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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  InterfaceBuilderLoader
 A class for loading InterfaceBuilders into the XML parser's basic::datacache::DataMap. More...
 
class  InterfaceBuilderLoaderCreator
 
class  InterfaceScoreCalculator
 
class  InterfaceScoreCalculatorCreator
 
struct  Ligand_info
 
class  LigandArea
 
class  LigandAreaLoader
 
class  LigandAreaLoaderCreator
 
class  LigandBaseProtocol
 Shared functionality for protocols that dock ligands. More...
 
class  LigandDesign
 
class  LigandDesignCreator
 
class  LigandDockMain
 
class  LigandDockProtocol
 
class  MinimizeBackbone
 
class  MinimizeBackboneCreator
 
class  MinimizeLigand
 
class  MolarMassFilter
 
class  MolarMassFilterCreator
 
class  MolecularMassFilter
 
class  MolecularMassFilterCreator
 
class  MoveMapBuilder
 
class  MoveMapBuilderLoader
 A class for loading MoveMapBuilders into the XML parser's basic::datacache::DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder. More...
 
class  MoveMapBuilderLoaderCreator
 
class  ProtLigEnsemble
 
class  ProtLigEnsembleCreator
 
struct  ProtLigPair_info
 
class  RandomConformerMover
 Replace the residue at the given position with a randomly selected conformer from its rotamer library. More...
 
class  RandomConformers
 
class  RandomConformersCreator
 
class  ResidueTorsionRestraints
 Manages harmonic restraints on torsions, so they can be turned off for packing. More...
 
class  RigidSearchMover
 An optimized mover for Monte Carlo trial of rigid body perturbations. More...
 
class  Rotate
 
struct  Rotate_info
 
class  RotateCreator
 
class  Rotates
 
class  RotatesCreator
 
class  SlideTogether
 
class  SlideTogetherCreator
 
class  StartFrom
 
class  StartFromCreator
 
class  TetherLigand
 
class  Transform
 
struct  Transform_info
 
class  TransformCreator
 
class  TransformEnsemble
 
struct  TransformEnsemble_info
 
class  TransformEnsembleCreator
 
class  Translate
 
struct  Translate_info
 
class  TranslateCreator
 
class  UnconstrainedTorsionsMover
 Juggles torsional constraints with packing or rotamer trials. More...
 
class  WriteLigandMolFile
 
class  WriteLigandMolFileCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AddHydrogen
AddHydrogenOP
 
typedef
utility::pointer::shared_ptr
< AddHydrogen const > 
AddHydrogenCOP
 
typedef
utility::pointer::shared_ptr
< AddHydrogens
AddHydrogensOP
 
typedef
utility::pointer::shared_ptr
< AddHydrogens const > 
AddHydrogensCOP
 
typedef
utility::pointer::shared_ptr
< ComputeLigandRDF
ComputeLigandRDFOP
 
typedef
utility::pointer::shared_ptr
< ComputeLigandRDF const > 
ComputeLigandRDFCOP
 
typedef
utility::pointer::shared_ptr
< FinalMinimizer
FinalMinimizerOP
 
typedef
utility::pointer::shared_ptr
< FinalMinimizer const > 
FinalMinimizerCOP
 
typedef utility::vector1
< FinalMinimizerOP
FinalMinimizerOPs
 
typedef utility::vector1
< FinalMinimizerCOP
FinalMinimizerCOPs
 
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_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.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)
 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)
 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::Sizeget_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::Realget_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::Realget_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::Realget_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::Realget_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::Realget_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::Realget_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::Realget_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::Realget_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::Realget_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::Sizeget_incomplete_connections (core::conformation::ResidueCOP residue)
 
utility::vector1< core::Sizefind_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

