protocols::ligand_docking Namespace Reference

Namespaces
	ligand_options
	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	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	InterfaceScoreCalculator
class	InterfaceScoreCalculatorCreator
class	LigandDockMain
class	LigandArea
class	LigandBaseProtocol
	Shared functionality for protocols that dock ligands. More...
class	LigandDesign
class	LigandDesignCreator
class	InterfaceBuilderLoaderCreator
class	MoveMapBuilderLoaderCreator
class	LigandAreaLoaderCreator
class	InterfaceBuilderLoader
	A class for loading InterfaceBuilders into the XML parser's DataMap. More...
class	MoveMapBuilderLoader
	A class for loading MoveMapBuilders into the XML parser's DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder. More...
class	LigandAreaLoader
class	LigandDockProtocol
class	MinimizeBackbone
class	MinimizeBackboneCreator
class	MinimizeLigand
class	MolarMassFilter
class	MolarMassFilterCreator
class	MolecularMassFilter
class	MolecularMassFilterCreator
class	MoveMapBuilder
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...
struct	Rotate_info
struct	Ligand_info
class	Rotate
class	RotateCreator
class	Rotates
class	RotatesCreator
class	SlideTogether
class	SlideTogetherCreator
class	StartFrom
class	StartFromCreator
class	TetherLigand
struct	Transform_info
class	Transform
class	TransformCreator
struct	Translate_info
class	Translate
class	TranslateCreator
class	UnconstrainedTorsionsMover
	Juggles torsional constraints with packing or rotamer trials. More...

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

Enumerations
enum	Distribution { Uniform, Gaussian }
enum	MoveType { conformerMove, transformMove }

Functions
std::string	generate_unique_name (std::string)
static basic::Tracer	add_hydrogen_tracer ("protocols.ligand_docking.AddHydrogen", basic::t_debug)
static basic::Tracer	add_hydrogens_tracer ("protocols.ligand_docking.LigandDesign", basic::t_debug)
static basic::Tracer	atom_tracer ("protocols.ligand_docking.AtomCountFilter")
static basic::Tracer	atom_tracer ("protocols.ligand_docking.ChainExistsFilter")
static basic::Tracer	complete_connections_tracer ("protocols.ligand_docking.CompleteConnectionsFilter")
static basic::Tracer	translate_tracer ("protocols.ligand_docking.CompoundTranslate", basic::t_debug)
Distribution	get_distribution (std::string distribution_str)
static basic::Tracer	FinalMinimizer_tracer ("protocols.ligand_docking.ligand_options.FinalMinimizer", basic::t_debug)
static basic::Tracer	TR ("protocols.ligand_docking.grid_functions", basic::t_debug)
static numeric::random::RandomGenerator	my_RG (810329)
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::owning_ptr< core::grid::CartGrid< int > >grid, core::pose::Pose const &pose, core::Real const rep_rad)
utility::pointer::owning_ptr < core::grid::CartGrid< int > >	make_atr_rep_grid (core::pose::Pose const &pose, core::Vector const &center)
	this function assumes there is only one ligand so it only considers protein residues More...
utility::pointer::owning_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)
	this function assumes excludes one ligand from the grid More...
utility::pointer::owning_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 basic::Tracer	grow_ligand_tracer ("protocols.ligand_docking.GrowLigand", basic::t_debug)
static basic::Tracer	hbond_acceptor_tracer ("protocols.ligand_docking.HBondAcceptorFilter")
static basic::Tracer	hbond_donor_tracer ("protocols.ligand_docking.HBondDonorFilter")
static basic::Tracer	heavy_atom_tracer ("protocols.ligand_docking.HeavyAtomFilter")
static basic::Tracer	high_res_docker_tracer ("protocols.ligand_docking.ligand_options.Protocol", basic::t_debug)
static basic::Tracer	interface_builder_tracer ("protocols.ligand_docking.ligand_options.InterfaceBuilder", basic::t_debug)
static basic::Tracer	InterfaceScoreCalculator_tracer ("protocols.ligand_docking.ligand_options.InterfaceScoreCalculator", basic::t_debug)
basic::Tracer	TR ("protocols.ligand_docking.main")
static 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)
	append interface_delta scores More...
void	append_ligand_travel (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after)
	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)
void	append_radius_of_gyration (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before)
	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)
void	append_multi_residue_ligand_RMSD (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after)
void	append_automorphic_rmsd (core::Size ligand_residue_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after)
static basic::Tracer	ligand_scores_tracer ("protocols.ligand_docking.ligand_scores", basic::t_debug)
static basic::Tracer	ligand_area_tracer ("protocols.ligand_docking.ligand_options.LigandArea", basic::t_debug)
static basic::Tracer	TR ("protocols.ligand_docking.LigandBaseProtocol")
static numeric::random::RandomGenerator	my_RG (810323)
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 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 basic::Tracer	TR ("protocols.ligand_docking.LigandDockingLoaders")
static numeric::random::RandomGenerator	my_RG (4049988)
static 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 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 basic::Tracer	MinimizeLigand_tracer ("protocols.ligand_docking.MinimizeLigand", basic::t_debug)
static basic::Tracer	atom_tracer ("protocols.ligand_docking.MolarMassFilter")
static basic::Tracer	molecular_mass_tracer ("protocols.ligand_docking.MolecularMassFilter")
static 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 basic::Tracer	random_conformer_tracer ("protocols.ligand_docking.ligand_options.RandomConformers", basic::t_debug)
static basic::Tracer	TR ("protocols.ligand_dock.ResidueTorsionRestraints", basic::t_debug)
static 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 basic::Tracer	rotates_tracer ("protocols.ligand_docking.ligand_options.rotates", basic::t_debug)
static basic::Tracer	slide_together_tracer ("protocols.ligand_docking.ligand_options.slide_together")
static 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 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 numeric::random::RandomGenerator	RG (23459)
static basic::Tracer	transform_tracer ("protocols.ligand_docking.ligand_options.transform", basic::t_debug)
static basic::Tracer	translate_tracer ("protocols.ligand_docking.ligand_options.translate", basic::t_debug)

