Rosetta
Namespaces | Classes | Typedefs | Enumerations | Functions
protocols::ligand_docking Namespace Reference

Namespaces

 ga_ligand_dock
 
 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  HighResEnsemble
 
class  HighResEnsembleCreator
 
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 basic::datacache::DataMap. More...
 
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  LigandAreaLoader
 
class  LigandDockProtocol
 
class  MinimizeBackbone
 
class  MinimizeBackboneCreator
 
class  MinimizeLigand
 
class  MolarMassFilter
 
class  MolarMassFilterCreator
 
class  MolecularMassFilter
 
class  MolecularMassFilterCreator
 
class  MoveMapBuilder
 
struct  ProtLigPair_info
 
class  ProtLigEnsemble
 
class  ProtLigEnsembleCreator
 
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  TransformEnsemble_info
 
class  TransformEnsemble
 
class  TransformEnsembleCreator
 
struct  Translate_info
 
class  Translate
 
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
 
using CartGridIntOP = utility::pointer::shared_ptr< core::grid::CartGrid< int > >
 
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< HighResEnsemble > HighResEnsembleOP
 
typedef utility::pointer::shared_ptr< HighResEnsemble const > HighResEnsembleCOP
 
typedef utility::vector1< HighResEnsembleOP > HighResEnsembleOPs
 
typedef utility::vector1< HighResEnsembleCOP > HighResEnsembleCOPs
 
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
 
using LigandDockMainOP = utility::pointer::shared_ptr< LigandDockMain >
 
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< ProtLigEnsemble > ProtLigEnsembleOP
 
typedef utility::pointer::shared_ptr< ProtLigEnsemble const > ProtLigEnsembleCOP
 
typedef utility::vector1< ProtLigEnsembleOP > ProtLigEnsembleOPs
 
typedef utility::vector1< ProtLigEnsembleCOP > ProtLigEnsembleCOPs
 
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 basic::Tracer add_hydrogens_tracer ("protocols.ligand_docking.LigandDesign", basic::t_debug)
 
static basic::Tracer atom_tracer ("protocols.ligand_docking.AtOOomCountFilter")
 
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)
 
static basic::Tracer compute_rdf_tracer ("protocols.ligand_docking.ComputeLigandRDF")
 
Distribution get_distribution (std::string distribution_str)
 
static basic::Tracer TR ("protocols.ligand_docking.ligand_options.FinalMinimizer")
 
static 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, core::pack::task::PackerTask const &packertask, 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, core::pack::task::PackerTask const &packertask)
 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, core::pack::task::PackerTask const &packertask)
 
void rotamers_for_trials (core::pose::Pose &pose, core::Size rsd_no, utility::vector1< core::conformation::ResidueOP > &conformers_out, core::pack::task::PackerTask const &packertask)
 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)
 @detail this function assumes there is only one ligand so it only considers protein residues 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)
 @detail this function assumes excludes one ligand from the grid 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 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 TR ("protocols.ligand_docking.ligand_options.Protocol")
 
static basic::Tracer high_res_docker_tracer ("protocols.ligand_docking.ligand_options.Protocol", basic::t_debug)
 
void vector_to_rank (utility::vector1< std::pair< core::Size, core::Real > > &vector)
 
core::Real spearman (utility::vector1< std::pair< core::Size, core::Real > > vector_exp, utility::vector1< std::pair< core::Size, core::Real > > vector_rosetta)
 
bool sort_by_second (std::pair< core::Size, core::Real > left_lig, std::pair< core::Size, core::Real > right_lig)
 
static basic::Tracer interface_builder_tracer ("protocols.ligand_docking.ligand_options.InterfaceBuilder", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.ligand_options.InterfaceScoreCalculator")
 
static 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...
 
static basic::Tracer TR ("protocols.ligand_docking.ligand_scores")
 
std::map< std::string, core::Real > get_interface_deltas (char chain, core::pose::Pose const &after, const core::scoring::ScoreFunctionOP scorefxn, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function, bool score_in_mem)
 
void output_interface_deltas (std::map< std::string, core::Real > &score_map, char chain, const core::scoring::ScoreFunctionOP scorefxn, core::scoring::EnergyMap const &together_energies, core::scoring::EnergyMap const &separated_energies, utility::vector1< core::conformation::ResidueCOP > const &residues, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
std::map< std::string, core::Real > get_ligand_travel (char chain, core::pose::Pose const &test_pose, core::pose::Pose const &ref_pose, std::string const &prefix="", bool use_ensemble_best=false)
 Another interesting metric – how far does the ligand centroid move? Large values indicate we're outside of the intended binding site. More...
 
