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protocols::ligand_docking::ga_ligand_dock Namespace Reference

Classes

struct  atmInfo
 
class  AtomProperties
 the atom properties important in constraint generation More...
 
struct  ChiInfo
 
class  ConstraintInfo
 Constraint information about AtomProperties and/or Pharmacophores. More...
 
class  EntropyEstimator
 Estimates entropy change by ligand binding using short MC simulation. More...
 
struct  GADockStageParams
 represent options for a single "phase" of ligand docking More...
 
class  GALigandDock
 Ligand Docking protocol using Genetic Algorithm. More...
 
class  GALigandDockCreator
 
class  GAOptimizer
 Genetic Algorithm Optimizer called by GALigandDock. More...
 
class  GriddedAtomTreeMultifunc
 Atom tree multifunction class. More...
 
class  GridHash3D
 
class  GridScorer
 Grid representation of scorefunction. More...
 
struct  hbAcc
 
struct  hbDon
 
class  LigandAligner
 Aligns ligand using defined constraint information. More...
 
class  LigandConformer
 Gene representation of ligand & flexible sidechains in receptor. More...
 
class  OutputStructureStore
 helper class to manage multiple outputs More...
 
class  Pharmacophore
 Pharmacophore (aka binding-motif) definition. More...
 
struct  PlaceableRotamer
 
class  ReweightableRepEnergy
 Rotamer data used for packing in GALigandDock. More...
 
class  RotamerPairEnergies
 
struct  StructInfo
 
class  StructInfoComp
 

Typedefs

typedef
utility::pointer::shared_ptr
< GALigandDock
GALigandDockOP
 
typedef
utility::pointer::shared_ptr
< GALigandDock const > 
GALigandDockCOP
 
typedef
utility::pointer::shared_ptr
< GAOptimizer
GAOptimizerOP
 
typedef
utility::pointer::shared_ptr
< GAOptimizer const > 
GAOptimizerCOP
 
typedef
utility::pointer::shared_ptr
< GridScorer
GridScorerOP
 
typedef
utility::pointer::shared_ptr
< GridScorer const > 
GridScorerCOP
 
typedef
utility::pointer::shared_ptr
< LigandAligner
LigandAlignerOP
 
typedef
utility::pointer::shared_ptr
< LigandAligner const > 
LigandAlignerCOP
 
typedef utility::vector1
< LigandConformer
LigandConformers
 
typedef utility::vector1
< PlaceableRotamer
PlaceableRotamers
 

Functions

static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.EntropyEstimator")
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.GALigandDock")
 
std::string gadock_subelement_ct_name (std::string const &name)
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.GAOptimizer")
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.GriddedAtomTreeMultifunc")
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.GridScorer")
 
core::Real ipow (core::Real base, core::Size exp)
 
core::Real xform_rep (core::Real rep)
 
core::Real ixform_rep (core::Real xfrep)
 
core::Real dxform_rep (core::Real xfrep)
 
core::Real xform_atr (core::Real atr)
 
core::Real ixform_atr (core::Real xfatr)
 
core::Real dxform_atr (core::Real)
 
core::Real get_hbond_score_weighted (core::scoring::ScoreFunctionOP sf, core::scoring::hbonds::HBondDatabaseCOP database, core::scoring::hbonds::HBondOptions const &hbopt, core::scoring::hbonds::HBEvalTuple const &hbt, numeric::xyzVector< core::Real > const &D, numeric::xyzVector< core::Real > const &H, numeric::xyzVector< core::Real > const &A, numeric::xyzVector< core::Real > const &B, numeric::xyzVector< core::Real > const &B_0)
 
static basic::Tracer TR ("ligand_align")
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.LigandConformer")
 
LigandConformer mutate (LigandConformer const &l)
 
LigandConformer crossover (LigandConformer const &l1, LigandConformer const &l2)
 
LigandConformer crossover_ft (LigandConformer const &l1, LigandConformer const &l2)
 
core::Real distance_slow (LigandConformer const &gene1, LigandConformer const &gene2)
 
core::Real distance_fast (LigandConformer &gene1, LigandConformer &gene2)
 
std::pair< core::Real, core::Realdistance_internal (LigandConformer const &gene1, LigandConformer const &gene2)
 
static basic::Tracer TS ("protocols.ligand_docking.GALigandDock.RotamerData")
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock")
 
core::Size count_neighbors_on_coord (core::pose::Pose const &pose, core::Vector const &xyz1, std::string const atomname, core::Real const dcut)
 
utility::vector1< core::Sizecount_neighbors (core::pose::Pose const &pose, std::string const atomname, core::Real const dcut)
 
utility::vector1< core::Sizeget_atomic_contacting_sidechains (core::pose::Pose const &pose, core::Size const ligid, core::Real const atomic_distance_cut)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< GALigandDock const > protocols::ligand_docking::ga_ligand_dock::GALigandDockCOP
typedef utility::pointer::shared_ptr< GAOptimizer const > protocols::ligand_docking::ga_ligand_dock::GAOptimizerCOP
typedef utility::pointer::shared_ptr< GridScorer const > protocols::ligand_docking::ga_ligand_dock::GridScorerCOP
typedef utility::pointer::shared_ptr< LigandAligner const > protocols::ligand_docking::ga_ligand_dock::LigandAlignerCOP

