Rotates > protocols::ligand_docking::RotatesOP

typedef utility::vector1<RotatesOP> protocols::ligand_docking::RotatesOPs

typedef utility::pointer::shared_ptr<StartFrom> protocols::ligand_docking::StartFromOP

typedef utility::pointer::shared_ptr< TetherLigand const > protocols::ligand_docking::TetherLigandCOP

typedef utility::vector1<TetherLigandCOP> protocols::ligand_docking::TetherLigandCOPs

typedef utility::pointer::shared_ptr< TetherLigand > protocols::ligand_docking::TetherLigandOP

typedef utility::vector1<TetherLigandOP> protocols::ligand_docking::TetherLigandOPs

typedef utility::pointer::shared_ptr< Translate const > protocols::ligand_docking::TranslateCOP

typedef utility::vector1<TranslateCOP> protocols::ligand_docking::TranslateCOPs

typedef utility::pointer::shared_ptr< Translate > protocols::ligand_docking::TranslateOP

typedef utility::vector1<TranslateOP> protocols::ligand_docking::TranslateOPs

typedef utility::pointer::shared_ptr< UnconstrainedTorsionsMover const > protocols::ligand_docking::UnconstrainedTorsionsMoverCOP

typedef utility::pointer::shared_ptr< UnconstrainedTorsionsMover > protocols::ligand_docking::UnconstrainedTorsionsMoverOP

typedef utility::pointer::shared_ptr<WriteLigandMolFile> protocols::ligand_docking::WriteLigandMolFileOP

Enumeration Type Documentation

enum protocols::ligand_docking::Distribution

Enumerator
Uniform
Gaussian

Function Documentation

static thread_local basic::Tracer protocols::ligand_docking::add_hydrogen_tracer ( "protocols.ligand_docking.AddHydrogen"  , basic::t_debug    )

static

static thread_local basic::Tracer protocols::ligand_docking::add_hydrogens_tracer ( "protocols.ligand_docking.LigandDesign"  , basic::t_debug    )

static

void protocols::ligand_docking::add_ligand_conditionally	(	Ligand_info const &	ligand_info,
		utility::vector1< Ligand_info > &	ligands,
		core::Size const	heavy_atom_number
	)

References check_RMSD(), and check_score().

Referenced by protocols::ligand_docking::Rotate::create_random_rotations().

void protocols::ligand_docking::append_automorphic_rmsd	(	core::Size	ligand_residue_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		core::pose::Pose const &	after,
		std::string const &	prefix
	)

References core::scoring::automorphic_rmsd(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

Referenced by append_ligand_RMSD().

void protocols::ligand_docking::append_interface_deltas	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	after,
		const core::scoring::ScoreFunctionOP	scorefxn,
		std::string const &	prefix
	)

append interface_delta scores

References protocols::rigid::RigidBodyTransMover::apply(), core::scoring::fa_rep, core::pose::get_chain_from_jump_id(), core::scoring::n_score_types, name_from_score_type(), numeric::xyzVector< class >::negate(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

void protocols::ligand_docking::append_interface_deltas	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	after,
		const core::scoring::ScoreFunctionOP	scorefxn,
		std::string const &	prefix,
		protocols::qsar::scoring_grid::ScoreNormalizationOP	normalization_function
	)

References core::scoring::fa_rep, core::pose::get_chain_from_jump_id(), core::pose::get_chain_id_from_jump_id(), core::pose::get_chain_residues(), core::scoring::n_score_types, and name_from_score_type().

void protocols::ligand_docking::append_ligand_grid_scores	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	after,
		std::string const &	prefix
	)

References center, protocols::geometry::downstream_centroid_by_jump(), protocols::qsar::scoring_grid::GridManager::get_cached_scores(), core::pose::get_chain_from_jump_id(), core::pose::get_chain_id_from_jump_id(), protocols::qsar::scoring_grid::GridManager::get_instance(), grid_score(), protocols::qsar::scoring_grid::GridManager::initialize_all_grids(), ligand_scores_tracer(), protocols::qsar::scoring_grid::GridManager::size(), total_score, protocols::qsar::scoring_grid::GridManager::total_score(), and protocols::qsar::scoring_grid::GridManager::update_grids().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

void protocols::ligand_docking::append_ligand_grid_scores	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	after,
		std::string const &	prefix,
		protocols::qsar::scoring_grid::ScoreNormalizationOP	normalization_function
	)

