Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
core::scoring::hbonds Namespace Reference

Namespaces

 graph
 
 hbtrie
 

Classes

struct  AssignmentScaleAndDerivVectID
 Classes (that probably shouldn't be in here!!! ) ///. More...
 
class  FadeInterval
 Classic FadeInterval. More...
 
class  HBDerivAssigner
 
class  HBEvalTuple
 
class  HBond
 
class  HBondDatabase
 
struct  HBondDerivs
 
class  HBondEnergy
 
class  HBondEnergyCreator
 
class  HBondOptions
 
class  HBondResidueMinData
 A class to hold data for the HBondEnergy class used in score and derivative evaluation. More...
 
class  HBondResPairMinData
 
class  HBondSet
 A class that holds Hbond objects and helps setup Hbonds for scoring. More...
 
class  HBondTypeManager
 
class  NPDHBondEnergy
 First pass implementation; somewhat ineffecient. The NPDHbondEnergy will cache a map of all hbonds by donor and acceptor in the Pose during setup_for_scoring, and will then retrieve these values during calls to residue_pair_energy. Doesn't work properly for packing. More...
 
class  NPDHBondEnergyCreator
 
class  NPDHBondSet
 A class that holds Hbond objects and helps setup Hbonds for scoring. More...
 
class  Polynomial_1d
 
struct  SSWeightParameters
 Weights and Options ///. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< HBondEnergy
HBondEnergyOP
 
typedef
utility::pointer::shared_ptr
< HBondEnergy const > 
HBondEnergyCOP
 
typedef
utility::pointer::shared_ptr
< HBondEnergy const > 
HBondEnergyCAP
 
typedef
utility::pointer::shared_ptr
< FadeInterval
FadeIntervalOP
 
typedef
utility::pointer::shared_ptr
< FadeInterval const > 
FadeIntervalCOP
 
typedef
utility::pointer::shared_ptr
< HBondDatabase
HBondDatabaseOP
 
typedef
utility::pointer::shared_ptr
< HBondDatabase const > 
HBondDatabaseCOP
 
using HBondResidueMinDataOP = utility::pointer::shared_ptr< HBondResidueMinData >
 
using HBondResidueMinDataCOP = utility::pointer::shared_ptr< const HBondResidueMinData >
 
using HBondResPairMinDataOP = utility::pointer::shared_ptr< HBondResPairMinData >
 
using HBondResPairMinDataCOP = utility::pointer::shared_ptr< const HBondResPairMinData >
 
typedef
utility::pointer::shared_ptr
< HBondOptions
HBondOptionsOP
 
typedef
utility::pointer::shared_ptr
< HBondOptions const > 
HBondOptionsCOP
 
typedef
utility::pointer::shared_ptr
< HBond
HBondOP
 
typedef
utility::pointer::shared_ptr
< HBond const > 
HBondCOP
 
typedef
utility::pointer::shared_ptr
< HBondSet
HBondSetOP
 
typedef
utility::pointer::shared_ptr
< HBondSet const > 
HBondSetCOP
 
typedef
utility::pointer::shared_ptr
< HBondTypeManager
HBondTypeManagerOP
 
typedef
utility::pointer::shared_ptr
< HBondTypeManager const > 
HBondTypeManagerCOP
 
typedef
utility::pointer::shared_ptr
< NPDHBondSet
NPDHBondSetOP
 
typedef
utility::pointer::shared_ptr
< NPDHBondSet const > 
NPDHBondSetCOP
 
typedef
utility::pointer::shared_ptr
< Polynomial_1d
Polynomial_1dOP
 
typedef
utility::pointer::shared_ptr
< Polynomial_1d const > 
Polynomial_1dCOP
 

Enumerations

enum  HBondWeightType {
  hbw_NONE = 1, hbw_SR_BB, hbw_LR_BB, hbw_SR_BB_SC,
  hbw_LR_BB_SC, hbw_SC, hbw_MAX = hbw_SC
}
 
enum  HBAccChemType {
  hbacc_NONE = 1, hbacc_PBA, hbacc_CXA, hbacc_CXL,
  hbacc_IMD, hbacc_IME, hbacc_AHX, hbacc_HXL,
  hbacc_PCA_DNA, hbacc_PES_DNA, hbacc_RRI_DNA, hbacc_PCA_RNA,
  hbacc_PES_RNA, hbacc_RRI_RNA, hbacc_H2O, hbacc_GENERIC_SP2BB,
  hbacc_GENERIC_SP2SC, hbacc_GENERIC_SP3BB, hbacc_GENERIC_SP3SC, hbacc_GENERIC_RINGBB,
  hbacc_GENERIC_RINGSC, hbacc_MAX = hbacc_GENERIC_RINGSC
}
 