core::Real get_ligand_travel_ensemble_best (core::pose::Pose const &test_pose, core::pose::Pose const &ref_pose, core::Size test_residue_id, utility::vector1< core::Size > const &ref_residue_ids)
 Another interesting metric – how far does the ligand centroid move? Returns the smallest distance from any of the residues in the reference structure. More...
 
std::map< std::string, core::Real > get_ligand_grid_scores (protocols::qsar::scoring_grid::GridSet const &grid_set_prototype, char chain, core::pose::Pose const &test_pose, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
std::map< std::string, core::Real > get_ligand_grid_scores (protocols::qsar::scoring_grid::GridSet const &grid_set_prototype, core::Size jump_id, core::pose::Pose const &test_pose, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
std::map< std::string, core::Real > get_ligand_grid_scores (protocols::qsar::scoring_grid::GridSet const &grid_set_prototype, utility::vector1< core::Size > const &test_resi, std::string const &chain, core::pose::Pose const &test_pose, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
std::map< std::string, core::Real > get_radius_of_gyration (char chain, core::pose::Pose const &test_pose, std::string const &prefix)
 Calculate radius of gyration for downstream non-H atoms. More...
 
std::map< std::string, core::Real > get_ligand_RMSDs (char chain, core::pose::Pose const &test_pose, core::pose::Pose const &ref_pose, std::string const &prefix, bool use_ensemble_best)
 
std::map< std::string, core::Real > get_automorphic_RMSDs (core::pose::Pose const &test_pose, core::pose::Pose const &ref_pose, core::Size test_residue_id, utility::vector1< core::Size > const &ref_residue_ids, std::string const &prefix)
 
std::map< std::string, core::Real > get_multi_residue_ligand_RMSDs (core::pose::Pose const &test_pose, core::pose::Pose const &ref_pose, utility::vector1< core::Size > const &test_residue_ids, utility::vector1< core::Size > const &ref_residue_ids, char chain, std::string const &prefix)
 
static basic::Tracer ligand_area_tracer ("protocols.ligand_docking.ligand_options.LigandArea", basic::t_debug)
 
static 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 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 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 TR ("protocols.ligand_docking.ligand_options.MinimizeBackbone")
 
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 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 TR ("protocols.ligand_docking.ligand_options.Protocol")
 
ProtLigPair_info process_line (std::string &line)
 
void info_to_rank (utility::vector1< ProtLigPair_info > &vector)
 
bool sort_by_binding (const ProtLigPair_info &left_pair, const ProtLigPair_info &right_pair)
 
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 TR ("protocols.ligand_docking.ligand_options.rotate")
 
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 TR ("protocols.ligand_docking.StartFrom")
 
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 basic::Tracer TR ("protocols.ligand_docking.Transform")
 
static basic::Tracer transform_tracer ("protocols.ligand_docking.TransformEnsemble", basic::t_debug)
 
static basic::Tracer translate_tracer ("protocols.ligand_docking.ligand_options.translate", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.util")
 
void move_ligand_to_desired_centroid (std::string const &chain, core::Vector const &desired_centroid, core::pose::Pose &pose)
 Move the center of specified chain to the desired_centroid. More...
 
void move_ligand_to_desired_centroid (utility::vector1< std::string > const &chains, core::Vector const &desired_centroid, core::pose::Pose &pose)
 Move the center of specified multiple chains to the desired_centroid. More...
 
void move_ligand_to_desired_centroid (core::Size const jump_id, core::Vector const &desired_centroid, core::pose::Pose &pose)
 Move the center of the object(s) downstream of jump_id to the desired_centroid. More...
 
void move_ligand_neighbor_to_desired_position (utility::vector1< std::string > const &chains, core::Vector const &desired_position, core::pose::Pose &pose)
 Move the neighbor atom of the specified multiple chains to the desired_position. More...
 
void move_ligand_neighbor_to_desired_position (std::string const &chain, core::Vector const &desired_position, core::pose::Pose &pose)
 Move the neighbor atom of the specified chain to the desired_position. More...
 
