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Rosetta
2020.50
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Namespaces | |
lkbtrie | |
Classes | |
class | LK_Ball_BB_BB_E_Invoker |
class | LK_Ball_BB_SC_E_Invoker |
class | LK_Ball_RPE_Invoker |
class | LK_Ball_SC_SC_E_Invoker |
class | LK_BallEnergy |
class | LK_BallEnergyCreator |
class | LK_BallInvoker |
class | LKB_ResidueInfo |
LKB_ResidueInfo holds the coordinates of the waters attached to a Residue More... | |
class | LKB_ResiduesInfo |
class | LKB_ResPairMinData |
class | LKBallDatabase |
A singleton class which stores data for LKBall terms. This is a separate singleton class, rather than static data on the LKB_ResidueInfo class so that the ResidueType destruction observer has a stable object to call back to. More... | |
struct | ScoredBridgingWater |
class | WaterBuilder |
class | WaterBuilderForRestype |
Typedefs | |
using | LKB_ResPairMinDataOP = utility::pointer::shared_ptr< LKB_ResPairMinData > |
using | LKB_ResPairMinDataCOP = utility::pointer::shared_ptr< const LKB_ResPairMinData > |
typedef utility::pointer::shared_ptr < LK_BallEnergy > | LK_BallEnergyOP |
typedef utility::pointer::shared_ptr < LK_BallEnergy const > | LK_BallEnergyCOP |
typedef utility::vector1< Vector > | WaterCoords |
typedef utility::fixedsizearray1 < Vector, MAX_N_WATERS_PER_ATOM > | WaterDerivVectors |
typedef utility::fixedsizearray1< Real, MAX_N_WATERS_PER_ATOM > | WaterDerivContributions |
typedef numeric::xyzMatrix< Real > | WaterDerivMatrix |
typedef utility::fixedsizearray1< Real, 2 > | AtomWeights |
typedef utility::vector1 < WaterBuilder > | WaterBuilders |
typedef utility::vector1 < WaterBuilders > | WaterBuildersList |
typedef utility::pointer::shared_ptr < WaterBuildersList > | WaterBuildersListOP |
typedef utility::pointer::shared_ptr < WaterBuildersList const > | WaterBuildersListCOP |
typedef utility::pointer::shared_ptr < WaterBuilderForRestype > | WaterBuilderForRestypeOP |
typedef utility::pointer::shared_ptr < WaterBuilderForRestype const > | WaterBuilderForRestypeCOP |
typedef utility::pointer::shared_ptr < LKB_ResidueInfo > | LKB_ResidueInfoOP |
typedef utility::pointer::shared_ptr < const LKB_ResidueInfo > | LKB_ResidueInfoCOP |
typedef LKB_ResiduesInfo | LKB_PoseInfo |
typedef LKB_ResiduesInfo | LKB_RotamerSetInfo |
typedef utility::pointer::shared_ptr < LKB_PoseInfo > | LKB_PoseInfoOP |
typedef utility::pointer::shared_ptr < LKB_RotamerSetInfo > | LKB_RotamerSetInfoOP |
Functions | |
static basic::Tracer | TR ("core.scoring.methods.LK_BallEnergy") |
void | evaluate_lk_ball_energy_for_atom_ranges (LK_BallEnergy const &lk_ball, conformation::Residue const &rsd1, LKB_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKB_ResidueInfo const &rsd2_info, ScoreFunction const &sfxn, etable::count_pair::CountPairFunction const &cpfxn, Size const res1_start_atom, Size const res1_end_atom, Size const res2_start_atom, Size const res2_end_atom, EnergyMap &emap) |
LKB_RotamerSetInfo const & | retrieve_lkb_rotamer_set_info (conformation::RotamerSetBase const &set) |
inline retrieval functions here: More... | |
void | update_cached_lkb_resinfo (conformation::Residue const &rsd, basic::datacache::BasicDataCache &residue_data_cache, bool compute_derivs) |
LKB_ResidueInfo const & | retrieve_lkb_resdata (conformation::Residue const &res) |
template<class CPDAT > | |
void | create_rotamer_descriptor (conformation::Residue const &res, LKB_ResidueInfo const &lkb_resinfo, trie::CPDataCorrespondence const &cpdata_map, trie::RotamerDescriptor< lkbtrie::LKBAtom, CPDAT > &rotamer_descriptor) |
static basic::Tracer | TR ("core.scoring.methods.LK_BallInfo") |
static Real const | optimal_water_distance (2.65) |
Vector | build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz) |
utility::vector1< Vector > | build_optimal_water_Os_on_acceptor (Size const acc_atm, conformation::Residue const &acc_rsd, Vector const &a_xyz, Vector b1_xyz, Vector b2_xyz, chemical::Hybridization const &hybrid) |
void | setup_water_builders_for_residue_type (ResidueType const &rsd_type, bool const sidechain_only, utility::vector1< WaterBuilders > &rsd_water_builders) |
Variables | |
int const | MAX_N_WATERS_PER_ATOM = 4 |
typedef utility::fixedsizearray1< Real, 2 > core::scoring::lkball::AtomWeights |
typedef utility::pointer::shared_ptr< LK_BallEnergy const > core::scoring::lkball::LK_BallEnergyCOP |
typedef utility::pointer::shared_ptr< LK_BallEnergy > core::scoring::lkball::LK_BallEnergyOP |
typedef utility::pointer::shared_ptr< LKB_PoseInfo > core::scoring::lkball::LKB_PoseInfoOP |
typedef utility::pointer::shared_ptr< const LKB_ResidueInfo > core::scoring::lkball::LKB_ResidueInfoCOP |
typedef utility::pointer::shared_ptr< LKB_ResidueInfo > core::scoring::lkball::LKB_ResidueInfoOP |
using core::scoring::lkball::LKB_ResPairMinDataCOP = typedef utility::pointer::shared_ptr<const LKB_ResPairMinData> |
using core::scoring::lkball::LKB_ResPairMinDataOP = typedef utility::pointer::shared_ptr<LKB_ResPairMinData> |
typedef utility::pointer::shared_ptr< LKB_RotamerSetInfo > core::scoring::lkball::LKB_RotamerSetInfoOP |
typedef utility::pointer::shared_ptr< WaterBuilderForRestype const > core::scoring::lkball::WaterBuilderForRestypeCOP |
typedef utility::pointer::shared_ptr< WaterBuilderForRestype > core::scoring::lkball::WaterBuilderForRestypeOP |
typedef utility::vector1< WaterBuilder > core::scoring::lkball::WaterBuilders |
typedef utility::vector1< WaterBuilders > core::scoring::lkball::WaterBuildersList |
typedef utility::pointer::shared_ptr< WaterBuildersList const > core::scoring::lkball::WaterBuildersListCOP |
typedef utility::pointer::shared_ptr< WaterBuildersList > core::scoring::lkball::WaterBuildersListOP |
typedef utility::vector1< Vector > core::scoring::lkball::WaterCoords |
typedef utility::fixedsizearray1< Real, MAX_N_WATERS_PER_ATOM > core::scoring::lkball::WaterDerivContributions |
typedef numeric::xyzMatrix< Real > core::scoring::lkball::WaterDerivMatrix |
typedef utility::fixedsizearray1< Vector, MAX_N_WATERS_PER_ATOM > core::scoring::lkball::WaterDerivVectors |
Vector core::scoring::lkball::build_optimal_water_O_on_donor | ( | Vector const & | hxyz, |
Vector const & | dxyz | ||
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The next two functions were taken from protocols/water/rotamer_building_functions.cc with slight modifications
References optimal_water_distance().
Referenced by setup_water_builders_for_residue_type().
utility::vector1< Vector > core::scoring::lkball::build_optimal_water_Os_on_acceptor | ( | Size const | acc_atm, |
conformation::Residue const & | acc_rsd, | ||
Vector const & | a_xyz, | ||
Vector | b1_xyz, | ||
Vector | b2_xyz, | ||
chemical::Hybridization const & | hybrid | ||
) |
References core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::kinematics::distance(), core::conformation::Residue::has(), core::conformation::Residue::is_DNA(), MAX_N_WATERS_PER_ATOM, core::conformation::Residue::name(), optimal_water_distance(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, core::kinematics::Stub::spherical(), TR(), and core::conformation::Residue::xyz().