enum  HBDonChemType {
  hbdon_NONE = 1, hbdon_PBA, hbdon_CXA, hbdon_IMD,
  hbdon_IME, hbdon_IND, hbdon_AMO, hbdon_GDE,
  hbdon_GDH, hbdon_AHX, hbdon_HXL, hbdon_H2O,
  hbdon_GENERIC_BB, hbdon_GENERIC_SC, hbdon_MAX = hbdon_GENERIC_SC
}
 
enum  HBEvalType {
  hbe_UNKNOWN = 0, hbe_NONE =1, hbe_dPBAaPBAsepM4helix, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM4helix = hbe_dPBAaPBAsepM4helix,
  hbe_dPBAaPBAsepM3turn, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM3turn = hbe_dPBAaPBAsepM3turn, hbe_dPBAaPBAsepM2turn, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM2turn = hbe_dPBAaPBAsepM2turn,
  hbe_dPBAaPBAsepPM1, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepPM1 = hbe_dPBAaPBAsepPM1, hbe_dPBAaPBAsepP2turn, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP2turn = hbe_dPBAaPBAsepP2turn,
  hbe_dPBAaPBAsepP3turn, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP3turn = hbe_dPBAaPBAsepP3turn, hbe_dPBAaPBAsepP4helix, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP4helix = hbe_dPBAaPBAsepP4helix,
  hbe_dPBAaPBAsepother, hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepother = hbe_dPBAaPBAsepother, hbe_dCXAaPBAsepPM1, hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepPM1 = hbe_dCXAaPBAsepPM1,
  hbe_dIMDaPBAsepPM1, hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepPM1 = hbe_dIMDaPBAsepPM1, hbe_dIMEaPBAsepPM1, hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepPM1 = hbe_dIMEaPBAsepPM1,
  hbe_dINDaPBAsepPM1, hbe_dINDOLaPROTEIN_BB_AMIDEsepPM1 = hbe_dINDaPBAsepPM1, hbe_dAMOaPBAsepPM1, hbe_dAMINOaPROTEIN_BB_AMIDEsepPM1 = hbe_dAMOaPBAsepPM1,
  hbe_dGDEaPBAsepPM1, hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepPM1 = hbe_dGDEaPBAsepPM1, hbe_dGDHaPBAsepPM1, hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepPM1 = hbe_dGDHaPBAsepPM1,
  hbe_dAHXaPBAsepPM1, hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepPM1 = hbe_dAHXaPBAsepPM1, hbe_dHXLaPBAsepPM1, hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepPM1 = hbe_dHXLaPBAsepPM1,
  hbe_dCXAaPBAsepother, hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepother = hbe_dCXAaPBAsepother, hbe_dIMDaPBAsepother, hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepother = hbe_dIMDaPBAsepother,
  hbe_dIMEaPBAsepother, hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepother = hbe_dIMEaPBAsepother, hbe_dINDaPBAsepother, hbe_dINDOLaPROTEIN_BB_AMIDEsepother = hbe_dINDaPBAsepother,
  hbe_dAMOaPBAsepother, hbe_dAMINOaPROTEIN_BB_AMIDEsepother = hbe_dAMOaPBAsepother, hbe_dGDEaPBAsepother, hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepother = hbe_dGDEaPBAsepother,
  hbe_dGDHaPBAsepother, hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepother = hbe_dGDHaPBAsepother, hbe_dAHXaPBAsepother, hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepother = hbe_dAHXaPBAsepother,
  hbe_dHXLaPBAsepother, hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepother = hbe_dHXLaPBAsepother, hbe_dH2OaPBA, hbe_WATERaPROTEIN_BB_AMIDE = hbe_dH2OaPBA,