static basic::Tracer write_ligand_tracer ("protocols.ligand_docking.WriteLigandMolFile")
 

Typedef Documentation

◆ AddHydrogenCOP

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

◆ AddHydrogenOP

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

◆ AddHydrogensCOP

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

◆ AddHydrogensOP

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

◆ CartGridIntOP

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

◆ ComputeLigandRDFCOP

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

◆ ComputeLigandRDFOP

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

◆ FinalMinimizerCOP

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

◆ FinalMinimizerCOPs

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

◆ FinalMinimizerOP

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

◆ FinalMinimizerOPs

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

◆ GrowLigandCOP

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

◆ GrowLigandOP

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

◆ HighResDockerCOP

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

◆ HighResDockerCOPs

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

◆ HighResDockerOP

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

◆ HighResDockerOPs

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

◆ HighResEnsembleCOP

typedef utility::pointer::shared_ptr< HighResEnsemble const > protocols::ligand_docking::HighResEnsembleCOP

◆ HighResEnsembleCOPs

typedef utility::vector1<HighResEnsembleCOP> protocols::ligand_docking::HighResEnsembleCOPs

◆ HighResEnsembleOP

typedef utility::pointer::shared_ptr< HighResEnsemble > protocols::ligand_docking::HighResEnsembleOP

◆ HighResEnsembleOPs

typedef utility::vector1<HighResEnsembleOP> protocols::ligand_docking::HighResEnsembleOPs

◆ InterfaceBuilderCOP

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

◆ InterfaceBuilderCOPs

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

◆ InterfaceBuilderOP

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

◆ InterfaceBuilderOPs

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

◆ InterfaceScoreCalculatorCOP

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

◆ InterfaceScoreCalculatorCOPs

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

◆ InterfaceScoreCalculatorOP

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

◆ InterfaceScoreCalculatorOPs

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

◆ LigandAreaCOP

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

◆ LigandAreaCOPs

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

◆ LigandAreaOP

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

◆ LigandAreaOPs

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

◆ LigandAreas

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

◆ LigandBaseProtocolCOP

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

◆ LigandBaseProtocolOP

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

◆ LigandDesignCOP

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

◆ LigandDesignOP

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

◆ LigandDockMainOP

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

◆ LigandDockProtocolCOP

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

◆ LigandDockProtocolOP

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

◆ MinimizeBackboneCOP

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

◆ MinimizeBackboneCOPs

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

◆ MinimizeBackboneOP

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

◆ MinimizeBackboneOPs

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

◆ MinimizeLigandCOP

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

◆ MinimizeLigandCOPs

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

◆ MinimizeLigandOP

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

◆ MinimizeLigandOPs

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

◆ MoveMapBuilderCOP

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

◆ MoveMapBuilderCOPs

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

◆ MoveMapBuilderOP

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

◆ MoveMapBuilderOPs

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

◆ ProtLigEnsembleCOP

typedef utility::pointer::shared_ptr< ProtLigEnsemble const > protocols::ligand_docking::ProtLigEnsembleCOP

◆ ProtLigEnsembleCOPs

typedef utility::vector1<ProtLigEnsembleCOP> protocols::ligand_docking::ProtLigEnsembleCOPs

◆ ProtLigEnsembleOP

typedef utility::pointer::shared_ptr< ProtLigEnsemble > protocols::ligand_docking::ProtLigEnsembleOP

◆ ProtLigEnsembleOPs

typedef utility::vector1<ProtLigEnsembleOP> protocols::ligand_docking::ProtLigEnsembleOPs

◆ RandomConformerMoverCOP

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

◆ RandomConformerMoverOP

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

◆ ResidueTorsionRestraintsCOP

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

◆ ResidueTorsionRestraintsOP

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

◆ RigidSearchMoverCOP

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

◆ RigidSearchMoverOP

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

◆ RotateCOP

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

◆ RotateCOPs

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

◆ RotateOP

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

◆ RotateOPs

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

◆ RotatesCOP

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

◆ RotatesCOPs

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

◆ RotatesOP

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

◆ RotatesOPs

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

◆ StartFromOP

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

◆ TetherLigandCOP

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

◆ TetherLigandCOPs

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

◆ TetherLigandOP

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

◆ TetherLigandOPs

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

◆ TranslateCOP

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

◆ TranslateCOPs

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

◆ TranslateOP

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

◆ TranslateOPs

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

◆ UnconstrainedTorsionsMoverCOP

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

◆ UnconstrainedTorsionsMoverOP

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

◆ WriteLigandMolFileOP

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

Enumeration Type Documentation

◆ Distribution

enum protocols::ligand_docking::Distribution
Enumerator
Uniform 
Gaussian 

Function Documentation

◆ add_hydrogens_tracer()

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

◆ add_ligand_conditionally()

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().