typedef utility::pointer::shared_ptr< AddHydrogen const > protocols::ligand_docking::AddHydrogenCOP
typedef utility::pointer::shared_ptr< AddHydrogen > protocols::ligand_docking::AddHydrogenOP
typedef utility::pointer::shared_ptr< AddHydrogens const > protocols::ligand_docking::AddHydrogensCOP
typedef utility::pointer::shared_ptr< AddHydrogens > protocols::ligand_docking::AddHydrogensOP
using protocols::ligand_docking::CartGridIntOP = typedef utility::pointer::shared_ptr<core::grid::CartGrid<int> >
typedef utility::pointer::shared_ptr< ComputeLigandRDF const > protocols::ligand_docking::ComputeLigandRDFCOP
typedef utility::pointer::shared_ptr< ComputeLigandRDF > protocols::ligand_docking::ComputeLigandRDFOP
typedef utility::pointer::shared_ptr< FinalMinimizer const > protocols::ligand_docking::FinalMinimizerCOP
typedef utility::pointer::shared_ptr< FinalMinimizer > protocols::ligand_docking::FinalMinimizerOP
typedef utility::pointer::shared_ptr< GrowLigand const > protocols::ligand_docking::GrowLigandCOP
typedef utility::pointer::shared_ptr< GrowLigand > protocols::ligand_docking::GrowLigandOP
typedef utility::pointer::shared_ptr< HighResDocker const > protocols::ligand_docking::HighResDockerCOP
typedef utility::pointer::shared_ptr< HighResDocker > protocols::ligand_docking::HighResDockerOP
typedef utility::pointer::shared_ptr< HighResEnsemble const > protocols::ligand_docking::HighResEnsembleCOP
typedef utility::pointer::shared_ptr< HighResEnsemble > protocols::ligand_docking::HighResEnsembleOP
typedef utility::pointer::shared_ptr< InterfaceBuilder const > protocols::ligand_docking::InterfaceBuilderCOP
typedef utility::pointer::shared_ptr< InterfaceBuilder > protocols::ligand_docking::InterfaceBuilderOP
typedef utility::pointer::shared_ptr< LigandArea const > protocols::ligand_docking::LigandAreaCOP
typedef utility::pointer::shared_ptr< LigandArea > protocols::ligand_docking::LigandAreaOP
typedef utility::pointer::shared_ptr< LigandBaseProtocol const > protocols::ligand_docking::LigandBaseProtocolCOP
typedef utility::pointer::shared_ptr< LigandDesign const > protocols::ligand_docking::LigandDesignCOP
typedef utility::pointer::shared_ptr< LigandDesign > protocols::ligand_docking::LigandDesignOP
using protocols::ligand_docking::LigandDockMainOP = typedef utility::pointer::shared_ptr<LigandDockMain>
typedef utility::pointer::shared_ptr< LigandDockProtocol const > protocols::ligand_docking::LigandDockProtocolCOP
typedef utility::pointer::shared_ptr< MinimizeBackbone const > protocols::ligand_docking::MinimizeBackboneCOP
typedef utility::pointer::shared_ptr< MinimizeBackbone > protocols::ligand_docking::MinimizeBackboneOP
typedef utility::pointer::shared_ptr< MinimizeLigand const > protocols::ligand_docking::MinimizeLigandCOP
typedef utility::pointer::shared_ptr< MinimizeLigand > protocols::ligand_docking::MinimizeLigandOP
typedef utility::pointer::shared_ptr< MoveMapBuilder const > protocols::ligand_docking::MoveMapBuilderCOP
typedef utility::pointer::shared_ptr< MoveMapBuilder > protocols::ligand_docking::MoveMapBuilderOP
typedef utility::pointer::shared_ptr< ProtLigEnsemble const > protocols::ligand_docking::ProtLigEnsembleCOP
typedef utility::pointer::shared_ptr< ProtLigEnsemble > protocols::ligand_docking::ProtLigEnsembleOP
typedef utility::pointer::shared_ptr< RandomConformerMover const > protocols::ligand_docking::RandomConformerMoverCOP
typedef utility::pointer::shared_ptr< RigidSearchMover const > protocols::ligand_docking::RigidSearchMoverCOP
typedef utility::pointer::shared_ptr< RigidSearchMover > protocols::ligand_docking::RigidSearchMoverOP
typedef utility::pointer::shared_ptr< Rotate const > protocols::ligand_docking::RotateCOP
typedef utility::pointer::shared_ptr< Rotate > protocols::ligand_docking::RotateOP
typedef utility::pointer::shared_ptr< Rotates const > protocols::ligand_docking::RotatesCOP
typedef utility::pointer::shared_ptr< Rotates > protocols::ligand_docking::RotatesOP
typedef utility::pointer::shared_ptr<StartFrom> protocols::ligand_docking::StartFromOP
typedef utility::pointer::shared_ptr< TetherLigand const > protocols::ligand_docking::TetherLigandCOP
typedef utility::pointer::shared_ptr< TetherLigand > protocols::ligand_docking::TetherLigandOP
typedef utility::pointer::shared_ptr< Translate const > protocols::ligand_docking::TranslateCOP
typedef utility::pointer::shared_ptr< Translate > protocols::ligand_docking::TranslateOP