  hbe_dPBAaCXAsepPM1, hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepPM1 = hbe_dPBAaCXAsepPM1, hbe_dPBAaCXAsepother, hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepother = hbe_dPBAaCXAsepother,
  hbe_dCXAaCXA, hbe_dCARBOXAMIDEaCARBOXAMIDE = hbe_dCXAaCXA, hbe_dIMDaCXA, hbe_dIMIDAZOL_DELTAaCARBOXAMIDE = hbe_dIMDaCXA,
  hbe_dIMEaCXA, hbe_dIMIDAZOL_EPSILONaCARBOXAMIDE = hbe_dIMEaCXA, hbe_dINDaCXA, hbe_dINDOLaCARBOXAMIDE = hbe_dINDaCXA,
  hbe_dAMOaCXA, hbe_dAMINOaCARBOXAMIDE = hbe_dAMOaCXA, hbe_dGDEaCXA, hbe_dGUANIDINIUM_EPSILONaCARBOXAMIDE = hbe_dGDEaCXA,
  hbe_dGDHaCXA, hbe_dDIHYDRO_GUANIDINIUMaCARBOXAMIDE = hbe_dGDHaCXA, hbe_dAHXaCXA, hbe_dAROMATIC_HYDROXYLaCARBOXAMIDE = hbe_dAHXaCXA,
  hbe_dHXLaCXA, hbe_dHYDROXYLaCARBOXAMIDE = hbe_dHXLaCXA, hbe_dH2OaCXA, hbe_dWATERaCARBOXAMIDE = hbe_dH2OaCXA,
  hbe_dPBAaCXLsepPM1, hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepPM1 = hbe_dPBAaCXLsepPM1, hbe_dPBAaCXLsepother, hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepother = hbe_dPBAaCXLsepother,
  hbe_dCXAaCXL, hbe_dCARBOXAMIDEaCARBOXYL = hbe_dCXAaCXL, hbe_dIMDaCXL, hbe_dIMIDAZOL_DELTAaCARBOXYL = hbe_dIMDaCXL,
  hbe_dIMEaCXL, hbe_dIMIDAZOL_EPSILONaCARBOXYL = hbe_dIMEaCXL, hbe_dINDaCXL, hbe_dINDOLaCARBOXYL = hbe_dINDaCXL,
  hbe_dAMOaCXL, hbe_dAMINOaCARBOXYL = hbe_dAMOaCXL, hbe_dGDEaCXL, hbe_dGUANIDINIUM_EPSILONaCARBOXYL = hbe_dGDEaCXL,
  hbe_dGDHaCXL, hbe_dDIHYDRO_GUANIDINIUMaCARBOXYL = hbe_dGDHaCXL, hbe_dAHXaCXL, hbe_dAROMATIC_HYDROXYLaCARBOXYL = hbe_dAHXaCXL,
  hbe_dHXLaCXL, hbe_dHYDROXYLaCARBOXYL = hbe_dHXLaCXL, hbe_dH2OaCXL, hbe_dWATERaCARBOXYL = hbe_dH2OaCXL,
  hbe_dPBAaIMDsepPM1, hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepPM1 = hbe_dPBAaIMDsepPM1, hbe_dPBAaIMDsepother, hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepother = hbe_dPBAaIMDsepother,
  hbe_dCXAaIMD, hbe_dCARBOXAMIDEaIMIDAZOL_DELTA = hbe_dCXAaIMD, hbe_dIMDaIMD, hbe_dIMIDAZOL_DELTAaIMIDAZOL_DELTA = hbe_dIMDaIMD,
  hbe_dIMEaIMD, hbe_dIMIDAZOL_EPSILONaIMIDAZOL_DELTA = hbe_dIMEaIMD, hbe_dINDaIMD, hbe_dINDOLaIMIDAZOL_DELTA = hbe_dINDaIMD,
  hbe_dAMOaIMD, hbe_dAMINOaIMIDAZOL_DELTA = hbe_dAMOaIMD, hbe_dGDEaIMD, hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_DELTA = hbe_dGDEaIMD,
  hbe_dGDHaIMD, hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_DELTA = hbe_dGDHaIMD, hbe_dAHXaIMD, hbe_dAROMATIC_HYDROXYLaIMIDAZOL_DELTA = hbe_dAHXaIMD,
  hbe_dHXLaIMD, hbe_dHYDROXYLaIMIDAZOL_DELTA = hbe_dHXLaIMD, hbe_dH2OaIMD, hbe_dWATERaIMIDAZOL_DELTA = hbe_dH2OaIMD,
  hbe_dPBAaIMEsepPM1, hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepPM1 = hbe_dPBAaIMEsepPM1, hbe_dPBAaIMEsepother, hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepother = hbe_dPBAaIMEsepother,
  hbe_dCXAaIME, hbe_dCARBOXAMIDEaIMIDAZOL_EPSILON = hbe_dCXAaIME, hbe_dIMDaIME, hbe_dIMIDAZOL_DELTAaIMIDAZOL_EPSILON = hbe_dIMDaIME,
  hbe_dIMEaIME, hbe_dIMIDAZOL_EPSILONaIMIDAZOL_EPSILON = hbe_dIMEaIME, hbe_dINDaIME, hbe_dINDOLaIMIDAZOL_EPSILON = hbe_dINDaIME,