Typedef Documentation

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

Definition at line 27 of file AddHydrogen.fwd.hh.

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

Definition at line 25 of file AddHydrogen.fwd.hh.

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

Definition at line 27 of file AddHydrogens.fwd.hh.

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

Definition at line 25 of file AddHydrogens.fwd.hh.

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

Definition at line 26 of file FinalMinimizer.fwd.hh.

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

Definition at line 28 of file FinalMinimizer.fwd.hh.

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

Definition at line 24 of file FinalMinimizer.fwd.hh.

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

Definition at line 27 of file FinalMinimizer.fwd.hh.

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

Definition at line 27 of file GrowLigand.fwd.hh.

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

Definition at line 25 of file GrowLigand.fwd.hh.

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

Definition at line 26 of file HighResDocker.fwd.hh.

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

Definition at line 28 of file HighResDocker.fwd.hh.

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

Definition at line 24 of file HighResDocker.fwd.hh.

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

Definition at line 27 of file HighResDocker.fwd.hh.

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

Definition at line 27 of file InterfaceBuilder.fwd.hh.

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

Definition at line 29 of file InterfaceBuilder.fwd.hh.

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

Definition at line 24 of file InterfaceBuilder.fwd.hh.

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

Definition at line 28 of file InterfaceBuilder.fwd.hh.

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

Definition at line 26 of file InterfaceScoreCalculator.fwd.hh.

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

Definition at line 28 of file InterfaceScoreCalculator.fwd.hh.

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

Definition at line 24 of file InterfaceScoreCalculator.fwd.hh.

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

Definition at line 27 of file InterfaceScoreCalculator.fwd.hh.

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

Definition at line 28 of file LigandArea.fwd.hh.

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

Definition at line 30 of file LigandArea.fwd.hh.

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

Definition at line 25 of file LigandArea.fwd.hh.

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

Definition at line 29 of file LigandArea.fwd.hh.

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

Definition at line 32 of file LigandArea.fwd.hh.

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

Definition at line 79 of file LigandBaseProtocol.hh.

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

Definition at line 77 of file LigandBaseProtocol.hh.

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

Definition at line 27 of file LigandDesign.fwd.hh.

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

Definition at line 25 of file LigandDesign.fwd.hh.

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

Definition at line 159 of file ligand_dock_impl.cc.

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

Definition at line 27 of file LigandDockProtocol.fwd.hh.

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

Definition at line 25 of file LigandDockProtocol.fwd.hh.

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

Definition at line 26 of file MinimizeBackbone.fwd.hh.

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

Definition at line 28 of file MinimizeBackbone.fwd.hh.

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

Definition at line 24 of file MinimizeBackbone.fwd.hh.

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

Definition at line 27 of file MinimizeBackbone.fwd.hh.

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

Definition at line 26 of file MinimizeLigand.fwd.hh.

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

Definition at line 28 of file MinimizeLigand.fwd.hh.

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

Definition at line 24 of file MinimizeLigand.fwd.hh.

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

Definition at line 27 of file MinimizeLigand.fwd.hh.

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

Definition at line 26 of file MoveMapBuilder.fwd.hh.

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

Definition at line 28 of file MoveMapBuilder.fwd.hh.

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

Definition at line 24 of file MoveMapBuilder.fwd.hh.

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

Definition at line 27 of file MoveMapBuilder.fwd.hh.

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

Definition at line 27 of file RandomConformerMover.fwd.hh.