Enumeration Type Documentation

Enumerator
Uniform 
Gaussian 

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 
)
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 
)
static basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.MolarMassFilter"  )
static
static basic::Tracer protocols::ligand_docking::atom_tracer ( "protocols.ligand_docking.AtOOomCountFilter"  )
static
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 
)
bool protocols::ligand_docking::check_score ( Ligand_info const &  ligand,
core::Size const  heavy_atom_number 
)
static basic::Tracer protocols::ligand_docking::complete_connections_tracer ( "protocols.ligand_docking.CompleteConnectionsFilter"  )
static
static basic::Tracer protocols::ligand_docking::compute_rdf_tracer ( "protocols.ligand_docking.ComputeLigandRDF"  )
static
void protocols::ligand_docking::constrain_ligand_torsions ( core::pose::Pose pose,
core::Real  stddev_degrees,
bool  constrain_all_torsions_equally 
)
core::Size protocols::ligand_docking::count_buried_unsat_Hbonds ( core::pose::Pose const &  pose)
core::Size protocols::ligand_docking::find_attach_pt ( core::Size const  jump_id,
ligand_options::Interface const &  interface,
core::pose::Pose const &  pose 
)
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 
)
utility::vector1< core::Size > protocols::ligand_docking::find_unconnected_residues ( core::pose::Pose const &  pose,
core::Size  start,
core::Size const  end 
)
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::ResidueType::natoms(), 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  )
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 
)
Distribution protocols::ligand_docking::get_distribution ( std::string  distribution_str)
utility::vector1< core::Size > protocols::ligand_docking::get_incomplete_connections ( core::conformation::ResidueCOP  residue)
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 
)
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 
)
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 
)
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 
)
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 
)
utility::vector1< core::Size > protocols::ligand_docking::get_ligand_seqpos ( core::pose::Pose const &  pose)
void protocols::ligand_docking::get_ligand_torsion_constraints ( core::pose::Pose pose,
core::Size  rsd_no,
core::Real  stddev_degrees,
utility::vector1< core::scoring::constraints::ConstraintOP > &  csts_out,
bool const  constrain_all_torsions_equally 
)

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

References core::conformation::Residue::clone(), core::pack::task::TaskFactory::create_packer_task(), 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::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().

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().

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 
)
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::pose::Pose::residue(), and core::id::to_string().

Referenced by protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_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 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,
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().

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().

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().

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 
)
template<typename T >
void protocols::ligand_docking::grid_to_kin ( std::ostream &  out,
core::grid::CartGrid< T > const &  grid,
min_val,
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(), and core::grid::CartGrid< T >::getValue().

bool protocols::ligand_docking::grow ( core::pose::Pose  pose,
core::Size  start,
core::Size  end 
)
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 
)
static basic::Tracer protocols::ligand_docking::hbond_acceptor_tracer ( "protocols.ligand_docking.HBondAcceptorFilter"  )
static
static basic::Tracer protocols::ligand_docking::hbond_donor_tracer ( "protocols.ligand_docking.HBondDonorFilter"  )
static
static basic::Tracer protocols::ligand_docking::heavy_atom_tracer ( "protocols.ligand_docking.HeavyAtomFilter"  )
static
static basic::Tracer protocols::ligand_docking::high_res_docker_tracer ( "protocols.ligand_docking.ligand_options.Protocol"  ,
basic::t_debug   
)
static
void protocols::ligand_docking::info_to_rank ( utility::vector1< ProtLigPair_info > &  vector)
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::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
utility::pointer::shared_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.