References center, protocols::geometry::downstream_centroid_by_jump(), protocols::qsar::scoring_grid::GridManager::get_cached_scores(), core::pose::get_chain_from_jump_id(), core::pose::get_chain_id_from_jump_id(), core::pose::get_chain_residues(), protocols::qsar::scoring_grid::GridManager::get_instance(), grid_score(), protocols::qsar::scoring_grid::GridManager::initialize_all_grids(), ligand_scores_tracer(), protocols::qsar::scoring_grid::GridManager::size(), total_score, protocols::qsar::scoring_grid::GridManager::total_score(), and protocols::qsar::scoring_grid::GridManager::update_grids().

void protocols::ligand_docking::append_ligand_RMSD	(	core::Size const	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		core::pose::Pose const &	after,
		std::string const &	prefix
	)

References append_automorphic_rmsd(), append_multi_residue_ligand_RMSD(), begin, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), end, core::pose::get_chain_id_from_jump_id(), and core::pose::Pose::num_jump().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

void protocols::ligand_docking::append_ligand_travel	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		core::pose::Pose const &	after,
		std::string const &	prefix
	)

Another interesting metric – how far does the ligand centroid move?

Large values indicate we're outside of the intended binding site.

References numeric::xyzVector< class >::distance(), protocols::geometry::downstream_centroid_by_jump(), and core::pose::get_chain_from_jump_id().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

void protocols::ligand_docking::append_multi_residue_ligand_RMSD	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		core::pose::Pose const &	after,
		std::string const &	prefix
	)

References core::pose::Pose::chain(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::get_chain_from_jump_id(), core::scoring::is_ligand_heavyatom(), core::pose::Pose::remove_constraints(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), and core::pose::Pose::split_by_chain().

Referenced by append_ligand_RMSD().

void protocols::ligand_docking::append_radius_of_gyration	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		std::string const &	prefix
	)

Calculate radius of gyration for downstream non-H atoms.

Ligands tend to bind in outstretched conformations...

References numeric::xyzVector< class >::distance_squared(), protocols::geometry::downstream_centroid_by_jump(), core::pose::Pose::fold_tree(), core::pose::get_chain_from_jump_id(), core::conformation::Residue::nheavyatoms(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

void protocols::ligand_docking::apply_rotate	(	protocols::rigid::RigidBodyMoverOP	mover,
		core::pose::Pose &	pose,
		core::Vector const &	center,
		core::Size	jump_id,
		utility::vector1< core::Size > const	tag_along_jumps
	)

References core::pose::Pose::update_actcoords().

Referenced by protocols::ligand_docking::Rotate::create_random_rotation().

static thread_local basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.MolarMassFilter"  )

static

static thread_local basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.AtOOomCountFilter"  )

static

Referenced by protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::ChainExistsFilter::parse_my_tag(), protocols::ligand_docking::AtomCountFilter::parse_my_tag(), and protocols::ligand_docking::MolarMassFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.ChainExistsFilter"  )

static

bool protocols::ligand_docking::check_RMSD	(	Ligand_info const	ligand,
		core::Size const	heavy_atom_number,
		utility::vector1< Ligand_info > const &	ligands
	)

References core::scoring::automorphic_rmsd(), protocols::ligand_docking::Ligand_info::get_residues(), core::scoring::is_ligand_heavyatom_residues(), rms, core::scoring::rmsd_no_super(), and runtime_assert.

Referenced by add_ligand_conditionally().

bool protocols::ligand_docking::check_score	(	Ligand_info const	ligand,
		core::Size const	heavy_atom_number
	)

Convenience Functions for use with Rotate.

References protocols::ligand_docking::Ligand_info::atr, and protocols::ligand_docking::Ligand_info::rep.

