Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Functions | Variables
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< VectorWaterCoords
 
typedef
utility::fixedsizearray1
< Vector,
MAX_N_WATERS_PER_ATOM
WaterDerivVectors
 
typedef
utility::fixedsizearray1< Real,
MAX_N_WATERS_PER_ATOM
WaterDerivContributions
 
typedef numeric::xyzMatrix< RealWaterDerivMatrix
 
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< 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)
 

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

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 
)
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 
)
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 
)
static Real const core::scoring::lkball::optimal_water_distance ( 2.  65)
static
LKB_ResidueInfo const& core::scoring::lkball::retrieve_lkb_resdata ( conformation::Residue const &  res)
inline
LKB_RotamerSetInfo const& core::scoring::lkball::retrieve_lkb_rotamer_set_info ( conformation::RotamerSetBase const &  set)
inline
void core::scoring::lkball::setup_water_builders_for_residue_type ( ResidueType const &  rsd_type,
bool const  sidechain_only,
utility::vector1< WaterBuilders > &  rsd_water_builders 
)
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
void core::scoring::lkball::update_cached_lkb_resinfo ( conformation::Residue const &  rsd,
basic::datacache::BasicDataCache &  residue_data_cache,
bool  compute_derivs 
)

Variable Documentation

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