Rosetta Protocols  2014.35
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
protocols::ligand_docking Namespace Reference

Namespaces

 ligand_options
 
 rdf
 
 scoring_grid
 

Classes

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

Typedefs

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

Enumerations

enum  Distribution { Uniform, Gaussian }
 

Functions

std::string generate_unique_name (std::string)
 
Distribution get_distribution (std::string distribution_str)
 
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, intget_rb_atr_and_rep_scores (core::grid::CartGrid< int > const &grid, core::pose::Pose const &pose, core::Size begin, core::Size end)
 a cleaner implementation of rb_grid_score_atr_rep More...
 
void grid_rotamer_trials (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no, int const min_score=0)
 Try all rotamers for the specified residue and install the first one that minimizes the grid score. Only tested with ligand residues w/ a conformer library. More...
 
void grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size rsd_no)
 Try all rotamers for the specified residue and install the first one that minimizes the repulsive score, breaking ties by the attractive score. Only tested with ligand residues w/ a conformer library. More...
 
void rb_grid_rotamer_trials_atr_rep (core::grid::CartGrid< int > const &grid, core::pose::Pose &pose, core::Size begin, core::Size end)
 
void rotamers_for_trials (core::pose::Pose &pose, core::Size rsd_no, utility::vector1< core::conformation::ResidueOP > &conformers_out)
 Internal helper function for rotamer trials; fills conformers_out. More...
 
void set_sphere (core::grid::CartGrid< int > &grid, core::Vector const &center, core::Real radius, int value)
 
void set_repulsive_bb_cores (utility::pointer::owning_ptr< core::grid::CartGrid< int > >grid, core::pose::Pose const &pose, core::Real const rep_rad)
 
utility::pointer::owning_ptr
< core::grid::CartGrid< int > > 
make_atr_rep_grid (core::pose::Pose const &pose, core::Vector const &center)
 Set the value for all grid boxes whose centers fall inside the sphere. More...
 
utility::pointer::owning_ptr
< core::grid::CartGrid< int > > 
make_atr_rep_grid_without_ligand (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
 Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude. More...
 
utility::pointer::owning_ptr
< core::grid::CartGrid< int > > 
make_atr_rep_grid_without_ligands (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
 Make a grid around the specified point with attractive (negative) and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude. More...
 
template<typename T >
void grid_to_kin (std::ostream &out, core::grid::CartGrid< T > const &grid, T min_val, T max_val, int stride)
 
basic::Tracer TR ("protocols.ligand_docking.main")
 
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...
 
void append_interface_deltas (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, const core::scoring::ScoreFunctionOP scorefxn, std::string const &prefix)
 append interface_delta scores More...
 
void append_interface_deltas (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, const core::scoring::ScoreFunctionOP scorefxn, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
void append_ligand_travel (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
 Another interesting metric – how far does the ligand centroid move? More...
 
void append_ligand_grid_scores (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, std::string const &prefix)
 
void append_ligand_grid_scores (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &after, std::string const &prefix, protocols::qsar::scoring_grid::ScoreNormalizationOP normalization_function)
 
void append_radius_of_gyration (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, std::string const &prefix)
 Calculate radius of gyration for downstream non-H atoms. More...
 
void append_ligand_RMSD (core::Size const jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
 
void append_multi_residue_ligand_RMSD (core::Size jump_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
 
void append_automorphic_rmsd (core::Size ligand_residue_id, protocols::jd2::JobOP job, core::pose::Pose const &before, core::pose::Pose const &after, std::string const &prefix)
 
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...
 
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)
 
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...
 
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)
 
void set_jumps (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap, LigandAreas ligand_areas)
 
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)
 
void move_ligand_to_desired_centroid (core::Size const jump_id, core::Vector const desired_centroid, core::pose::Pose &pose)
 
core::scoring::constraints::ConstraintCOP restrain_ligand_nbr_atom (core::Size const lig_id, core::Real const stddev_Angstroms, core::pose::Pose &pose)
 

Variables

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")
 
static basic::Tracer FinalMinimizer_tracer ("protocols.ligand_docking.ligand_options.FinalMinimizer", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.grid_functions", basic::t_debug)
 
static
numeric::random::RandomGenerator 
my_RG (810329)
 
static basic::Tracer grow_ligand_tracer ("protocols.ligand_docking.GrowLigand", basic::t_debug)
 
static basic::Tracer hbond_acceptor_tracer ("protocols.ligand_docking.HBondAcceptorFilter")
 
static basic::Tracer hbond_donor_tracer ("protocols.ligand_docking.HBondDonorFilter")
 
static basic::Tracer heavy_atom_tracer ("protocols.ligand_docking.HeavyAtomFilter")
 
static basic::Tracer high_res_docker_tracer ("protocols.ligand_docking.ligand_options.Protocol", basic::t_debug)
 