Referenced by add_ligand_conditionally(), and protocols::abinitio::IterativeBase::add_structure().

static thread_local basic::Tracer protocols::ligand_docking::complete_connections_tracer ( "protocols.ligand_docking.CompleteConnectionsFilter"  )

static

Referenced by protocols::ligand_docking::CompleteConnectionsFilter::apply(), and protocols::ligand_docking::CompleteConnectionsFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::compute_rdf_tracer ( "protocols.ligand_docking.ComputeLigandRDF"  )

static

Referenced by protocols::ligand_docking::ComputeLigandRDF::apply(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::ligand_docking::ComputeLigandRDF::parse_my_tag(), and protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf().

void protocols::ligand_docking::constrain_ligand_torsions	(	core::pose::Pose &	pose,
		core::Real	stddev_degrees,
		bool	constrain_all_torsions_equally
	)

Call get_ligand_torsion_constraints() for all non-polymer residues and add the resulting constraints to the Pose.

References core::pose::Pose::constraint_set(), get_ligand_torsion_constraints(), core::chemical::ResidueType::is_polymer(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), and protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis().

core::Size protocols::ligand_docking::count_buried_unsat_Hbonds

(

core::pose::Pose const &

pose

)

Helper function to tame the PoseMetricCalculator madness.

References core::pose::metrics::EnergyDependentCalculator::get().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores().

static thread_local basic::Tracer protocols::ligand_docking::FinalMinimizer_tracer ( "protocols.ligand_docking.ligand_options.FinalMinimizer"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::FinalMinimizer::apply(), and protocols::ligand_docking::FinalMinimizer::get_final_min_mover().

core::Size protocols::ligand_docking::find_attach_pt	(	core::Size const	jump_id,
		ligand_options::Interface const	interface,
		core::pose::Pose const &	pose
	)

References numeric::xyzVector< class >::distance_squared(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), protocols::ligand_docking::ligand_options::InterfaceInfo::non_interface, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::MinimizeBackbone::find_attach_pts().

core::Size protocols::ligand_docking::find_peptide_attach_pt	(	int const &	start,
		int const &	stop,
		std::map< core::Size, core::Size > const	jump_to_attach
	)

References end.

Referenced by protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts().

utility::vector1< core::Size > protocols::ligand_docking::find_unconnected_residues	(	core::pose::Pose const &	pose,
		core::Size	start,
		core::Size const	end
	)

References core::conformation::Residue::has_incomplete_connection(), core::pose::Pose::residue(), and protocols::loops::start.

Referenced by protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::AddHydrogens::apply(), and protocols::ligand_docking::GrowLigand::apply().

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.

Currently considers only heavy atoms, not hydrogens.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), numeric::xyzVector< class >::length_squared(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::type(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores().

std::string protocols::ligand_docking::generate_unique_name

(

std::string

)

References a(), protocols::match::upstream::b, c, core::chemical::FA_STANDARD, core::chemical::ResidueTypeSet::has_name(), core::chemical::ChemicalManager::nonconst_residue_type_set(), and numeric::random::random_range().

Referenced by protocols::ligand_docking::AddHydrogen::apply().

Distribution protocols::ligand_docking::get_distribution

(

std::string

distribution_str

)

References protocols::ligand_docking::DistributionMap::get_instance().

Referenced by protocols::ligand_docking::CompoundTranslate::parse_my_tag(), protocols::ligand_docking::Rotates::parse_my_tag(), protocols::ligand_docking::Translate::parse_my_tag(), and protocols::ligand_docking::Rotate::parse_my_tag().

utility::vector1< core::Size > protocols::ligand_docking::get_incomplete_connections

(

core::conformation::ResidueCOP

residue

)

Referenced by protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::LigandDesign::fragments_to_string(), and random_connection().

utility::vector1< core::Size > protocols::ligand_docking::get_ligand_seqpos

(

core::pose::Pose const &

pose

)

simple function to scan the pose for all ligand residues

References core::chemical::ResidueType::is_ligand(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply().

void protocols::ligand_docking::get_ligand_torsion_constraints	(	core::pose::Pose &	pose,
		core::Size	rsd_no,
		core::Real	stddev_degrees,
		utility::vector1< core::scoring::constraints::ConstraintOP > &	csts_out,
		bool const	constrain_all_torsions_equally
	)

Produce dihedral restraints for all chi angles in the specified residue, from chi_rotamers() if available, and from the rotamer library otherwise.

