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
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
class	TorsionDistrParams
class	TorsionSampler
struct	TorsionType
	Gene representation of ligand & flexible sidechains in receptor. More...

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

Enumerations
enum	ReadMode {   rmNONE, rmATOM, rmBOND, rmANGLE,   rmTORSION, rmIMPROPER }

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)
core::Real	distance_slow (LigandConformer &gene1, LigandConformer &gene2)
core::Real	distance_fast (LigandConformer &gene1, LigandConformer &gene2)
std::pair< core::Real, core::Real >	distance_internal (LigandConformer const &gene1, LigandConformer const &gene2)
static basic::Tracer	TS ("protocols.ligand_docking.GALigandDock.RotamerData")
static basic::Tracer	TR ("protocols.ligand_docking.GALigandDock.TorsionSampler")
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::Size >	count_neighbors (core::pose::Pose const &pose, std::string const atomname, core::Real const dcut)
utility::vector1< core::Size >	get_atomic_contacting_sidechains (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, 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< GALigandDock > protocols::ligand_docking::ga_ligand_dock::GALigandDockOP

typedef utility::pointer::shared_ptr< GAOptimizer const > protocols::ligand_docking::ga_ligand_dock::GAOptimizerCOP

typedef utility::pointer::shared_ptr< GAOptimizer > protocols::ligand_docking::ga_ligand_dock::GAOptimizerOP

typedef utility::pointer::shared_ptr< GridScorer const > protocols::ligand_docking::ga_ligand_dock::GridScorerCOP

typedef utility::pointer::shared_ptr< GridScorer > protocols::ligand_docking::ga_ligand_dock::GridScorerOP

typedef utility::pointer::shared_ptr< LigandAligner const > protocols::ligand_docking::ga_ligand_dock::LigandAlignerCOP

typedef utility::pointer::shared_ptr< LigandAligner > protocols::ligand_docking::ga_ligand_dock::LigandAlignerOP

typedef utility::vector1< LigandConformer > protocols::ligand_docking::ga_ligand_dock::LigandConformers

typedef utility::vector1< PlaceableRotamer > protocols::ligand_docking::ga_ligand_dock::PlaceableRotamers

Enumeration Type Documentation

enum protocols::ligand_docking::ga_ligand_dock::ReadMode

Enumerator
rmNONE
rmATOM
rmBOND
rmANGLE
rmTORSION
rmIMPROPER

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
	)

References core::pose::Pose::energies(), core::conformation::Residue::has(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_filters::ResidueBurialFilter::apply(), protocols::enzdes::LigBurialFilter::apply(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::NonSequentialNeighborsFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::switches::GraftSwitchMover::init_burial_filter(), protocols::simple_filters::ResidueBurialFilter::report(), protocols::enzdes::LigBurialFilter::report(), protocols::simple_filters::ResidueBurialFilter::report_sm(), protocols::enzdes::LigBurialFilter::report_sm(), and protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors().

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
	)

References core::conformation::Residue::has(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

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::ligids_, 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().

core::Real protocols::ligand_docking::ga_ligand_dock::distance_fast	(	LigandConformer &	gene1,
		LigandConformer &	gene2
	)

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), and protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_pool().

std::pair< core::Real, core::Real > protocols::ligand_docking::ga_ligand_dock::distance_internal	(	LigandConformer const &	gene1,
		LigandConformer const &	gene2
	)

References protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchi(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchis(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_rg(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::quat(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::trans().

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().

core::Real protocols::ligand_docking::ga_ligand_dock::distance_slow	(	LigandConformer &	gene1,
		LigandConformer &	gene2
	)

References core::scoring::automorphic_rmsd(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::distance_fast, protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligids_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status().

core::Real protocols::ligand_docking::ga_ligand_dock::dxform_atr ( core::Real  )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives().

core::Real protocols::ligand_docking::ga_ligand_dock::dxform_rep ( core::Real  xfrep )

inline

References ipow().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives().

std::string protocols::ligand_docking::ga_ligand_dock::gadock_subelement_ct_name

(

std::string const &

name

)

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::provide_xml_schema().

utility::vector1< core::Size > protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	ligids,
		core::Real const	atomic_distance_cut
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::Residue::atom_is_backbone(), protocols::membrane::com(), core::conformation::Residue::is_protein(), protocols::mean_field::min(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin().

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

References core::scoring::hbonds::DUMMY_DERIVS, protocols::buns::energy, core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::get_hbond_weight_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::hbonds::hbw_LR_BB_SC, core::scoring::hbonds::hbw_SC, core::scoring::hbonds::hbw_SR_BB_SC, and core::scoring::hbonds::HBondOptions::max_hb_energy().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy().

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

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::point_energy().

core::Real protocols::ligand_docking::ga_ligand_dock::ixform_rep ( core::Real  xfrep )

inline

References ipow().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::point_clash_energy(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::point_energy().

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::ligids_, 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.TorsionSampler"  )

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_ligand(), 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::TorsionDistrParams::normalize(), 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::TorsionSampler::read_database(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), protocols::ligand_docking::ga_ligand_dock::TorsionSampler::sample(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_conformation(), protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::sample_mode(), 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::update_conf().

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.LigandConformer"  )

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

Referenced by protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::finalize().

core::Real protocols::ligand_docking::ga_ligand_dock::xform_atr ( core::Real  atr )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid().

core::Real protocols::ligand_docking::ga_ligand_dock::xform_rep ( core::Real  rep )

inline

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid().