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Classes | Typedefs | Enumerations | Functions
protocols::ligand_docking::ga_ligand_dock Namespace Reference

Classes

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

Typedefs

typedef utility::pointer::shared_ptr< GALigandDock > GALigandDockOP
 
typedef utility::pointer::shared_ptr< GALigandDock const > GALigandDockCOP
 
typedef std::map< std::pair< core::Size, core::Size >, std::vector< core::Size > > HbondMap
 
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< std::pair< core::Size, core::Size > > SizePairVec
 
typedef utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size > DihedralAtomTuple
 
typedef std::map< utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size >, core::Size > DihedralAtomTuple2ChiIdxMap
 
typedef utility::pointer::shared_ptr< MCSAligner > MCSAlignerOP
 
typedef utility::pointer::shared_ptr< MCSAligner const > MCSAlignerCOP
 
typedef utility::vector1< PlaceableRotamer > PlaceableRotamers
 
typedef utility::pointer::shared_ptr< TorsionSampler > TorsionSamplerOP
 
typedef utility::pointer::shared_ptr< TorsionSampler const > TorsionSamplerCOP
 

Enumerations

enum  OptHMode {
  OPTH_NONE , OPTH_FULL , OPTH_NO_FLIP_HNQ , OPTH_FLEXIBLE_SIDECHAINS ,
  OPTH_REDEFINE_SIDECHAINS
}
 
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_fast (LigandConformer &gene1, LigandConformer &gene2)
 
std::pair< core::Real, core::Real > distance_internal (LigandConformer const &gene1, LigandConformer const &gene2)
 
core::Real distance_slow (LigandConformer &gene1, LigandConformer &gene2)
 
static basic::Tracer TR ("protocols.ligand_docking.GALigandDock.MCSAligner")
 
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.util")
 
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)
 
void constraint_relax (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &movable_scs, core::Real maxiter)
 
void make_ligand_only_pose (core::pose::PoseOP pose_new, core::pose::PoseCOP pose, utility::vector1< core::Size > const &lig_resnos)
 
void perturb_ligand_rb (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, core::Real trans_step, core::Real rot_step)
 
void perturb_ligand_torsions (core::pose::Pose &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &freeze_chi, core::Real chi_step)
 
core::Size get_ligand_jumpid (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids)
 
void get_ligand_resids (core::pose::Pose const &pose, utility::vector1< core::Size > &lig_resids)
 
bool is_hb_satisfied (core::scoring::ScoreFunctionOP sf, core::scoring::hbonds::HBondDatabaseCOP hb_database, core::scoring::hbonds::HBondOptions const &hbopt, hbAcc const &acc, hbDon const &don, core::Real const &maxHbdis2, core::Real const &hb_energy_cutoff, std::string const &metric)
 
void compute_nhbonds (core::pose::Pose const &pose, utility::vector1< core::Size > const &ligids, utility::vector1< core::Size > const &resids, core::Size &nhbonds_total, core::Size &nhbonds_max1, bool const &include_bb, std::string const &hb_metric)
 

Typedef Documentation

◆ DihedralAtomTuple

typedef utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size > protocols::ligand_docking::ga_ligand_dock::DihedralAtomTuple

◆ DihedralAtomTuple2ChiIdxMap

typedef std::map< utility::keys::Key4Tuple< core::Size, core::Size, core::Size, core::Size >, core::Size> protocols::ligand_docking::ga_ligand_dock::DihedralAtomTuple2ChiIdxMap

◆ GALigandDockCOP

typedef utility::pointer::shared_ptr< GALigandDock const > protocols::ligand_docking::ga_ligand_dock::GALigandDockCOP

◆ GALigandDockOP

typedef utility::pointer::shared_ptr< GALigandDock > protocols::ligand_docking::ga_ligand_dock::GALigandDockOP

◆ GAOptimizerCOP

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

◆ GAOptimizerOP

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

◆ GridScorerCOP

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

◆ GridScorerOP

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

◆ HbondMap

typedef std::map< std::pair < core::Size, core::Size >, std::vector < core::Size > > protocols::ligand_docking::ga_ligand_dock::HbondMap

◆ LigandAlignerCOP

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

◆ LigandAlignerOP

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

◆ LigandConformers

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

◆ MCSAlignerCOP

typedef utility::pointer::shared_ptr< MCSAligner const > protocols::ligand_docking::ga_ligand_dock::MCSAlignerCOP