Function Documentation

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::count_neighbors ( core::pose::Pose const &  pose,
std::string const  atomname,
core::Real const  dcut 
)
core::Size protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord ( core::pose::Pose const &  pose,
core::Vector const &  xyz1,
std::string const  atomname,
core::Real const  dcut 
)
LigandConformer protocols::ligand_docking::ga_ligand_dock::crossover ( LigandConformer const &  l1,
LigandConformer const &  l2 
)

References protocols::antibody::l1, protocols::antibody::l2, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchis_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandnus_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandtaus_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligid_, core::chemical::ResidueType::n_rings(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ref_pose_, core::scoring::rg, core::chemical::ResidueType::ring_atoms(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers(), and core::id::to_string().

Referenced by core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_backbone(), core::scoring::etable::BaseEtableEnergy< Derived >::bump_energy_full(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), protocols::stepwise::screener::PartitionContactScreener::check_screen(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::get_intrares_countpair(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy(), and core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy().

LigandConformer protocols::ligand_docking::ga_ligand_dock::crossover_ft ( LigandConformer const &  l1,
LigandConformer const &  l2 
)
core::Real protocols::ligand_docking::ga_ligand_dock::distance_fast ( LigandConformer &  gene1,
LigandConformer &  gene2 
)
std::pair< core::Real, core::Real > protocols::ligand_docking::ga_ligand_dock::distance_internal ( LigandConformer const &  gene1,
LigandConformer const &  gene2 
)
core::Real protocols::ligand_docking::ga_ligand_dock::distance_slow ( LigandConformer const &  gene1,
LigandConformer const &  gene2 
)
core::Real protocols::ligand_docking::ga_ligand_dock::dxform_atr ( core::Real  )
inline
core::Real protocols::ligand_docking::ga_ligand_dock::dxform_rep ( core::Real  xfrep)
inline
std::string protocols::ligand_docking::ga_ligand_dock::gadock_subelement_ct_name ( std::string const &  name)
utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains ( core::pose::Pose const &  pose,
core::Size const  ligid,
core::Real const  atomic_distance_cut 
)
core::Real protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted ( core::scoring::ScoreFunctionOP  sf,
core::scoring::hbonds::HBondDatabaseCOP  database,
core::scoring::hbonds::HBondOptions const &  hbopt,
core::scoring::hbonds::HBEvalTuple const &  hbt,
numeric::xyzVector< core::Real > const &  D,
numeric::xyzVector< core::Real > const &  H,
numeric::xyzVector< core::Real > const &  A,
numeric::xyzVector< core::Real > const &  B,
numeric::xyzVector< core::Real > const &  B_0 
)
inline
core::Real protocols::ligand_docking::ga_ligand_dock::ipow ( core::Real  base,
core::Size  exp 
)
inline

Referenced by dxform_rep(), and ixform_rep().

core::Real protocols::ligand_docking::ga_ligand_dock::ixform_atr ( core::Real  xfatr)
inline
core::Real protocols::ligand_docking::ga_ligand_dock::ixform_rep ( core::Real  xfrep)
inline
LigandConformer protocols::ligand_docking::ga_ligand_dock::mutate ( LigandConformer const &  l)

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandchis_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandnus_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandtaus_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligandxyz_synced_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligchimutWidth_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligid_, core::chemical::ResidueType::n_rings(), protocols::simple_filters::R2quat(), core::scoring::motif::random_rotation(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::rb_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ref_pose_, core::scoring::rg, core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::rotmutWidth_, protocols::ligand_docking::ga_ligand_dock::LigandConformer::rtmutationRate_, core::scoring::sa, protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_generation_tag(), core::id::to_string(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::torsmutationRate_, and protocols::ligand_docking::ga_ligand_dock::LigandConformer::transmutWidth_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::tcr::match_template_and_target_sequence(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), and protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset().

static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.GriddedAtomTreeMultifunc"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.EntropyEstimator"  )
static

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_all_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_receptor(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::optimize_generation(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), protocols::ligand_docking::ga_ligand_dock::GridScorer::score(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::set_default(), protocols::ligand_docking::ga_ligand_dock::GridScorer::set_grid_dim_with_maxRad(), protocols::ligand_docking::ga_ligand_dock::GridScorer::set_smoothing(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_ligand_aligner(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame().

static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.LigandConformer"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.GAOptimizer"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.GridScorer"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "ligand_align"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "protocols.ligand_docking.GALigandDock.GALigandDock"  )
static
static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TS ( "protocols.ligand_docking.GALigandDock.RotamerData"  )
static
core::Real protocols::ligand_docking::ga_ligand_dock::xform_atr ( core::Real  atr)
inline
core::Real protocols::ligand_docking::ga_ligand_dock::xform_rep ( core::Real  rep)
inline