Referenced by setup_water_builders_for_residue_type().
void core::scoring::lkball::create_rotamer_descriptor | ( | conformation::Residue const & | res, |
LKB_ResidueInfo const & | lkb_resinfo, | ||
trie::CPDataCorrespondence const & | cpdata_map, | ||
trie::RotamerDescriptor< lkbtrie::LKBAtom, CPDAT > & | rotamer_descriptor | ||
) |
References core::scoring::trie::RotamerDescriptor< AT, CPDAT >::atom(), core::conformation::Residue::atom(), core::scoring::lkball::LKB_ResidueInfo::atom_weights(), core::scoring::trie::initialize_cpdata_for_atom(), core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::scoring::trie::RotamerDescriptor< AT, CPDAT >::natoms(), core::conformation::Residue::nheavyatoms(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), and core::scoring::lkball::LKB_ResidueInfo::waters().
Referenced by core::scoring::lkball::LK_BallEnergy::create_rotamer_trie().
void core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges | ( | LK_BallEnergy const & | lk_ball, |
conformation::Residue const & | rsd1, | ||
LKB_ResidueInfo const & | rsd1_info, | ||
conformation::Residue const & | rsd2, | ||
LKB_ResidueInfo const & | rsd2_info, | ||
ScoreFunction const & | sfxn, | ||
etable::count_pair::CountPairFunction const & | cpfxn, | ||
Size const | res1_start_atom, | ||
Size const | res1_end_atom, | ||
Size const | res2_start_atom, | ||
Size const | res2_end_atom, | ||
EnergyMap & | emap | ||
) |
References core::scoring::lkball::LK_BallEnergy::accumulate_single_atom_contributions(), core::scoring::etable::Etable::analytic_lk_energy(), core::conformation::Residue::atom(), core::scoring::lkball::LKB_ResidueInfo::atom_weights(), core::scoring::etable::count_pair::CountPairFunction::count(), core::scoring::lkball::LK_BallEnergy::etable(), core::scoring::lkball::LK_BallEnergy::etable_bins_per_A2(), core::scoring::lkball::LK_BallEnergy::fasol_max_dis2(), core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution(), core::scoring::ScoreFunction::get_weight(), protocols::antibody::l1, core::scoring::lk_ball_bridge, core::scoring::lk_ball_bridge_uncpl, core::scoring::lkball::LK_BallEnergy::lkb_max_dis2(), core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(), core::scoring::lkball::LK_BallEnergy::slim_etable(), core::scoring::lkball::LK_BallEnergy::solv1(), core::scoring::lkball::LK_BallEnergy::solv2(), core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(), core::scoring::lkball::LKB_ResidueInfo::waters(), and core::conformation::Residue::xyz().
Referenced by core::scoring::lkball::LK_Ball_RPE_Invoker::invoke(), core::scoring::lkball::LK_Ball_BB_BB_E_Invoker::invoke(), core::scoring::lkball::LK_Ball_BB_SC_E_Invoker::invoke(), and core::scoring::lkball::LK_Ball_SC_SC_E_Invoker::invoke().
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Referenced by build_optimal_water_O_on_donor(), and build_optimal_water_Os_on_acceptor().
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inline retrieval functions here:
References core::conformation::RotamerSetBase::data(), and core::conformation::RotamerSetCacheableDataType::LK_BALL_ROTAMER_SET_INFO.
Referenced by core::scoring::lkball::LK_BallEnergy::create_rotamer_trie().
void core::scoring::lkball::setup_water_builders_for_residue_type | ( | ResidueType const & | rsd_type, |
bool const | sidechain_only, | ||
utility::vector1< WaterBuilders > & | rsd_water_builders | ||
) |
References core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_gln, core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), build_optimal_water_O_on_donor(), build_optimal_water_Os_on_acceptor(), core::conformation::ResidueFactory::create_residue(), core::io::pdb::dump_pdb_residue(), core::chemical::element::F, core::chemical::AtomType::hybridization(), core::chemical::element::I, core::chemical::AtomType::name(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::conformation::membrane::out, core::chemical::SP3_HYBRID, and TR().
Referenced by core::scoring::lkball::LKBallDatabase::initialize_residue_type().
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void core::scoring::lkball::update_cached_lkb_resinfo | ( | conformation::Residue const & | rsd, |
basic::datacache::BasicDataCache & | residue_data_cache, | ||
bool | compute_derivs | ||
) |
References core::conformation::residue_datacache::LK_BALL_INFO.
Referenced by core::scoring::lkball::LK_BallEnergy::setup_for_derivatives_for_residue(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().
int const core::scoring::lkball::MAX_N_WATERS_PER_ATOM = 4 |
Referenced by build_optimal_water_Os_on_acceptor().