◆ MCSAlignerOP

typedef utility::pointer::shared_ptr< MCSAligner > protocols::ligand_docking::ga_ligand_dock::MCSAlignerOP

◆ PlaceableRotamers

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

◆ SizePairVec

typedef utility::vector1<std::pair<core::Size, core::Size> > protocols::ligand_docking::ga_ligand_dock::SizePairVec

◆ TorsionSamplerCOP

typedef utility::pointer::shared_ptr< TorsionSampler const > protocols::ligand_docking::ga_ligand_dock::TorsionSamplerCOP

◆ TorsionSamplerOP

typedef utility::pointer::shared_ptr< TorsionSampler > protocols::ligand_docking::ga_ligand_dock::TorsionSamplerOP

Enumeration Type Documentation

◆ OptHMode

enum protocols::ligand_docking::ga_ligand_dock::OptHMode
Enumerator
OPTH_NONE 
OPTH_FULL 
OPTH_NO_FLIP_HNQ 
OPTH_FLEXIBLE_SIDECHAINS 
OPTH_REDEFINE_SIDECHAINS 

◆ ReadMode

enum protocols::ligand_docking::ga_ligand_dock::ReadMode
Enumerator
rmNONE 
rmATOM 
rmBOND 
rmANGLE 
rmTORSION 
rmIMPROPER 

Function Documentation

◆ compute_nhbonds()

void protocols::ligand_docking::ga_ligand_dock::compute_nhbonds ( core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  ligids,
utility::vector1< core::Size > const &  resids,
core::Size &  nhbonds_total,
core::Size &  nhbonds_max1,
bool const &  include_bb,
std::string const &  hb_metric 
)

References protocols::ligand_docking::ga_ligand_dock::hbAcc::A, core::conformation::Residue::abase2(), core::conformation::Residue::accpt_pos(), protocols::ligand_docking::ga_ligand_dock::hbAcc::acctype, core::conformation::Residue::atom_base(), protocols::ligand_docking::ga_ligand_dock::hbAcc::B, protocols::ligand_docking::ga_ligand_dock::hbAcc::B_0, protocols::ligand_docking::ga_ligand_dock::hbDon::D, protocols::ligand_docking::ga_ligand_dock::hbDon::dontype, core::conformation::Residue::first_sidechain_hydrogen(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::get_score_function(), protocols::ligand_docking::ga_ligand_dock::hbDon::H, core::conformation::Residue::Hpos_polar(), is_hb_satisfied(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::scoring::hbonds::HBondOptions::params_database_tag(), core::select::resids(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

◆ constraint_relax()

void protocols::ligand_docking::ga_ligand_dock::constraint_relax ( core::pose::Pose &  pose,
utility::vector1< core::Size > const &  ligids,
utility::vector1< core::Size > const &  movable_scs,
core::Real  maxiter 
)

References core::pose::Pose::add_constraint(), core::scoring::all_atom_rmsd_nosuper(), core::scoring::cart_bonded, core::scoring::coordinate_constraint, core::pose::Pose::fold_tree(), get_ligand_jumpid(), core::scoring::get_score_function(), core::optimization::MinimizerOptions::max_iter(), core::scoring::pro_close, core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::optimization::CartesianMinimizer::run(), core::pose::setPoseExtraScore(), TR(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

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

◆ count_neighbors()

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

◆ count_neighbors_on_coord()

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().

◆ crossover()

LigandConformer protocols::ligand_docking::ga_ligand_dock::crossover ( LigandConformer const &  l1,
LigandConformer const &  l2 
)

Referenced by core::scoring::lkball::LK_BallEnergy::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::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::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::etable::count_pair::CountPairFactory::create_intrares_count_pair_function(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), 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_DomeEnergy::residue_pair_energy(), core::scoring::lkball::LK_DomeEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().

◆ distance_fast()

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

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

◆ distance_internal()

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

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

◆ distance_slow()

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

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

◆ dxform_atr()

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

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

◆ dxform_rep()

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().

◆ gadock_subelement_ct_name()

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().

◆ get_atomic_contacting_sidechains()

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::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), 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_ligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH().

◆ get_hbond_score_weighted()

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::chemical::element::B, core::id::D, core::scoring::hbonds::DUMMY_DERIVS, protocols::buns::energy, core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::get_hbond_weight_type(), core::chemical::element::H, 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(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), and is_hb_satisfied().

◆ get_ligand_jumpid()

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

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::get_jump_edges().

Referenced by constraint_relax().