References core::conformation::Residue::clone(), option, core::pose::Pose::residue(), core::pose::Pose::residue_type(), rotamers_for_trials(), torsion_constraints_from_chi_rotamers(), and torsion_constraints_from_rotamers().

Referenced by constrain_ligand_torsions().

std::pair< int, int > protocols::ligand_docking::get_rb_atr_and_rep_scores	(	core::grid::CartGrid< int > const &	grid,
		core::pose::Pose const &	pose,
		core::Size	begin,
		core::Size	end
	)

a cleaner implementation of rb_grid_score_atr_rep

References rb_grid_score_atr_rep().

Referenced by protocols::ligand_docking::Rotate::create_random_rotation().

void protocols::ligand_docking::grid_rotamer_trials	(	core::grid::CartGrid< int > const &	grid,
		core::pose::Pose &	pose,
		core::Size	rsd_no,
		int const	min_score
	)

Try all rotamers for the specified residue and install the first one that minimizes the grid score. Only tested with ligand residues w/ a conformer library.

min_score exists so you can search for the rotamer that clashes with the grid a minimal ammount instead of none, to disfavor free-floating, non-interacting poses.

References grid_score(), core::pose::Pose::replace_residue(), rotamers_for_trials(), and TR().

void protocols::ligand_docking::grid_rotamer_trials_atr_rep	(	core::grid::CartGrid< int > const &	grid,
		core::pose::Pose &	pose,
		core::Size	rsd_no
	)

Try all rotamers for the specified residue and install the first one that minimizes the repulsive score, breaking ties by the attractive score. Only tested with ligand residues w/ a conformer library.

References grid_score_atr_rep(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), rotamers_for_trials(), and TR().

Referenced by protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), and rb_grid_rotamer_trials_atr_rep().

int protocols::ligand_docking::grid_score	(	core::grid::CartGrid< int > const &	grid,
		core::conformation::Residue const &	rsd,
		int	max_score
	)

Sum the grid values for all heavy atoms in the residue.

If score exceeds max_score, stop counting and return (faster). Atoms that fall outside the grid are scored as zero.

References core::grid::CartGrid< class >::getValue(), core::grid::CartGrid< class >::is_in_grid(), core::conformation::Residue::nheavyatoms(), TR(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by append_ligand_grid_scores(), protocols::qsar::scoring_grid::SingleGrid::atom_score(), grid_rotamer_trials(), and protocols::qsar::scoring_grid::SingleGrid::score().

void protocols::ligand_docking::grid_score_atr_rep	(	core::grid::CartGrid< int > const &	grid,
		core::conformation::Residue const &	rsd,
		int &	atr_out,
		int &	rep_out,
		int	max_rep
	)

Sum the grid values for all heavy atoms in the residue.

If rep exceeds max_rep, atr is likely to be incorrect.

References core::grid::CartGrid< class >::getValue(), core::grid::CartGrid< class >::is_in_grid(), core::conformation::Residue::nheavyatoms(), TR(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by grid_rotamer_trials_atr_rep(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), and rb_grid_score_atr_rep().

template<typename T >

void protocols::ligand_docking::grid_to_kin	(	std::ostream &	out,
		core::grid::CartGrid< T > const &	grid,
		T	min_val,
		T	max_val,
		int	stride
	)

Just writes the points – you have to write @ dotlist, etc.

References core::grid::CartGrid< class >::coords(), core::grid::CartGrid< class >::getNumberOfPoints(), core::grid::CartGrid< class >::getValue(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

bool protocols::ligand_docking::grow	(	core::pose::Pose	pose,
		core::Size	start,
		core::Size	end
	)

References has_incomplete_connections(), and passes_filters().