static basic::Tracer interface_builder_tracer ("protocols.ligand_docking.ligand_options.InterfaceBuilder", basic::t_debug)
 
static basic::Tracer InterfaceScoreCalculator_tracer ("protocols.ligand_docking.ligand_options.InterfaceScoreCalculator", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.ligand_functions")
 
static basic::Tracer ligand_scores_tracer ("protocols.ligand_docking.ligand_scores", basic::t_debug)
 
static basic::Tracer ligand_area_tracer ("protocols.ligand_docking.ligand_options.LigandArea", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.LigandBaseProtocol")
 
static
numeric::random::RandomGenerator 
my_RG (810323)
 
static basic::Tracer ligand_design_tracer ("protocols.ligand_docking.LigandDesign", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_docking.LigandDockingLoaders")
 
static
numeric::random::RandomGenerator 
my_RG (4049988)
 
static basic::Tracer TR ("protocols.ligand_docking.LigandDockProtocol")
 
static basic::Tracer minimize_backbone_tracer ("protocols.ligand_docking.ligand_options.MinimizeBackbone", basic::t_debug)
 
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)
 
static basic::Tracer random_conformer_tracer ("protocols.ligand_docking.ligand_options.RandomConformers", basic::t_debug)
 
static basic::Tracer TR ("protocols.ligand_dock.ResidueTorsionRestraints", basic::t_debug)
 
static basic::Tracer rotate_tracer ("protocols.ligand_docking.ligand_options.rotate", basic::t_debug)
 
static basic::Tracer rotates_tracer ("protocols.ligand_docking.ligand_options.rotates", basic::t_debug)
 
static basic::Tracer slide_together_tracer ("protocols.ligand_docking.ligand_options.slide_together")
 
static basic::Tracer start_from_tracer ("protocols.ligand_docking.ligand_options.Start_from", basic::t_debug)
 
static basic::Tracer tether_ligand_tracer ("protocols.ligand_docking.ligand_options.Tether_ligand", basic::t_debug)
 
static
numeric::random::RandomGenerator 
RG (23459)
 
static basic::Tracer transform_tracer ("protocols.ligand_docking.Transform")
 
static basic::Tracer translate_tracer ("protocols.ligand_docking.ligand_options.translate", basic::t_debug)
 
basic::Tracer write_ligand_tracer ("protocols.ligand_docking.WriteLigandMolFile")
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
Uniform 
Gaussian 

Function Documentation

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

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

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

References protocols::jd2::Job::add_string_real_pair(), centroid, numeric::xyzVector< class >::distance(), protocols::geometry::downstream_centroid_by_jump(), and core::pose::get_chain_from_jump_id().

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

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

Helper function to tame the PoseMetricCalculator madness.

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

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

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 
)
std::string protocols::ligand_docking::generate_unique_name ( std::string  )
Distribution protocols::ligand_docking::get_distribution ( std::string  distribution_str)
utility::vector1< core::Size > protocols::ligand_docking::get_incomplete_connections ( core::conformation::ResidueCOP  residue)
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(), option, core::pose::Pose::residue(), core::pose::Pose::residue_type(), rotamers_for_trials(), torsion_constraints_from_chi_rotamers(), and torsion_constraints_from_rotamers().

Referenced by constrain_ligand_torsions().

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

a cleaner implementation of rb_grid_score_atr_rep

References rb_grid_score_atr_rep().

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

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

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

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

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

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

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

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

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

int protocols::ligand_docking::grid_score ( core::grid::CartGrid< int > const &  grid,
core::conformation::Residue const &  rsd,
int  max_score 
)
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,
T  min_val,
T  max_val,
int  stride 
)
bool protocols::ligand_docking::grow ( core::pose::Pose  pose,
core::Size  start,
core::Size  end 
)
bool protocols::ligand_docking::has_incomplete_connections ( core::pose::Pose  pose,
core::Size  start,
core::Size const  end 
)
utility::pointer::owning_ptr< core::grid::CartGrid< int > > protocols::ligand_docking::make_atr_rep_grid ( core::pose::Pose const &  pose,
core::Vector const &  center 
)

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

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

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

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

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

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

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

this function assumes excludes one ligand from the grid

References make_atr_rep_grid_without_ligands().

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

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

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

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

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

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

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

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

Referenced by get_rb_atr_and_rep_scores().

void protocols::ligand_docking::reorder_with_first_non_mobile_as_root ( core::kinematics::FoldTreeOP  f,
ligand_options::Interface const &  interface,
core::pose::Pose pose 
)
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 
)
void protocols::ligand_docking::select_best_poses ( core::import_pose::atom_tree_diffs::ScoresPairList const &  scores_in,
core::import_pose::atom_tree_diffs::ScoresPairList scores_out,
core::Real  to_keep 
)

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

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

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

Referenced by select_best_poses().

void protocols::ligand_docking::select_best_poses ( core::import_pose::atom_tree_diffs::AtomTreeDiff const &  atdiff,
core::import_pose::atom_tree_diffs::ScoresPairList scores_out,
core::Real  to_keep 
)

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

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

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

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

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

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

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

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

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

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

Referenced by get_ligand_torsion_constraints().

