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core::scoring::lkball Namespace Reference

Namespaces

 lkbtrie
 

Classes

class  LK_BallInvoker
 
class  LK_Ball_RPE_Invoker
 
class  LK_Ball_BB_BB_E_Invoker
 
class  LK_Ball_BB_SC_E_Invoker
 
class  LK_Ball_SC_SC_E_Invoker
 
class  LKB_ResPairMinData
 
struct  ScoredBridgingWater
 
class  LK_BallEnergy
 
class  LK_BallEnergyCreator
 
class  WaterBuilder
 
class  WaterBuilderForRestype
 
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...
 
class  LKB_ResidueInfo
 LKB_ResidueInfo holds the coordinates of the waters attached to a Residue More...
 
class  LKB_ResiduesInfo
 
class  LK_DomeInvoker
 
class  LK_Dome_RPE_Invoker
 
class  LKD_ResPairMinData
 
class  LK_DomeEnergy
 
struct  DerivativeFinder
 
struct  DerivativeFinderWadj
 
class  LK_DomeEnergyCreator
 
class  LKD_ResidueInfo
 

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_BallEnergyLK_BallEnergyOP
 
typedef utility::pointer::shared_ptr< LK_BallEnergy const > LK_BallEnergyCOP
 
typedef utility::vector1< VectorWaterCoords
 
typedef utility::fixedsizearray1< Vector, MAX_N_WATERS_PER_ATOMWaterDerivVectors
 
typedef utility::fixedsizearray1< Real, MAX_N_WATERS_PER_ATOMWaterDerivContributions
 
typedef numeric::xyzMatrix< RealWaterDerivMatrix
 
typedef utility::fixedsizearray1< Real, 2 > AtomWeights
 
typedef utility::vector1< WaterBuilderWaterBuilders
 
typedef utility::vector1< WaterBuildersWaterBuildersList
 
typedef utility::pointer::shared_ptr< WaterBuildersListWaterBuildersListOP
 
typedef utility::pointer::shared_ptr< WaterBuildersList const > WaterBuildersListCOP
 
typedef utility::pointer::shared_ptr< WaterBuilderForRestypeWaterBuilderForRestypeOP
 
typedef utility::pointer::shared_ptr< WaterBuilderForRestype const > WaterBuilderForRestypeCOP
 
typedef utility::pointer::shared_ptr< LKB_ResidueInfoLKB_ResidueInfoOP
 
typedef utility::pointer::shared_ptr< const LKB_ResidueInfoLKB_ResidueInfoCOP
 
typedef LKB_ResiduesInfo LKB_PoseInfo
 
typedef LKB_ResiduesInfo LKB_RotamerSetInfo
 
typedef utility::pointer::shared_ptr< LKB_PoseInfoLKB_PoseInfoOP
 
typedef utility::pointer::shared_ptr< LKB_RotamerSetInfoLKB_RotamerSetInfoOP
 
using LKD_ResPairMinDataOP = utility::pointer::shared_ptr< LKD_ResPairMinData >
 
using LKD_ResPairMinDataCOP = utility::pointer::shared_ptr< const LKD_ResPairMinData >
 
typedef utility::pointer::shared_ptr< LK_DomeEnergyLK_DomeEnergyOP
 
typedef utility::pointer::shared_ptr< LK_DomeEnergy const > LK_DomeEnergyCOP
 
typedef utility::fixedsizearray1< Real, MAX_N_WATERS_PER_ATOMWaterOcclusions
 
typedef utility::fixedsizearray1< Real, MAX_N_WATERS_PER_ATOMWaterSolValues
 
typedef utility::pointer::shared_ptr< LKD_ResidueInfoLKD_ResidueInfoOP
 
typedef utility::pointer::shared_ptr< const LKD_ResidueInfoLKD_ResidueInfoCOP
 

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< Vectorbuild_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)
 
void evaluate_lk_dome_energy_for_atom_ranges (LK_DomeEnergy const &lk_dome, conformation::Residue const &rsd1, LKD_ResidueInfo const &rsd1_info, conformation::Residue const &rsd2, LKD_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)
 
Real cubed_root (Real val)
 
LKD_ResidueInfo const & retrieve_lkd_resdata (conformation::Residue const &res)
 
static basic::Tracer TR ("core.scoring.methods.LK_DomeInfo")
 

Variables

int const MAX_N_WATERS_PER_ATOM = 4
 

Typedef Documentation

◆ AtomWeights

typedef utility::fixedsizearray1< Real, 2 > core::scoring::lkball::AtomWeights

◆ LK_BallEnergyCOP

typedef utility::pointer::shared_ptr< LK_BallEnergy const > core::scoring::lkball::LK_BallEnergyCOP

◆ LK_BallEnergyOP

typedef utility::pointer::shared_ptr< LK_BallEnergy > core::scoring::lkball::LK_BallEnergyOP