Referenced by protocols::ligand_docking::LigandDesign::apply(), and protocols::forge::build::Bridge::modify_impl().

static thread_local basic::Tracer protocols::ligand_docking::grow_ligand_tracer ( "protocols.ligand_docking.GrowLigand"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::GrowLigand::fragments_to_string(), protocols::ligand_docking::GrowLigand::parse_my_tag(), and protocols::ligand_docking::GrowLigand::set_fragments().

bool protocols::ligand_docking::has_incomplete_connections	(	core::pose::Pose	pose,
		core::Size	start,
		core::Size const	end
	)

References core::conformation::Residue::has_incomplete_connection(), ligand_design_tracer(), core::conformation::Residue::name(), core::pose::Pose::residue(), and protocols::loops::start.

Referenced by grow().

static thread_local basic::Tracer protocols::ligand_docking::hbond_acceptor_tracer ( "protocols.ligand_docking.HBondAcceptorFilter"  )

static

Referenced by protocols::ligand_docking::HBondAcceptorFilter::apply(), and protocols::ligand_docking::HBondAcceptorFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::hbond_donor_tracer ( "protocols.ligand_docking.HBondDonorFilter"  )

static

Referenced by protocols::ligand_docking::HBondDonorFilter::apply(), and protocols::ligand_docking::HBondDonorFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::heavy_atom_tracer ( "protocols.ligand_docking.HeavyAtomFilter"  )

static

Referenced by protocols::ligand_docking::HeavyAtomFilter::apply(), and protocols::ligand_docking::HeavyAtomFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::high_res_docker_tracer ( "protocols.ligand_docking.ligand_options.Protocol"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::HighResDocker::apply(), and protocols::ligand_docking::HighResDocker::make_packer_task_from_vector().

static thread_local basic::Tracer protocols::ligand_docking::interface_builder_tracer ( "protocols.ligand_docking.ligand_options.InterfaceBuilder"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::InterfaceBuilder::build(), and protocols::ligand_docking::InterfaceBuilder::find_interface_residues().

static thread_local basic::Tracer protocols::ligand_docking::InterfaceScoreCalculator_tracer ( "protocols.ligand_docking.ligand_options.InterfaceScoreCalculator"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::append_ligand_docking_scores().

static thread_local basic::Tracer protocols::ligand_docking::ligand_area_tracer ( "protocols.ligand_docking.ligand_options.LigandArea"  , basic::t_debug    )

static

static thread_local basic::Tracer protocols::ligand_docking::ligand_design_tracer ( "protocols.ligand_docking.LigandDesign"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::LigandDesign::fragments_to_string(), has_incomplete_connections(), protocols::ligand_docking::LigandDesign::parse_my_tag(), passes_filters(), and protocols::ligand_docking::LigandDesign::set_fragments().

static thread_local basic::Tracer protocols::ligand_docking::ligand_scores_tracer ( "protocols.ligand_docking.ligand_scores"  , basic::t_debug    )

static

Referenced by append_ligand_grid_scores().

utility::pointer::shared_ptr< core::grid::CartGrid< int > > protocols::ligand_docking::make_atr_rep_grid	(	core::pose::Pose const &	pose,
		core::Vector const &	center
	)

Set the value for all grid boxes whose centers fall inside the sphere.

this function assumes there is only one ligand so it only considers protein residues

Make a grid around the specified point with attractive (negative) and repulsive (positive) values for the protein backbone.

References a(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), set_repulsive_bb_cores(), set_sphere(), core::pose::Pose::total_residue(), TR(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by protocols::ligand_docking::LigandDockProtocol::optimize_orientation3().

utility::pointer::shared_ptr< core::grid::CartGrid< int > > protocols::ligand_docking::make_atr_rep_grid_without_ligand	(	core::pose::Pose const &	pose,
		core::Vector const &	center,
		core::Size const &	ligand_chain_id_to_exclude
	)

Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude.

this function assumes excludes one ligand from the grid

References make_atr_rep_grid_without_ligands().

utility::pointer::shared_ptr< core::grid::CartGrid< int > > protocols::ligand_docking::make_atr_rep_grid_without_ligands	(	core::pose::Pose const &	pose,
		core::Vector const &	center,
		utility::vector1< core::Size >	ligand_chain_ids_to_exclude
	)

Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude.

Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_ids_to_exclude.