  hbe_dAMOaIME, hbe_dAMINOaIMIDAZOL_EPSILON = hbe_dAMOaIME, hbe_dGDEaIME, hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_EPSILON = hbe_dGDEaIME,
  hbe_dGDHaIME, hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_EPSILON = hbe_dGDHaIME, hbe_dAHXaIME, hbe_dAROMATIC_HYDROXYLaIMIDAZOL_EPSILON = hbe_dAHXaIME,
  hbe_dHXLaIME, hbe_dHYDROXYLaIMIDAZOL_EPSILON = hbe_dHXLaIME, hbe_dH2OaIME, hbe_dWATERaIMIDAZOL_EPSILON = hbe_dH2OaIME,
  hbe_dPBAaAHXsepPM1, hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepPM1 = hbe_dPBAaAHXsepPM1, hbe_dPBAaAHXsepother, hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepother = hbe_dPBAaAHXsepother,
  hbe_dCXAaAHX, hbe_dCARBOXAMIDEaAROMATIC_HYDROXYL = hbe_dCXAaAHX, hbe_dIMDaAHX, hbe_dIMIDAZOL_DELTAaAROMATIC_HYDROXYL = hbe_dIMDaAHX,
  hbe_dIMEaAHX, hbe_dIMIDAZOL_EPSILONaAROMATIC_HYDROXYL = hbe_dIMEaAHX, hbe_dINDaAHX, hbe_dINDOLaAROMATIC_HYDROXYL = hbe_dINDaAHX,
  hbe_dAMOaAHX, hbe_dAMINOaAROMATIC_HYDROXYL = hbe_dAMOaAHX, hbe_dGDEaAHX, hbe_dGUANIDINIUM_EPSILONaAROMATIC_HYDROXYL = hbe_dGDEaAHX,
  hbe_dGDHaAHX, hbe_dDIHYDRO_GUANIDINIUMaAROMATIC_HYDROXYL = hbe_dGDHaAHX, hbe_dAHXaAHX, hbe_dAROMATIC_HYDROXYLaAROMATIC_HYDROXYL = hbe_dAHXaAHX,
  hbe_dHXLaAHX, hbe_dHYDROXYLaAROMATIC_HYDROXYL = hbe_dHXLaAHX, hbe_dH2OaAHX, hbe_dWATERaAROMATIC_HYDROXYL = hbe_dH2OaAHX,
  hbe_dPBAaHXLsepPM1, hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepPM1 = hbe_dPBAaHXLsepPM1, hbe_dPBAaHXLsepother, hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepother = hbe_dPBAaHXLsepother,
  hbe_dCXAaHXL, hbe_dCARBOXAMIDEaHYDROXYL = hbe_dCXAaHXL, hbe_dIMDaHXL, hbe_dIMIDAZOL_DELTAaHYDROXYL = hbe_dIMDaHXL,
  hbe_dIMEaHXL, hbe_dIMIDAZOL_EPSILONaHYDXROXYL = hbe_dIMEaHXL, hbe_dINDaHXL, hbe_dINDOLaHYDROXYL = hbe_dINDaHXL,
  hbe_dAMOaHXL, hbe_dAMINOaHYDROXYL = hbe_dAMOaHXL, hbe_dGDEaHXL, hbe_dGUANIDINIUM_EPSILONaHYDROXYL = hbe_dGDEaHXL,
  hbe_dGDHaHXL, hbe_dDIHYDRO_GUANIDINIUMaHYDROXYL = hbe_dGDHaHXL, hbe_dAHXaHXL, hbe_dAROMATIC_HYDROXYLaHYDROXYL = hbe_dAHXaHXL,
  hbe_dHXLaHXL, hbe_dHYDROXYLaHYDROXYL = hbe_dHXLaHXL, hbe_dH2OaHXL, hbe_dWATERaHYDROXYL = hbe_dH2OaHXL,
  hbe_dPBAaPCA_DNAsepPM1, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepPM1 = hbe_dPBAaPCA_DNAsepPM1, hbe_dPBAaPCA_DNAsepother, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepother = hbe_dPBAaPCA_DNAsepother,
  hbe_dCXAaPCA_DNA, hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_DNA = hbe_dCXAaPCA_DNA, hbe_dIMDaPCA_DNA, hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_DNA = hbe_dIMDaPCA_DNA,
  hbe_dIMEaPCA_DNA, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_DNA = hbe_dIMEaPCA_DNA, hbe_dINDaPCA_DNA, hbe_dINDOLaPHOSPHATE_CARBONYL_DNA = hbe_dINDaPCA_DNA,
  hbe_dAMOaPCA_DNA, hbe_dAMINOaPHOSPHATE_CARBONYL_DNA = hbe_dAMOaPCA_DNA, hbe_dGDEaPCA_DNA, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_DNA = hbe_dGDEaPCA_DNA,
  hbe_dGDHaPCA_DNA, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_DNA = hbe_dGDHaPCA_DNA, hbe_dAHXaPCA_DNA, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_DNA = hbe_dAHXaPCA_DNA,