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

Variable Documentation

basic::Tracer protocols::ligand_docking::add_hydrogen_tracer("protocols.ligand_docking.AddHydrogen", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::add_hydrogens_tracer("protocols.ligand_docking.LigandDesign", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::atom_tracer("protocols.ligand_docking.ChainExistsFilter")
static
basic::Tracer protocols::ligand_docking::atom_tracer("protocols.ligand_docking.AtOOomCountFilter")
static
basic::Tracer protocols::ligand_docking::atom_tracer("protocols.ligand_docking.MolarMassFilter")
static
basic::Tracer protocols::ligand_docking::complete_connections_tracer("protocols.ligand_docking.CompleteConnectionsFilter")
static
basic::Tracer protocols::ligand_docking::compute_rdf_tracer("protocols.ligand_docking.ComputeLigandRDF")
static
basic::Tracer protocols::ligand_docking::FinalMinimizer_tracer("protocols.ligand_docking.ligand_options.FinalMinimizer", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::grow_ligand_tracer("protocols.ligand_docking.GrowLigand", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::hbond_acceptor_tracer("protocols.ligand_docking.HBondAcceptorFilter")
static
basic::Tracer protocols::ligand_docking::hbond_donor_tracer("protocols.ligand_docking.HBondDonorFilter")
static
basic::Tracer protocols::ligand_docking::heavy_atom_tracer("protocols.ligand_docking.HeavyAtomFilter")
static
basic::Tracer protocols::ligand_docking::high_res_docker_tracer("protocols.ligand_docking.ligand_options.Protocol", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::interface_builder_tracer("protocols.ligand_docking.ligand_options.InterfaceBuilder", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::InterfaceScoreCalculator_tracer("protocols.ligand_docking.ligand_options.InterfaceScoreCalculator", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::ligand_area_tracer("protocols.ligand_docking.ligand_options.LigandArea", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::ligand_design_tracer("protocols.ligand_docking.LigandDesign", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::ligand_scores_tracer("protocols.ligand_docking.ligand_scores", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::mass_tracer("protocols.ligand_docking.MolecularMassFilter")
static
basic::Tracer protocols::ligand_docking::minimize_backbone_tracer("protocols.ligand_docking.ligand_options.MinimizeBackbone", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::MinimizeLigand_tracer("protocols.ligand_docking.MinimizeLigand", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::MoveMapBuilder_tracer("protocols.ligand_docking.ligand_options.MoveMapBuilder", basic::t_debug)
static
numeric::random::RandomGenerator protocols::ligand_docking::my_RG(810329)
static
numeric::random::RandomGenerator protocols::ligand_docking::my_RG(810323)
static
numeric::random::RandomGenerator protocols::ligand_docking::my_RG(4049988)
static
basic::Tracer protocols::ligand_docking::random_conformer_tracer("protocols.ligand_docking.ligand_options.RandomConformers", basic::t_debug)
static
numeric::random::RandomGenerator protocols::ligand_docking::RG(23459)
static
basic::Tracer protocols::ligand_docking::rotate_tracer("protocols.ligand_docking.ligand_options.rotate", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::rotates_tracer("protocols.ligand_docking.ligand_options.rotates", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::slide_together_tracer("protocols.ligand_docking.ligand_options.slide_together")
static
basic::Tracer protocols::ligand_docking::start_from_tracer("protocols.ligand_docking.ligand_options.Start_from", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::tether_ligand_tracer("protocols.ligand_docking.ligand_options.Tether_ligand", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_docking.main") ( "protocols.ligand_docking.grid_functions"  ,
basic::t_debug   
)
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_dock.ResidueTorsionRestraints", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_docking.LigandDockingLoaders")
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_docking.ligand_functions")
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_docking.LigandBaseProtocol")
static
basic::Tracer protocols::ligand_docking::TR("protocols.ligand_docking.LigandDockProtocol")
static
basic::Tracer protocols::ligand_docking::transform_tracer("protocols.ligand_docking.Transform")
static
basic::Tracer protocols::ligand_docking::translate_tracer("protocols.ligand_docking.CompoundTranslate", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::translate_tracer("protocols.ligand_docking.ligand_options.translate", basic::t_debug)
static
basic::Tracer protocols::ligand_docking::write_ligand_tracer("protocols.ligand_docking.WriteLigandMolFile")