References a(), core::conformation::Residue::chain(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), set_repulsive_bb_cores(), set_sphere(), core::pose::Pose::total_residue(), TR(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Rotate::apply(), and make_atr_rep_grid_without_ligand().

static thread_local basic::Tracer protocols::ligand_docking::mass_tracer ( "protocols.ligand_docking.MolecularMassFilter"  )

static

Referenced by protocols::ligand_docking::MolecularMassFilter::apply(), and protocols::ligand_docking::MolecularMassFilter::parse_my_tag().

static thread_local basic::Tracer protocols::ligand_docking::minimize_backbone_tracer ( "protocols.ligand_docking.ligand_options.MinimizeBackbone"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::ligand_docking::MinimizeBackbone::apply(), protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), and protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calphas().

static thread_local basic::Tracer protocols::ligand_docking::MinimizeLigand_tracer ( "protocols.ligand_docking.MinimizeLigand"  , basic::t_debug    )

static

void protocols::ligand_docking::move_ligand_to_desired_centroid	(	core::Size const	jump_id,
		core::Vector const	desired_centroid,
		core::pose::Pose &	pose
	)

References protocols::rigid::RigidBodyTransMover::apply(), protocols::geometry::downstream_centroid_by_jump(), numeric::xyzVector< class >::length(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by protocols::ligand_docking::StartFrom::apply().

static thread_local basic::Tracer protocols::ligand_docking::MoveMapBuilder_tracer ( "protocols.ligand_docking.ligand_options.MoveMapBuilder"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::MoveMapBuilder::build(), and protocols::ligand_docking::MoveMapBuilder::set_all_chi().

bool protocols::ligand_docking::passes_filters	(	core::pose::Pose const &	pose,
		core::Size	start,
		core::Size const	end
	)

References ligand_design_tracer(), core::pose::num_chi_angles(), and core::pose::num_heavy_atoms().

Referenced by protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::abinitio::AbrelaxApplication::fold(), and grow().

void protocols::ligand_docking::print_buried_unsat_Hbonds	(	core::pose::Pose const &	bound,
		core::pose::Pose const &	unbound
	)

Because inquiring minds want to know: what Hbonds are precluded by this docking?

References a(), core::chemical::ResidueType::atom_name(), core::pose::metrics::EnergyDependentCalculator::get(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), and TR().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores().

static thread_local basic::Tracer protocols::ligand_docking::random_conformer_tracer ( "protocols.ligand_docking.ligand_options.RandomConformers"  , basic::t_debug    )

static

core::Size protocols::ligand_docking::random_connection

(

core::conformation::ResidueCOP

residue

)

References get_incomplete_connections(), numeric::random::RandomGenerator::random_element(), and numeric::random::rg().

Referenced by protocols::ligand_docking::LigandDesign::apply(), and protocols::ligand_docking::GrowLigand::apply().

void protocols::ligand_docking::rb_grid_rotamer_trials_atr_rep	(	core::grid::CartGrid< int > const &	grid,
		core::pose::Pose &	pose,
		core::Size	begin,
		core::Size	end
	)

References grid_rotamer_trials_atr_rep(), and TR().

Referenced by protocols::ligand_docking::Rotate::create_random_rotation().

void protocols::ligand_docking::rb_grid_score_atr_rep	(	core::grid::CartGrid< int > const &	grid,
		core::pose::Pose const &	pose,
		core::Size	begin,
		core::Size const	end,
		int &	atr_out,
		int &	rep_out,
		int	max_rep
	)

Sum the grid values for all heavy atoms in the residue.

References grid_score_atr_rep(), and core::pose::Pose::residue().

Referenced by get_rb_atr_and_rep_scores().

void protocols::ligand_docking::reorder_with_first_non_mobile_as_root	(	core::kinematics::FoldTreeOP	f,
		ligand_options::Interface const &	interface,
		core::pose::Pose &	pose
	)

References core::conformation::Residue::is_polymer(), core::pose::Pose::n_residue(), protocols::ligand_docking::ligand_options::InterfaceInfo::non_interface, core::pose::Pose::residue(), and utility_exit_with_message.