References core::pose::motif::a(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), set_repulsive_bb_cores(), set_sphere(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

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

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

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

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

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

void protocols::ligand_docking::move_ligand_to_desired_centroid ( utility::vector1< std::string > const &  chains,
core::Vector const &  desired_centroid,
core::pose::Pose pose 
)
void protocols::ligand_docking::move_ligand_to_desired_centroid ( core::Size const  jump_id,
core::Vector const &  desired_centroid,
core::pose::Pose pose 
)
static basic::Tracer protocols::ligand_docking::MoveMapBuilder_tracer ( "protocols.ligand_docking.ligand_options.MoveMapBuilder"  ,
basic::t_debug   
)
static
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 
)
bool protocols::ligand_docking::passes_filters ( core::pose::Pose const &  pose,
core::Size  start,
core::Size const  end 
)
void protocols::ligand_docking::print_buried_unsat_Hbonds ( core::pose::Pose const &  bound,
core::pose::Pose const &  unbound 
)
ProtLigPair_info protocols::ligand_docking::process_line ( std::string &  line)
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)
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 
)
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().

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

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.

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

void protocols::ligand_docking::select_best_poses ( core::import_pose::atom_tree_diffs::AtomTreeDiff const &  atdiff,
std::set< std::string > &  tags_out 
)

Convenience wrapper: selects the best ligand docking results from a silent file and appends their tags to the supplied set.

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

void protocols::ligand_docking::set_jumps ( core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  movemap,
LigandAreas  ligand_areas 
)
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 
)
void protocols::ligand_docking::set_sphere ( core::grid::CartGrid< int > &  grid,
core::Vector const &  center,
core::Real  radius,
int  value 
)

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

References core::grid::CartGrid< 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().

static basic::Tracer protocols::ligand_docking::slide_together_tracer ( "protocols.ligand_docking.ligand_options.slide_together"  )
static
bool protocols::ligand_docking::sort_by_binding ( const ProtLigPair_info &  left_pair,
const ProtLigPair_info &  right_pair 
)
bool protocols::ligand_docking::sort_by_second ( std::pair< core::Size, core::Real left_lig,
std::pair< core::Size, core::Real right_lig 
)
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 
)
static basic::Tracer protocols::ligand_docking::tether_ligand_tracer ( "protocols.ligand_docking.ligand_options.Tether_ligand"  ,
basic::t_debug   
)
static
core::scoring::constraints::ConstraintOP protocols::ligand_docking::torsion_constraints_from_chi_rotamers ( core::Size  rsd_no,
core::Size  chino,
core::chemical::ResidueType const &  rsdtype 
)

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

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

Referenced by get_ligand_torsion_constraints().

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

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.util"  )
static
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.grid_functions"  ,
basic::t_debug   
)
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_functions"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.InterfaceScoreCalculator"  )
static
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::RigidSearchMover::apply(), protocols::ligand_docking::FinalMinimizer::apply(), protocols::ligand_docking::MinimizeBackbone::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::HighResDocker::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::Rotate::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(), ligand_dock_main(), protocols::ligand_docking::LigandBaseProtocol::LigandBaseProtocol(), protocols::ligand_docking::InterfaceBuilderLoader::load_data(), protocols::ligand_docking::MoveMapBuilderLoader::load_data(), protocols::ligand_docking::LigandAreaLoader::load_data(), make_atr_rep_grid(), make_atr_rep_grid_without_ligands(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), move_ligand_neighbor_to_desired_position(), 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::MinimizeBackbone::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::LigandBaseProtocol::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().

static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.main"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.rotate"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_scores"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.MinimizeBackbone"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.StartFrom"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.Transform"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.Protocol"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.LigandDockProtocol"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.LigandBaseProtocol"  )
static
static basic::Tracer protocols::ligand_docking::TR ( "protocols.ligand_docking.ligand_options.Protocol"  )
static
static basic::Tracer protocols::ligand_docking::transform_tracer ( "protocols.ligand_docking.TransformEnsemble"  ,
basic::t_debug   
)
static
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
void protocols::ligand_docking::vector_to_rank ( utility::vector1< std::pair< core::Size, core::Real > > &  vector)
static basic::Tracer protocols::ligand_docking::write_ligand_tracer ( "protocols.ligand_docking.WriteLigandMolFile"  )
static