  hbe_dHXLaPCA_DNA, hbe_dHYDROXYLaPHOSPHATE_CARBONYL_DNA = hbe_dHXLaPCA_DNA, hbe_dH2OaPCA_DNA, hbe_dWATERaPHOSPHATE_CARBONYL_DNA = hbe_dH2OaPCA_DNA,
  hbe_dPBAaPCA_RNAsepPM1, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dPBAaPCA_RNAsepPM1, hbe_dPBAaPCA_RNAsepother, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepother = hbe_dPBAaPCA_RNAsepother,
  hbe_dCXAaPCA_RNAsepPM1, hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dCXAaPCA_RNAsepPM1, hbe_dCXAaPCA_RNAsepother, hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepother = hbe_dCXAaPCA_RNAsepother,
  hbe_dIMDaPCA_RNAsepPM1, hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dIMDaPCA_RNAsepPM1, hbe_dIMDaPCA_RNAsepother, hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepother = hbe_dIMDaPCA_RNAsepother,
  hbe_dIMEaPCA_RNAsepPM1, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dIMEaPCA_RNAsepPM1, hbe_dIMEaPCA_RNAsepother, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepother = hbe_dIMEaPCA_RNAsepother,
  hbe_dINDaPCA_RNAsepPM1, hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dINDaPCA_RNAsepPM1, hbe_dINDaPCA_RNAsepother, hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepother = hbe_dINDaPCA_RNAsepother,
  hbe_dAMOaPCA_RNAsepPM1, hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dAMOaPCA_RNAsepPM1, hbe_dAMOaPCA_RNAsepother, hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepother = hbe_dAMOaPCA_RNAsepother,
  hbe_dGDEaPCA_RNAsepPM1, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dGDEaPCA_RNAsepPM1, hbe_dGDEaPCA_RNAsepother, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepother = hbe_dGDEaPCA_RNAsepother,
  hbe_dGDHaPCA_RNAsepPM1, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepPM1 = hbe_dGDHaPCA_RNAsepPM1, hbe_dGDHaPCA_RNAsepother, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepother = hbe_dGDHaPCA_RNAsepother,
  hbe_dAHXaPCA_RNAsepPM1, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dAHXaPCA_RNAsepPM1, hbe_dAHXaPCA_RNAsepother, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepother = hbe_dAHXaPCA_RNAsepother,
  hbe_dHXLaPCA_RNAsepPM1, hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 = hbe_dHXLaPCA_RNAsepPM1, hbe_dHXLaPCA_RNAsepother, hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepother = hbe_dHXLaPCA_RNAsepother,
  hbe_dH2OaPCA_RNA, hbe_dWATERaPHOSPHATE_CARBONYL_RNA = hbe_dH2OaPCA_RNA, hbe_dPBAaPES_DNAsepPM1, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepPM1 = hbe_dPBAaPES_DNAsepPM1,
  hbe_dPBAaPES_DNAsepother, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepother = hbe_dPBAaPES_DNAsepother, hbe_dCXAaPES_DNA, hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_DNA = hbe_dCXAaPES_DNA,
  hbe_dIMDaPES_DNA, hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_DNA = hbe_dIMDaPES_DNA, hbe_dIMEaPES_DNA, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_DNA = hbe_dIMEaPES_DNA,
  hbe_dINDaPES_DNA, hbe_dINDOLaPHOSPHATE_ESTER_DNA = hbe_dINDaPES_DNA, hbe_dAMOaPES_DNA, hbe_dAMINOaPHOSPHATE_ESTER_DNA = hbe_dAMOaPES_DNA,