◆ get_ligand_resids()

void protocols::ligand_docking::ga_ligand_dock::get_ligand_resids ( core::pose::Pose const &  pose,
utility::vector1< core::Size > &  lig_resids 
)

References core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_virtual_residue(), core::chemical::ResidueType::lower_connect_id(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::replace_ligand().

◆ ipow()

core::Real protocols::ligand_docking::ga_ligand_dock::ipow ( core::Real  base,
core::Size  exp 
)
inline

Referenced by dxform_rep(), and ixform_rep().

◆ is_hb_satisfied()

bool protocols::ligand_docking::ga_ligand_dock::is_hb_satisfied ( core::scoring::ScoreFunctionOP  sf,
core::scoring::hbonds::HBondDatabaseCOP  hb_database,
core::scoring::hbonds::HBondOptions const &  hbopt,
hbAcc const &  acc,
hbDon const &  don,
core::Real const &  maxHbdis2,
core::Real const &  hb_energy_cutoff,
std::string const &  metric 
)

References protocols::comparative_modeling::features::A, protocols::ligand_docking::ga_ligand_dock::hbAcc::A, core::scoring::hbonds::HBEvalTuple::acc_type(), protocols::ligand_docking::ga_ligand_dock::hbAcc::acctype, core::chemical::element::B, protocols::ligand_docking::ga_ligand_dock::hbAcc::B, protocols::ligand_docking::ga_ligand_dock::hbAcc::B_0, core::id::D, protocols::ligand_docking::ga_ligand_dock::hbDon::D, core::scoring::hbonds::HBEvalTuple::don_type(), protocols::ligand_docking::ga_ligand_dock::hbDon::dontype, get_hbond_score_weighted(), core::chemical::element::H, protocols::ligand_docking::ga_ligand_dock::hbDon::H, core::scoring::hbonds::hb_energy(), and core::scoring::hbonds::MAX_R2.

Referenced by compute_nhbonds().

◆ ixform_atr()

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().

◆ ixform_rep()

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().

◆ make_ligand_only_pose()

void protocols::ligand_docking::ga_ligand_dock::make_ligand_only_pose ( core::pose::PoseOP  pose_new,
core::pose::PoseCOP  pose,
utility::vector1< core::Size > const &  lig_resnos 
)

References core::pose::create_subpose(), core::pose::getPoseExtraScore(), core::scoring::rms, and core::pose::setPoseExtraScore().

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

◆ mutate()

LigandConformer protocols::ligand_docking::ga_ligand_dock::mutate ( LigandConformer const &  l)

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().

◆ perturb_ligand_rb()

void protocols::ligand_docking::ga_ligand_dock::perturb_ligand_rb ( core::pose::Pose &  pose,
utility::vector1< core::Size > const &  ligids,
core::Real  trans_step,
core::Real  rot_step 
)

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool().

◆ perturb_ligand_torsions()

void protocols::ligand_docking::ga_ligand_dock::perturb_ligand_torsions ( core::pose::Pose &  pose,
utility::vector1< core::Size > const &  ligids,
utility::vector1< core::Size > const &  freeze_chi,
core::Real  chi_step 
)

References core::chemical::ResidueType::bond_type(), core::pose::Pose::chi(), core::chemical::ResidueType::chi_atoms(), core::chemical::DoubleBond, core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueType::nchi(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool().

◆ TR() [1/10]

static basic::Tracer protocols::ligand_docking::ga_ligand_dock::TR ( "ligand_align"  )
static

◆ TR() [2/10]

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

Referenced by protocols::ligand_docking::ga_ligand_dock::MCSAligner::align_pose(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::assign_neighbors(), 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::GALigandDock::compare_hbonds_to_native(), constraint_relax(), 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_ligand_multibody_phores(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::erode_points(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose_helper(), 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_ligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_optH(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_biggest_skeleton(), 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::EntropyEstimator::get_contacting_reslist(), 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::GridScorer::get_hbond_map(), 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::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::MCEntropy(), 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::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::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::LigandAligner::select_points(), 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::MCSAligner::set_torsion_and_align(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::show_status(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::SimpleEntropy(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf().

◆ TR() [3/10]

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

◆ TR() [4/10]

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

◆ TR() [5/10]

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

◆ TR() [6/10]

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

◆ TR() [7/10]

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

◆ TR() [8/10]

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

◆ TR() [9/10]

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

◆ TR() [10/10]

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

◆ TS()

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().

◆ xform_atr()

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().

◆ xform_rep()

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().

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