◆ apply_rotate()

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::conformation::membrane::center, and core::pose::Pose::update_actcoords().

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

◆ atom_tracer() [1/3]

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

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

◆ atom_tracer() [2/3]

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

◆ atom_tracer() [3/3]

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

◆ check_RMSD()

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(), core::scoring::is_ligand_heavyatom_residues(), protocols::sewing::data_storage::ligand, core::scoring::rms, and core::scoring::rmsd_no_super().

Referenced by add_ligand_conditionally().

◆ check_score()

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

Convenience Functions for use with Rotate.

References protocols::sewing::data_storage::ligand.

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

◆ complete_connections_tracer()

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

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

◆ compute_rdf_tracer()

static 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().

◆ constrain_ligand_torsions()

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::ResidueTypeBase::is_polymer(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

◆ count_buried_unsat_Hbonds()

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(), and protocols::hybridization::val.

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

◆ find_attach_pt()

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

References 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().

◆ find_peptide_attach_pt()

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 core::sequence::end, protocols::loops::start, and protocols::loops::stop.

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

◆ find_unconnected_residues()

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

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

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

◆ frac_atoms_within()

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(), core::chemical::ResidueTypeBase::name3(), 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().

◆ generate_unique_name()

std::string protocols::ligand_docking::generate_unique_name ( std::string  )

References core::pose::motif::a(), protocols::match::upstream::b, core::chemical::FA_STANDARD, and core::chemical::ChemicalManager::residue_type_set().

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

◆ get_automorphic_RMSDs()

std::map< std::string, core::Real > protocols::ligand_docking::get_automorphic_RMSDs ( core::pose::Pose const &  test_pose,
core::pose::Pose const &  ref_pose,
core::Size  test_residue_id,
utility::vector1< core::Size > const &  ref_residue_ids,
std::string const &  prefix 
)

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

Referenced by get_ligand_RMSDs().

◆ get_distribution()

Distribution protocols::ligand_docking::get_distribution ( std::string  distribution_str)

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

◆ get_incomplete_connections()

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().

◆ get_interface_deltas()

std::map< std::string, core::Real > protocols::ligand_docking::get_interface_deltas ( char  chain,
core::pose::Pose const &  after,
const core::scoring::ScoreFunctionOP  scorefxn,
std::string const &  prefix,
protocols::qsar::scoring_grid::ScoreNormalizationOP  normalization_function,
bool  score_in_mem 
)

References protocols::rigid::RigidBodyTransMover::apply(), core::select::residue_selector::ChainSelector::apply(), core::scoring::fa_rep, core::kinematics::get_foldtree_which_partitions(), core::kinematics::jump_which_partitions(), output_interface_deltas(), protocols::rigid::RigidBodyTransMover::step_size(), protocols::kinmatch::str(), TR(), and protocols::rigid::RigidBodyTransMover::trans_axis().

Referenced by protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), LigandDiscoverySearch::discover(), and protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores().

◆ get_ligand_grid_scores() [1/3]

std::map< std::string, core::Real > protocols::ligand_docking::get_ligand_grid_scores ( protocols::qsar::scoring_grid::GridSet const &  grid_set_prototype,
char  chain,
core::pose::Pose const &  test_pose,
std::string const &  prefix = "",
protocols::qsar::scoring_grid::ScoreNormalizationOP  normalization_function = nullptr 
)

normalizaton_function will only be used if the Grids do not have their own normalization

References core::pose::get_resnums_for_chain(), and core::id::to_string().

Referenced by protocols::ligand_docking::TransformEnsemble::apply(), protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores(), and get_ligand_grid_scores().