  hbe_dGDEaPES_DNA, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_DNA = hbe_dGDEaPES_DNA, hbe_dGDHaPES_DNA, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_DNA = hbe_dGDHaPES_DNA,
  hbe_dAHXaPES_DNA, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_DNA = hbe_dAHXaPES_DNA, hbe_dHXLaPES_DNA, hbe_dHYDROXYLaPHOSPHATE_ESTER_DNA = hbe_dHXLaPES_DNA,
  hbe_dH2OaPES_DNA, hbe_dWATERaPHOSPHATE_ESTER_DNA = hbe_dH2OaPES_DNA, hbe_dPBAaPES_RNAsepPM1, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dPBAaPES_RNAsepPM1,
  hbe_dPBAaPES_RNAsepother, hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepother = hbe_dPBAaPES_RNAsepother, hbe_dCXAaPES_RNAsepPM1, hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dCXAaPES_RNAsepPM1,
  hbe_dCXAaPES_RNAsepother, hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepother = hbe_dCXAaPES_RNAsepother, hbe_dIMDaPES_RNAsepPM1, hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dIMDaPES_RNAsepPM1,
  hbe_dIMDaPES_RNAsepother, hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepother = hbe_dIMDaPES_RNAsepother, hbe_dIMEaPES_RNAsepPM1, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dIMEaPES_RNAsepPM1,
  hbe_dIMEaPES_RNAsepother, hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepother = hbe_dIMEaPES_RNAsepother, hbe_dINDaPES_RNAsepPM1, hbe_dINDOLaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dINDaPES_RNAsepPM1,
  hbe_dINDaPES_RNAsepother, hbe_dINDOLaPHOSPHATE_ESTER_RNAsepother = hbe_dINDaPES_RNAsepother, hbe_dAMOaPES_RNAsepPM1, hbe_dAMINOaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dAMOaPES_RNAsepPM1,
  hbe_dAMOaPES_RNAsepother, hbe_dAMINOaPHOSPHATE_ESTER_RNAsepother = hbe_dAMOaPES_RNAsepother, hbe_dGDEaPES_RNAsepPM1, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dGDEaPES_RNAsepPM1,
  hbe_dGDEaPES_RNAsepother, hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepother = hbe_dGDEaPES_RNAsepother, hbe_dGDHaPES_RNAsepPM1, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dGDHaPES_RNAsepPM1,
  hbe_dGDHaPES_RNAsepother, hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepother = hbe_dGDHaPES_RNAsepother, hbe_dAHXaPES_RNAsepPM1, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dAHXaPES_RNAsepPM1,
  hbe_dAHXaPES_RNAsepother, hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepother = hbe_dAHXaPES_RNAsepother, hbe_dHXLaPES_RNAsepPM1, hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 = hbe_dHXLaPES_RNAsepPM1,
  hbe_dHXLaPES_RNAsepother, hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepother = hbe_dHXLaPES_RNAsepother, hbe_dH2OaPES_RNA, hbe_dWATERaPHOSPHATE_ESTER_RNAsepother = hbe_dH2OaPES_RNA,
  hbe_dPBAaRRI_DNAsepPM1, hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepPM1 = hbe_dPBAaRRI_DNAsepPM1, hbe_dPBAaRRI_DNAsepother, hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepother = hbe_dPBAaRRI_DNAsepother,
  hbe_dCXAaRRI_DNA, hbe_dCARBOXAMIDEaRIBOSE_RING_DNA = hbe_dCXAaRRI_DNA, hbe_dIMDaRRI_DNA, hbe_dIMIDAZOL_DELTAaRIBOSE_RING_DNA = hbe_dIMDaRRI_DNA,