Referenced by protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions().

core::scoring::constraints::ConstraintCOP protocols::ligand_docking::restrain_ligand_nbr_atom	(	core::Size const	lig_id,
		core::Real const	stddev_Angstroms,
		core::pose::Pose &	pose
	)

References core::pose::Pose::add_constraint(), core::pose::Pose::atom_tree(), core::pose::Pose::residue(), core::kinematics::AtomTree::root(), and tether_ligand_tracer().

Referenced by protocols::ligand_docking::TetherLigand::apply().

void protocols::ligand_docking::restrict_to_protein_residues	(	ligand_options::Interface &	interface,
		core::pose::Pose const &	pose
	)

References protocols::ligand_docking::ligand_options::InterfaceInfo::is_interface, core::conformation::Residue::is_ligand(), protocols::ligand_docking::ligand_options::InterfaceInfo::non_interface, and core::pose::Pose::residue().

Referenced by protocols::ligand_docking::MinimizeBackbone::apply().

void protocols::ligand_docking::rotamers_for_trials	(	core::pose::Pose &	pose,
		core::Size	rsd_no,
		utility::vector1< core::conformation::ResidueOP > &	conformers_out
	)

Internal helper function for rotamer trials; fills conformers_out.

References core::chemical::ResidueType::get_self_ptr(), numeric::random::random_permutation(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and numeric::random::rg().

Referenced by protocols::ligand_docking::Transform::apply(), get_ligand_torsion_constraints(), grid_rotamer_trials(), and grid_rotamer_trials_atr_rep().

static thread_local basic::Tracer protocols::ligand_docking::rotate_tracer ( "protocols.ligand_docking.ligand_options.rotate"  , basic::t_debug    )

static

static thread_local basic::Tracer protocols::ligand_docking::rotates_tracer ( "protocols.ligand_docking.ligand_options.rotates"  , basic::t_debug    )

static

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
	)

Trims scores_in based on ligand_is_touching (if present) and then by total_score.

First discards ligands that aren't touching, then takes the top 5% by total_score. (Take given number of poses if to_keep > 1.0).

References core::import_pose::atom_tree_diffs::AtomTreeDiff::sort_by(), and utility_exit_with_message.

Referenced by select_best_poses().

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
	)

Selects the best ligand docking results from a silent file and appends their scores to the supplied list.

References core::import_pose::atom_tree_diffs::AtomTreeDiff::scores(), and select_best_poses().

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.

References core::import_pose::atom_tree_diffs::AtomTreeDiff::scores(), and select_best_poses().

void protocols::ligand_docking::set_jumps	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP	movemap,
		LigandAreas	ligand_areas
	)

References core::pose::get_jump_ids_from_chain().

Referenced by protocols::ligand_docking::MoveMapBuilder::build().

void protocols::ligand_docking::set_repulsive_bb_cores	(	utility::pointer::shared_ptr< core::grid::CartGrid< int > >	grid,
		core::pose::Pose const &	pose,
		core::Real const	rep_rad
	)

References core::conformation::Residue::has(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), set_sphere(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by make_atr_rep_grid(), and make_atr_rep_grid_without_ligands().

void protocols::ligand_docking::set_sphere	(	core::grid::CartGrid< int > &	grid,
		core::Vector const &	center,
		core::Real	radius,
		int	value
	)

Make a bounding box around the sphere, and visit all grid points that the box intersects. If the grid point center is within the sphere, fill that grid space with the specified value.

References core::grid::CartGrid< class >::coords(), numeric::xyzVector< class >::distance_squared(), core::grid::CartGrid< class >::getNumberOfPoints(), core::grid::CartGrid< class >::gridpt(), max(), min(), and core::grid::CartGrid< class >::setValue().