◆ get_ligand_grid_scores() [2/3]

std::map< std::string, core::Real > protocols::ligand_docking::get_ligand_grid_scores ( protocols::qsar::scoring_grid::GridSet const &  grid_set_prototype,
core::Size  jump_id,
core::pose::Pose const &  test_pose,
std::string const &  prefix = "",
protocols::qsar::scoring_grid::ScoreNormalizationOP  normalization_function = nullptr 
)

normalizaton_function will only be used if the Grids do not have their own normalization

References core::pose::Pose::fold_tree(), core::pose::get_chain_from_jump_id(), get_ligand_grid_scores(), core::pose::Pose::num_jump(), core::kinematics::residues_downstream_of_jump(), and core::id::to_string().

◆ get_ligand_grid_scores() [3/3]

std::map< std::string, core::Real > protocols::ligand_docking::get_ligand_grid_scores ( protocols::qsar::scoring_grid::GridSet const &  grid_set_prototype,
utility::vector1< core::Size > const &  residues,
std::string const &  chain_label,
core::pose::Pose const &  test_pose,
std::string const &  prefix,
protocols::qsar::scoring_grid::ScoreNormalizationOP  normalization_function 
)

normalizaton_function will only be used if the Grids do not have their own normalization

References core::pose::all_atom_center(), core::conformation::membrane::center, core::conformation::Residue::get_self_ptr(), grid_score(), core::pose::Pose::residue(), protocols::qsar::scoring_grid::GridSet::size(), core::scoring::total_score, and TR().

◆ get_ligand_RMSDs()

std::map< std::string, core::Real > protocols::ligand_docking::get_ligand_RMSDs ( char  chain,
core::pose::Pose const &  test_pose,
core::pose::Pose const &  ref_pose,
std::string const &  prefix,
bool  use_ensemble_best 
)

References get_automorphic_RMSDs(), get_multi_residue_ligand_RMSDs(), core::pose::get_resnums_for_chain(), and TR().

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

◆ get_ligand_seqpos()

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::size().

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

◆ get_ligand_torsion_constraints()

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::chemical::ResidueType::chi_rotamers(), core::conformation::Residue::clone(), core::pack::task::TaskFactory::create_packer_task(), core::chemical::ResidueType::nchi(), 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().

◆ get_ligand_travel()

std::map< std::string, core::Real > protocols::ligand_docking::get_ligand_travel ( char  chain,
core::pose::Pose const &  test_pose,
core::pose::Pose const &  ref_pose,
std::string const &  prefix,
bool  use_ensemble_best 
)

Another interesting metric – how far does the ligand centroid move? Large values indicate we're outside of the intended binding site.

References core::pose::all_atom_center(), get_ligand_travel_ensemble_best(), core::pose::get_resnums_for_chain(), and core::id::to_string().

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

◆ get_ligand_travel_ensemble_best()

core::Real protocols::ligand_docking::get_ligand_travel_ensemble_best ( core::pose::Pose const &  test_pose,
core::pose::Pose const &  ref_pose,
core::Size  test_residue_id,
utility::vector1< core::Size > const &  ref_residue_ids 
)

Another interesting metric – how far does the ligand centroid move? Returns the smallest distance from any of the residues in the reference structure.

References core::conformation::all_atom_center(), and core::pose::Pose::residue().

Referenced by get_ligand_travel().

◆ get_multi_residue_ligand_RMSDs()

std::map< std::string, core::Real > protocols::ligand_docking::get_multi_residue_ligand_RMSDs ( core::pose::Pose const &  test_pose,
core::pose::Pose const &  ref_pose,
utility::vector1< core::Size > const &  test_residue_ids,
utility::vector1< core::Size > const &  ref_residue_ids,
char  chain,
std::string const &  prefix 
)

References core::scoring::is_ligand_heavyatom(), core::scoring::rmsd_no_super(), and core::scoring::rmsd_with_super().

Referenced by get_ligand_RMSDs().

◆ get_radius_of_gyration()

std::map< std::string, core::Real > protocols::ligand_docking::get_radius_of_gyration ( char  chain,
core::pose::Pose const &  test_pose,
std::string const &  prefix 
)

Calculate radius of gyration for downstream non-H atoms.

Ligands tend to bind in outstretched conformations...

References core::pose::all_atom_center(), core::pose::get_resnums_for_chain(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::id::to_string(), and core::conformation::Residue::xyz().

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

◆ get_rb_atr_and_rep_scores()

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 core::sequence::end, and rb_grid_score_atr_rep().