◆ LK_DomeEnergyCOP

typedef utility::pointer::shared_ptr< LK_DomeEnergy const > core::scoring::lkball::LK_DomeEnergyCOP

◆ LK_DomeEnergyOP

typedef utility::pointer::shared_ptr< LK_DomeEnergy > core::scoring::lkball::LK_DomeEnergyOP

◆ LKB_PoseInfo

◆ LKB_PoseInfoOP

typedef utility::pointer::shared_ptr< LKB_PoseInfo > core::scoring::lkball::LKB_PoseInfoOP

◆ LKB_ResidueInfoCOP

typedef utility::pointer::shared_ptr< const LKB_ResidueInfo > core::scoring::lkball::LKB_ResidueInfoCOP

◆ LKB_ResidueInfoOP

typedef utility::pointer::shared_ptr< LKB_ResidueInfo > core::scoring::lkball::LKB_ResidueInfoOP

◆ LKB_ResPairMinDataCOP

using core::scoring::lkball::LKB_ResPairMinDataCOP = typedef utility::pointer::shared_ptr<const LKB_ResPairMinData>

◆ LKB_ResPairMinDataOP

using core::scoring::lkball::LKB_ResPairMinDataOP = typedef utility::pointer::shared_ptr<LKB_ResPairMinData>

◆ LKB_RotamerSetInfo

◆ LKB_RotamerSetInfoOP

typedef utility::pointer::shared_ptr< LKB_RotamerSetInfo > core::scoring::lkball::LKB_RotamerSetInfoOP

◆ LKD_ResidueInfoCOP

typedef utility::pointer::shared_ptr< const LKD_ResidueInfo > core::scoring::lkball::LKD_ResidueInfoCOP

◆ LKD_ResidueInfoOP

typedef utility::pointer::shared_ptr< LKD_ResidueInfo > core::scoring::lkball::LKD_ResidueInfoOP

◆ LKD_ResPairMinDataCOP

using core::scoring::lkball::LKD_ResPairMinDataCOP = typedef utility::pointer::shared_ptr<const LKD_ResPairMinData>

◆ LKD_ResPairMinDataOP

using core::scoring::lkball::LKD_ResPairMinDataOP = typedef utility::pointer::shared_ptr<LKD_ResPairMinData>

◆ WaterBuilderForRestypeCOP

typedef utility::pointer::shared_ptr< WaterBuilderForRestype const > core::scoring::lkball::WaterBuilderForRestypeCOP

◆ WaterBuilderForRestypeOP

◆ WaterBuilders

◆ WaterBuildersList

◆ WaterBuildersListCOP

typedef utility::pointer::shared_ptr< WaterBuildersList const > core::scoring::lkball::WaterBuildersListCOP

◆ WaterBuildersListOP

typedef utility::pointer::shared_ptr< WaterBuildersList > core::scoring::lkball::WaterBuildersListOP

◆ WaterCoords

typedef utility::vector1< Vector > core::scoring::lkball::WaterCoords

◆ WaterDerivContributions

◆ WaterDerivMatrix

typedef numeric::xyzMatrix< Real > core::scoring::lkball::WaterDerivMatrix

◆ WaterDerivVectors

◆ WaterOcclusions

◆ WaterSolValues

Function Documentation

◆ build_optimal_water_O_on_donor()

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().

◆ build_optimal_water_Os_on_acceptor()

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 
)

◆ create_rotamer_descriptor()

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 
)

◆ cubed_root()

Real core::scoring::lkball::cubed_root ( Real  val)

◆ evaluate_lk_ball_energy_for_atom_ranges()

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 
)

◆ evaluate_lk_dome_energy_for_atom_ranges()

void core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges ( LK_DomeEnergy const &  lk_dome,
conformation::Residue const &  rsd1,
LKD_ResidueInfo const &  rsd1_info,
conformation::Residue const &  rsd2,
LKD_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 
)

◆ optimal_water_distance()

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

◆ retrieve_lkb_resdata()

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

◆ retrieve_lkb_rotamer_set_info()

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

◆ retrieve_lkd_resdata()

LKD_ResidueInfo const& core::scoring::lkball::retrieve_lkd_resdata ( conformation::Residue const &  res)
inline

◆ setup_water_builders_for_residue_type()

void core::scoring::lkball::setup_water_builders_for_residue_type ( ResidueType const &  rsd_type,
bool const  sidechain_only,
utility::vector1< WaterBuilders > &  rsd_water_builders 
)

◆ TR() [1/3]

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

◆ TR() [2/3]

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

◆ TR() [3/3]

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

◆ update_cached_lkb_resinfo()

void core::scoring::lkball::update_cached_lkb_resinfo ( conformation::Residue const &  rsd,
basic::datacache::BasicDataCache &  residue_data_cache,
bool  compute_derivs 
)

Variable Documentation

◆ MAX_N_WATERS_PER_ATOM

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