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

Definition at line 25 of file RandomConformerMover.fwd.hh.

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

Definition at line 25 of file ResidueTorsionRestraints.fwd.hh.

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

Definition at line 23 of file ResidueTorsionRestraints.fwd.hh.

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

Definition at line 27 of file RigidSearchMover.fwd.hh.

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

Definition at line 25 of file RigidSearchMover.fwd.hh.

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

Definition at line 26 of file Rotate.fwd.hh.

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

Definition at line 28 of file Rotate.fwd.hh.

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

Definition at line 24 of file Rotate.fwd.hh.

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

Definition at line 27 of file Rotate.fwd.hh.

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

Definition at line 26 of file Rotates.fwd.hh.

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

Definition at line 28 of file Rotates.fwd.hh.

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

Definition at line 24 of file Rotates.fwd.hh.

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

Definition at line 27 of file Rotates.fwd.hh.

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

Definition at line 21 of file StartFrom.fwd.hh.

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

Definition at line 26 of file TetherLigand.fwd.hh.

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

Definition at line 28 of file TetherLigand.fwd.hh.

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

Definition at line 24 of file TetherLigand.fwd.hh.

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

Definition at line 27 of file TetherLigand.fwd.hh.

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

Definition at line 26 of file Translate.fwd.hh.

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

Definition at line 28 of file Translate.fwd.hh.

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

Definition at line 24 of file Translate.fwd.hh.

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

Definition at line 27 of file Translate.fwd.hh.

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

Definition at line 26 of file UnconstrainedTorsionsMover.fwd.hh.

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

Definition at line 24 of file UnconstrainedTorsionsMover.fwd.hh.

Enumeration Type Documentation

enum protocols::ligand_docking::Distribution

Enumerator
Uniform
Gaussian

Definition at line 23 of file DistributionMap.hh.

enum protocols::ligand_docking::MoveType

Enumerator
conformerMove
transformMove

Definition at line 28 of file Transform.hh.

Function Documentation

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

static

static 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
	)

Definition at line 297 of file Rotate.cc.

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
	)

Definition at line 277 of file ligand_scores.cc.

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
	)

append interface_delta scores

Definition at line 64 of file ligand_scores.cc.

References protocols::rigid::RigidBodyTransMover::apply(), core::scoring::fa_rep, core::pose::get_chain_from_jump_id(), core::scoring::n_score_types, core::scoring::name_from_score_type(), 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_ligand_grid_scores	(	core::Size	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	after
	)

Definition at line 143 of file ligand_scores.cc.

References 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(), protocols::qsar::scoring_grid::GridManager::total_score(), core::scoring::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_RMSD	(	core::Size const	jump_id,
		protocols::jd2::JobOP	job,
		core::pose::Pose const &	before,
		core::pose::Pose const &	after
	)

Definition at line 211 of file ligand_scores.cc.

References append_automorphic_rmsd(), append_multi_residue_ligand_RMSD(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::sequence::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
	)

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

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

Definition at line 126 of file ligand_scores.cc.

References 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
	)

Definition at line 232 of file ligand_scores.cc.

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
	)

Calculate radius of gyration for downstream non-H atoms.

Ligands tend to bind in outstretched conformations...

Definition at line 179 of file ligand_scores.cc.

References 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
	)

Definition at line 310 of file Rotate.cc.

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

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

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

static

static basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.AtomCountFilter"  )

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 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
	)

Definition at line 342 of file Rotate.cc.

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

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.

Definition at line 333 of file Rotate.cc.

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 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().

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.

Definition at line 168 of file ligand_functions.cc.

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.

Definition at line 728 of file LigandDockProtocol.cc.

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

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

static 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
	)

Definition at line 421 of file MinimizeBackbone.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), 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
	)

Definition at line 398 of file MinimizeBackbone.cc.

References core::sequence::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
	)

Definition at line 192 of file LigandDesign.cc.

References core::sequence::end, 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.

Definition at line 273 of file LigandBaseProtocol.cc.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_hydrogen(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::chemical::AutomorphismIterator::next(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::type(), 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

)

Definition at line 126 of file AddHydrogen.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueTypeSet::has_name(), and core::chemical::ChemicalManager::nonconst_residue_type_set().

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

Distribution protocols::ligand_docking::get_distribution

(

std::string

distribution_str)

Definition at line 38 of file DistributionMap.cc.

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)

Definition at line 181 of file LigandDesign.cc.

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

Definition at line 190 of file ligand_functions.cc.

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.

Definition at line 127 of file ligand_functions.cc.

References core::conformation::Residue::clone(), 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

Definition at line 98 of file grid_functions.cc.

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.

Definition at line 112 of file grid_functions.cc.

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.

Definition at line 149 of file grid_functions.cc.

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.