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

◆ grid_rotamer_trials()

void protocols::ligand_docking::grid_rotamer_trials ( core::grid::CartGrid< int > const &  grid,
core::pose::Pose &  pose,
core::Size  rsd_no,
core::pack::task::PackerTask const &  packertask,
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().

◆ grid_rotamer_trials_atr_rep()

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

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().

◆ grid_score()

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

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

◆ grid_score_atr_rep()

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

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

◆ grid_to_kin()

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< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::getValue(), and core::conformation::membrane::out.

◆ grow()

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

References core::sequence::end, has_incomplete_connections(), passes_filters(), and protocols::loops::start.

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

◆ grow_ligand_tracer()

static 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(), and protocols::ligand_docking::GrowLigand::set_fragments().

◆ has_incomplete_connections()

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

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

Referenced by grow().

◆ hbond_acceptor_tracer()

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

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

◆ hbond_donor_tracer()

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

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

◆ heavy_atom_tracer()

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

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

◆ high_res_docker_tracer()

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

◆ info_to_rank()

void protocols::ligand_docking::info_to_rank ( utility::vector1< ProtLigPair_info > &  vector)

Referenced by protocols::ligand_docking::ProtLigEnsemble::read_qsar_file().

◆ interface_builder_tracer()

static 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().

◆ ligand_area_tracer()

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

◆ ligand_design_tracer()

static 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(), passes_filters(), and protocols::ligand_docking::LigandDesign::set_fragments().

◆ make_atr_rep_grid()

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

@detail 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.

References core::pose::motif::a(), core::conformation::membrane::center, 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::size(), TR(), and core::conformation::Residue::xyz().

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

◆ make_atr_rep_grid_without_ligand()

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 
)

@detail 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.

References core::conformation::membrane::center, and make_atr_rep_grid_without_ligands().

◆ 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 core::pose::motif::a(), core::conformation::membrane::center, 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::size(), TR(), and core::conformation::Residue::xyz().

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

◆ mass_tracer()

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

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

◆ MinimizeLigand_tracer()

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

◆ move_ligand_neighbor_to_desired_position() [1/2]

void protocols::ligand_docking::move_ligand_neighbor_to_desired_position ( std::string const &  chain,
core::Vector const &  desired_position,
core::pose::Pose &  pose 
)

Move the neighbor atom of the specified chain to the desired_position.

References protocols::rigid::RigidBodyTransMover::apply(), core::pose::get_chain_id_from_chain(), core::pose::get_chain_residues(), core::pose::get_jump_id_from_chain(), protocols::rigid::RigidBodyTransMover::step_size(), TR(), and protocols::rigid::RigidBodyTransMover::trans_axis().

◆ move_ligand_neighbor_to_desired_position() [2/2]

void protocols::ligand_docking::move_ligand_neighbor_to_desired_position ( utility::vector1< std::string > const &  chains,
core::Vector const &  desired_position,
core::pose::Pose &  pose 
)

Move the neighbor atom of the specified multiple chains to the desired_position.

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

◆ move_ligand_to_desired_centroid() [1/3]

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

Move the center of the object(s) downstream of jump_id to the desired_centroid.

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

◆ move_ligand_to_desired_centroid() [2/3]

void protocols::ligand_docking::move_ligand_to_desired_centroid ( std::string const &  chain,
core::Vector const &  desired_centroid,
core::pose::Pose &  pose 
)

Move the center of specified chain to the desired_centroid.

References core::pose::get_jump_id_from_chain().

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

◆ move_ligand_to_desired_centroid() [3/3]

void protocols::ligand_docking::move_ligand_to_desired_centroid ( utility::vector1< std::string > const &  chains,
core::Vector const &  desired_centroid,
core::pose::Pose &  pose 
)

Move the center of specified multiple chains to the desired_centroid.

References protocols::rigid::RigidBodyTransMover::apply(), protocols::geometry::centroid_by_chains(), protocols::rigid::RigidBodyMover::freeze(), core::pose::get_chain_ids_from_chain(), core::pose::get_jump_id_from_chain_id(), protocols::rigid::RigidBodyMover::rb_jump(), protocols::rigid::RigidBodyTransMover::step_size(), TR(), and protocols::rigid::RigidBodyTransMover::trans_axis().

◆ MoveMapBuilder_tracer()

static 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().