Referenced by make_atr_rep_grid(), make_atr_rep_grid_without_ligands(), and set_repulsive_bb_cores().

static thread_local basic::Tracer protocols::ligand_docking::slide_together_tracer ( "protocols.ligand_docking.ligand_options.slide_together"  )

static

Referenced by protocols::ligand_docking::SlideTogether::apply().

static thread_local basic::Tracer protocols::ligand_docking::start_from_tracer ( "protocols.ligand_docking.ligand_options.Start_from"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::StartFrom::apply(), and protocols::ligand_docking::StartFrom::parse_startfrom_file().

static thread_local basic::Tracer protocols::ligand_docking::tether_ligand_tracer ( "protocols.ligand_docking.ligand_options.Tether_ligand"  , basic::t_debug    )

static

Referenced by restrain_ligand_nbr_atom().

core::scoring::constraints::ConstraintOP protocols::ligand_docking::torsion_constraints_from_chi_rotamers	(	core::Size	rsd_no,
		core::Size	chino,
		core::chemical::ResidueType const &	rsdtype
	)

Produce an ambiguous dihedral restraint for the specified chi angle, assuming that ResidueType.chi_rotamers() lists (all) energetic minima.

References core::chemical::ResidueType::chi_rotamers(), and torsion_constraints_from_mean_sd().

Referenced by get_ligand_torsion_constraints().

core::scoring::constraints::ConstraintOP protocols::ligand_docking::torsion_constraints_from_mean_sd	(	core::Size	rsd_no,
		core::Size	chino,
		core::chemical::ResidueType const &	rsd_type,
		utility::vector1< std::pair< core::Real, core::Real > > const &	mean_sd_degrees
	)

Helper function.

References core::chemical::ResidueType::chi_atoms(), numeric::conversions::radians(), and TR().

Referenced by torsion_constraints_from_chi_rotamers(), and torsion_constraints_from_rotamers().

core::scoring::constraints::ConstraintOP protocols::ligand_docking::torsion_constraints_from_rotamers	(	core::Size	rsd_no,
		core::Size	chino,
		utility::vector1< core::conformation::ResidueCOP > const &	rsds,
		core::Real	stddev_degrees
	)

Produce an ambiguous dihedral restraint for the specified chi angle, assuming that the provided conformations represent (all) energetic minima.

References min(), numeric::nearest_angle_degrees(), and torsion_constraints_from_mean_sd().

Referenced by get_ligand_torsion_constraints().

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_dock.ResidueTorsionRestraints"  , basic::t_debug    )

static

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.grid_functions"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::RigidSearchMover::apply(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), grid_rotamer_trials(), grid_rotamer_trials_atr_rep(), grid_score(), grid_score_atr_rep(), ligand_dock_main(), protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol(), protocols::ligand_docking::InterfaceBuilderLoader::load_data(), protocols::ligand_docking::MoveMapBuilderLoader::load_data(), protocols::ligand_docking::LigandAreaLoader::load_data(), make_atr_rep_grid(), make_atr_rep_grid_without_ligands(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), print_buried_unsat_Hbonds(), rb_grid_rotamer_trials_atr_rep(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::ligand_docking::LigandDockProtocol::shear_min_protocol(), torsion_constraints_from_mean_sd(), and protocols::ligand_docking::ResidueTorsionRestraints::without_my_constraints().

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.LigandDockingLoaders"  )

static

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_functions"  )

static

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.main"  )

static

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.LigandBaseProtocol"  )

static

static thread_local basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.LigandDockProtocol"  )

static

static thread_local basic::Tracer protocols::ligand_docking::transform_tracer ( "protocols.ligand_docking.Transform"  )

static

Referenced by protocols::ligand_docking::Transform::apply(), and protocols::ligand_docking::Transform::transform_ligand().

static thread_local basic::Tracer protocols::ligand_docking::translate_tracer ( "protocols.ligand_docking.CompoundTranslate"  , basic::t_debug    )

static

Referenced by protocols::ligand_docking::Translate::gaussian_translate_ligand(), protocols::ligand_docking::Translate::translate_ligand(), and protocols::ligand_docking::Translate::uniform_translate_ligand().

static thread_local basic::Tracer protocols::ligand_docking::translate_tracer ( "protocols.ligand_docking.ligand_options.translate"  , basic::t_debug    )

static

static thread_local basic::Tracer protocols::ligand_docking::write_ligand_tracer ( "protocols.ligand_docking.WriteLigandMolFile"  )

static

Referenced by protocols::ligand_docking::WriteLigandMolFile::apply().