Definition at line 44 of file grid_functions.cc.

References core::grid::CartGrid< T >::getValue(), core::grid::CartGrid< T >::is_in_grid(), core::conformation::Residue::nheavyatoms(), TR(), and core::conformation::Residue::xyz().

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.

Definition at line 63 of file grid_functions.cc.

References core::grid::CartGrid< T >::getValue(), core::grid::CartGrid< T >::is_in_grid(), core::conformation::Residue::nheavyatoms(), TR(), and core::conformation::Residue::xyz().

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.

Definition at line 139 of file grid_functions.hh.

References core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), and core::pack::interaction_graph::T().

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

Definition at line 140 of file LigandDesign.cc.

References has_incomplete_connections(), and passes_filters().

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

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

static

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

Definition at line 144 of file LigandDesign.cc.

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

Referenced by grow().

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

static

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

static

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

static

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

static

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

static

static 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::owning_ptr< core::grid::CartGrid< int > > protocols::ligand_docking::make_atr_rep_grid	(	core::pose::Pose const &	pose,
		core::Vector const &	center
	)

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

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

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

Definition at line 289 of file grid_functions.cc.

References 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::grid::CartGrid< T >::setBase(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

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

utility::pointer::owning_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
	)

this function assumes excludes one ligand from the grid

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.

Definition at line 340 of file grid_functions.cc.

References make_atr_rep_grid_without_ligands().

utility::pointer::owning_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.

Definition at line 353 of file grid_functions.cc.

References 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::grid::CartGrid< T >::setBase(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

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

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

static

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

static

static basic::Tracer protocols::ligand_docking::molecular_mass_tracer ( "protocols.ligand_docking.MolecularMassFilter"  )

static

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

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

Definition at line 279 of file StartFrom.cc.

References protocols::rigid::RigidBodyTransMover::apply(), protocols::geometry::downstream_centroid_by_jump(), protocols::rigid::RigidBodyTransMover::step_size(), and protocols::rigid::RigidBodyTransMover::trans_axis().

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

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

static

static numeric::random::RandomGenerator protocols::ligand_docking::my_RG ( 810329  )

static

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), rotamers_for_trials(), and protocols::ligand_docking::LigandDockProtocol::shear_min_protocol().

static numeric::random::RandomGenerator protocols::ligand_docking::my_RG ( 4049988  )

static

static numeric::random::RandomGenerator protocols::ligand_docking::my_RG ( 810323  )

static

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

Definition at line 158 of file LigandDesign.cc.

References 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?

Definition at line 740 of file LigandDockProtocol.cc.

References 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 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)

Definition at line 173 of file LigandDesign.cc.

References get_incomplete_connections().

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
	)

Definition at line 188 of file grid_functions.cc.

References core::sequence::end, 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.

Definition at line 83 of file grid_functions.cc.

References core::sequence::end, 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
	)

Definition at line 176 of file MinimizeBackbone.cc.

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

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
	)

Definition at line 90 of file TetherLigand.cc.

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
	)

Definition at line 447 of file MinimizeBackbone.cc.

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().

static numeric::random::RandomGenerator protocols::ligand_docking::RG ( 23459  )

static

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

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.

Definition at line 202 of file grid_functions.cc.

References core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), my_RG(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

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

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

static

static 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).

Definition at line 214 of file LigandBaseProtocol.cc.

References core::import_pose::atom_tree_diffs::AtomTreeDiff::sort_by().

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.

Definition at line 249 of file LigandBaseProtocol.cc.

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.

Definition at line 259 of file LigandBaseProtocol.cc.

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
	)

Definition at line 60 of file MoveMapBuilder.cc.

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::owning_ptr< core::grid::CartGrid< int > >	grid,
		core::pose::Pose const &	pose,
		core::Real const	rep_rad
	)

Definition at line 275 of file grid_functions.cc.

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.

Definition at line 246 of file grid_functions.cc.

References core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::gridpt(), and core::grid::CartGrid< T >::setValue().

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

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

static

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

static

static 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.

Definition at line 116 of file ligand_functions.cc.

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.

Definition at line 45 of file ligand_functions.cc.

References core::chemical::ResidueType::chi_atoms(), 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.

Definition at line 83 of file ligand_functions.cc.

References torsion_constraints_from_mean_sd().

Referenced by get_ligand_torsion_constraints().

static 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::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(), 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::LigandDockProtocol::shear_min_protocol(), and torsion_constraints_from_mean_sd().

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

static

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

static

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

static

basic::Tracer protocols::ligand_docking::TR

(

"protocols.ligand_docking.main"

)

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

static

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

static

static basic::Tracer protocols::ligand_docking::transform_tracer ( "protocols.ligand_docking.ligand_options.transform"  , basic::t_debug    )

static

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

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

static

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

static