◆ output_interface_deltas()

void protocols::ligand_docking::output_interface_deltas ( std::map< std::string, core::Real > &  score_map,
char  chain,
const core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::EnergyMap const &  together_energies,
core::scoring::EnergyMap const &  separated_energies,
utility::vector1< core::conformation::ResidueCOP > const &  residues,
std::string const &  prefix,
protocols::qsar::scoring_grid::ScoreNormalizationOP  normalization_function 
)

References core::scoring::n_score_types, core::scoring::name_from_score_type(), and core::scoring::total_score.

Referenced by get_interface_deltas().

◆ passes_filters()

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

References core::sequence::end, ligand_design_tracer(), core::pose::num_chi_angles(), core::pose::num_heavy_atoms(), and protocols::loops::start.

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

◆ print_buried_unsat_Hbonds()

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

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

◆ process_line()

ProtLigPair_info protocols::ligand_docking::process_line ( std::string &  line)

References protocols::ligand_docking::ProtLigPair_info::bind_data, protocols::ligand_docking::ProtLigPair_info::has_bind, protocols::ligand_docking::ProtLigPair_info::lig_chain, protocols::ligand_docking::ProtLigPair_info::mut_resid, protocols::ligand_docking::ProtLigPair_info::mut_target, TR(), and protocols::ligand_docking::ProtLigPair_info::wild_type.

Referenced by protocols::ligand_docking::ProtLigEnsemble::read_qsar_file().

◆ random_conformer_tracer()

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

◆ random_connection()

core::Size protocols::ligand_docking::random_connection ( core::conformation::ResidueCOP  residue)

References get_incomplete_connections(), and core::scoring::rg.

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

◆ rb_grid_rotamer_trials_atr_rep()

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,
core::pack::task::PackerTask const &  packertask 
)

References core::sequence::end, grid_rotamer_trials_atr_rep(), and TR().

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

◆ rb_grid_score_atr_rep()

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 core::sequence::end, grid_score_atr_rep(), and core::pose::Pose::residue().

Referenced by get_rb_atr_and_rep_scores().

◆ reorder_with_first_non_mobile_as_root()

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(), protocols::ligand_docking::ligand_options::InterfaceInfo::non_interface, core::pose::Pose::residue(), and core::pose::Pose::size().

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

◆ restrain_ligand_nbr_atom()

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::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::kinematics::AtomTree::root(), and tether_ligand_tracer().

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

◆ restrict_to_protein_residues()

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, core::pose::Pose::residue(), and protocols::moves::Mover::type().

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

◆ rotamers_for_trials()

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

Internal helper function for rotamer trials; fills conformers_out.

References core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_ptr(), core::scoring::rg, and TR().

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

◆ rotates_tracer()

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

◆ select_best_poses() [1/3]

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().

◆ select_best_poses() [2/3]

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().

◆ select_best_poses() [3/3]

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().

Referenced by select_best_poses().

◆ set_jumps()

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().

◆ set_repulsive_bb_cores()

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::size(), and core::conformation::Residue::xyz().

Referenced by make_atr_rep_grid(), and make_atr_rep_grid_without_ligands().

◆ set_sphere()

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::conformation::membrane::center, core::grid::CartGrid< T >::coords(), core::grid::CartGrid< T >::getNumberOfPoints(), core::grid::CartGrid< T >::gridpt(), protocols::mean_field::max(), protocols::mean_field::min(), and core::grid::CartGrid< T >::setValue().

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

◆ slide_together_tracer()

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

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

◆ sort_by_binding()

bool protocols::ligand_docking::sort_by_binding ( const ProtLigPair_info &  left_pair,
const ProtLigPair_info &  right_pair 
)

References protocols::ligand_docking::ProtLigPair_info::bind_data, and protocols::ligand_docking::ProtLigPair_info::has_bind.

Referenced by protocols::ligand_docking::ProtLigEnsemble::read_qsar_file().

◆ sort_by_second()

bool protocols::ligand_docking::sort_by_second ( std::pair< core::Size, core::Real >  left_lig,
std::pair< core::Size, core::Real >  right_lig 
)

Referenced by protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::HighResEnsemble::qsar_correlation(), and protocols::ligand_docking::ProtLigEnsemble::qsar_correlation().

