core::scoring::lkball Namespace Reference

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 Documentation

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 LKB_ResiduesInfo core::scoring::lkball::LKB_PoseInfo

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 LKB_ResiduesInfo core::scoring::lkball::LKB_RotamerSetInfo

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

Function Documentation

Vector core::scoring::lkball::build_optimal_water_O_on_donor	(	Vector const &	hxyz,
		Vector const &	dxyz
	)

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().

template<class CPDAT >

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().

static Real const core::scoring::lkball::optimal_water_distance ( 2.  65 )

static

Referenced by build_optimal_water_O_on_donor(), and build_optimal_water_Os_on_acceptor().

LKB_ResidueInfo const& core::scoring::lkball::retrieve_lkb_resdata ( conformation::Residue const &  res )

inline

References core::conformation::Residue::data(), and core::conformation::residue_datacache::LK_BALL_INFO.

Referenced by core::scoring::lkball::LK_BallEnergy::create_rotamer_trie(), and core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives().

LKB_RotamerSetInfo const& core::scoring::lkball::retrieve_lkb_rotamer_set_info ( conformation::RotamerSetBase const &  set )

inline

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().

static basic::Tracer core::scoring::lkball::TR ( "core.scoring.methods.LK_BallInfo"  )

static

static basic::Tracer core::scoring::lkball::TR ( "core.scoring.methods.LK_BallEnergy"  )

static

Referenced by build_optimal_water_Os_on_acceptor(), core::scoring::lkball::LKBallDatabase::initialize_residue_type(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), and setup_water_builders_for_residue_type().

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().

Variable Documentation

int const core::scoring::lkball::MAX_N_WATERS_PER_ATOM = 4

Referenced by build_optimal_water_Os_on_acceptor().