◆ spearman()

core::Real protocols::ligand_docking::spearman ( utility::vector1< std::pair< core::Size, core::Real > >  vector_exp,
utility::vector1< std::pair< core::Size, core::Real > >  vector_rosetta 
)

Referenced by protocols::ligand_docking::HighResEnsemble::qsar_correlation(), and protocols::ligand_docking::ProtLigEnsemble::qsar_correlation().

◆ tether_ligand_tracer()

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().

◆ torsion_constraints_from_chi_rotamers()

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().

◆ torsion_constraints_from_mean_sd()

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(), and TR().

Referenced by torsion_constraints_from_chi_rotamers(), and torsion_constraints_from_rotamers().

◆ 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 protocols::mean_field::min(), and torsion_constraints_from_mean_sd().

Referenced by get_ligand_torsion_constraints().

◆ TR() [1/17]

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

◆ TR() [2/17]

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

◆ TR() [3/17]

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

◆ TR() [4/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.FinalMinimizer"  )
static

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::ligand_docking::FinalMinimizer::apply(), protocols::ligand_docking::HighResDocker::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::ligand_docking::MinimizeBackbone::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::ligand_docking::Rotate::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::Transform::check_conformers(), protocols::ligand_docking::Transform::convert_to_full_pose(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::ligand_docking::FinalMinimizer::get_final_min_mover(), get_interface_deltas(), protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores(), get_ligand_grid_scores(), get_ligand_RMSDs(), grid_rotamer_trials(), grid_rotamer_trials_atr_rep(), grid_score(), grid_score_atr_rep(), protocols::ligand_docking::HighResDocker::initialize_from_options(), protocols::ligand_docking::LigandBaseProtocol::initialize_scorefxns(), ligand_dock_main(), 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::HighResDocker::make_packer_task_from_vector(), move_ligand_neighbor_to_desired_position(), move_ligand_to_desired_centroid(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::ligand_docking::StartFrom::parse_my_tag(), protocols::ligand_docking::StartFrom::parse_pdb_file(), print_buried_unsat_Hbonds(), process_line(), protocols::ligand_docking::ProtLigEnsemble::qsar_correlation(), rb_grid_rotamer_trials_atr_rep(), protocols::ligand_docking::MinimizeBackbone::remove_cutpoints(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calphas(), rotamers_for_trials(), protocols::ligand_docking::Transform::score_ligand(), protocols::ligand_docking::Transform::setup_conformers(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::ligand_docking::LigandDockProtocol::shear_min_protocol(), torsion_constraints_from_mean_sd(), protocols::ligand_docking::Transform::transform_ligand(), and protocols::ligand_docking::ResidueTorsionRestraints::without_my_constraints().

◆ TR() [5/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.InterfaceScoreCalculator"  )
static

◆ TR() [6/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.MinimizeBackbone"  )
static

◆ TR() [7/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.Protocol"  )
static

◆ TR() [8/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.Protocol"  )
static

◆ TR() [9/17]

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.rotate"  )
static

◆ TR() [10/17]

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

◆ TR() [11/17]

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

◆ TR() [12/17]

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

◆ TR() [13/17]

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

◆ TR() [14/17]

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

◆ TR() [15/17]

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

◆ TR() [16/17]

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

◆ TR() [17/17]

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

◆ transform_tracer()

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

Referenced by protocols::ligand_docking::TransformEnsemble::apply(), protocols::ligand_docking::TransformEnsemble::change_conformer(), protocols::ligand_docking::TransformEnsemble::check_grid(), protocols::ligand_docking::TransformEnsemble::convert_to_full_pose(), protocols::ligand_docking::TransformEnsemble::monte_carlo(), protocols::ligand_docking::TransformEnsemble::print_xyz(), protocols::ligand_docking::TransformEnsemble::score_ligands(), and protocols::ligand_docking::TransformEnsemble::transform_ligand().

◆ translate_tracer() [1/2]

static 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().

◆ translate_tracer() [2/2]

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

◆ vector_to_rank()

void protocols::ligand_docking::vector_to_rank ( utility::vector1< std::pair< core::Size, core::Real > > &  vector)

Referenced by protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::HighResEnsemble::qsar_correlation(), and protocols::ligand_docking::ProtLigEnsemble::qsar_correlation().

◆ write_ligand_tracer()

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

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

Generated on Sat Mar 2 2024 12:18:37 for Rosetta by doxygen 1.9.1