  hbe_dIMEaRRI_DNA, hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_DNA = hbe_dIMEaRRI_DNA, hbe_dINDaRRI_DNA, hbe_dINDOLaRIBOSE_RING_DNA = hbe_dINDaRRI_DNA,
  hbe_dAMOaRRI_DNA, hbe_dAMINOaRIBOSE_RING_DNA = hbe_dAMOaRRI_DNA, hbe_dGDEaRRI_DNA, hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_DNA = hbe_dGDEaRRI_DNA,
  hbe_dGDHaRRI_DNA, hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_DNA = hbe_dGDHaRRI_DNA, hbe_dAHXaRRI_DNA, hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_DNA = hbe_dAHXaRRI_DNA,
  hbe_dHXLaRRI_DNA, hbe_dHYDROXYLaRIBOSE_RING_DNA = hbe_dHXLaRRI_DNA, hbe_dH2OaRRI_DNA, hbe_dWATERaRIBOSE_RING_DNA = hbe_dH2OaRRI_DNA,
  hbe_dPBAaRRI_RNAsepPM1, hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepPM1 = hbe_dPBAaRRI_RNAsepPM1, hbe_dPBAaRRI_RNAsepother, hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepother = hbe_dPBAaRRI_RNAsepother,
  hbe_dCXAaRRI_RNAsepPM1, hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepPM1 = hbe_dCXAaRRI_RNAsepPM1, hbe_dCXAaRRI_RNAsepother, hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepother = hbe_dCXAaRRI_RNAsepother,
  hbe_dIMDaRRI_RNAsepPM1, hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepPM1 = hbe_dIMDaRRI_RNAsepPM1, hbe_dIMDaRRI_RNAsepother, hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepother = hbe_dIMDaRRI_RNAsepother,
  hbe_dIMEaRRI_RNAsepPM1, hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepPM1 = hbe_dIMEaRRI_RNAsepPM1, hbe_dIMEaRRI_RNAsepother, hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepother = hbe_dIMEaRRI_RNAsepother,
  hbe_dINDaRRI_RNAsepPM1, hbe_dINDOLaRIBOSE_RING_RNAsepPM1 = hbe_dINDaRRI_RNAsepPM1, hbe_dINDaRRI_RNAsepother, hbe_dINDOLaRIBOSE_RING_RNAsepother = hbe_dINDaRRI_RNAsepother,
  hbe_dAMOaRRI_RNAsepPM1, hbe_dAMINOaRIBOSE_RING_RNAsepPM1 = hbe_dAMOaRRI_RNAsepPM1, hbe_dAMOaRRI_RNAsepother, hbe_dAMINOaRIBOSE_RING_RNAsepother = hbe_dAMOaRRI_RNAsepother,
  hbe_dGDEaRRI_RNAsepPM1, hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepPM1 = hbe_dGDEaRRI_RNAsepPM1, hbe_dGDEaRRI_RNAsepother, hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepother = hbe_dGDEaRRI_RNAsepother,
  hbe_dGDHaRRI_RNAsepPM1, hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepPM1 = hbe_dGDHaRRI_RNAsepPM1, hbe_dGDHaRRI_RNAsepother, hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepother = hbe_dGDHaRRI_RNAsepother,
  hbe_dAHXaRRI_RNAsepPM1, hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepPM1 = hbe_dAHXaRRI_RNAsepPM1, hbe_dAHXaRRI_RNAsepother, hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepother = hbe_dAHXaRRI_RNAsepother,
  hbe_dHXLaRRI_RNAsepPM1, hbe_dHYDROXYLaRIBOSE_RING_RNAsepPM1 = hbe_dHXLaRRI_RNAsepPM1, hbe_dHXLaRRI_RNAsepother, hbe_dHYDROXYLaRIBOSE_RING_RNAsepother = hbe_dHXLaRRI_RNAsepother,
  hbe_dH2OaRRI_RNA, hbe_dWATERaRIBOSE_RING_RNAsepother = hbe_dH2OaRRI_RNA, hbe_dPBAaH2O, hbe_dPROTEIN_BB_AMIDEaWATER = hbe_dPBAaH2O,
  hbe_dCXAaH2O, hbe_dCARBOXAMIDEaWATER = hbe_dCXAaH2O, hbe_dIMDaH2O, hbe_dIMIDAZOL_DELTAaWATER = hbe_dIMDaH2O,
  hbe_dIMEaH2O, hbe_dIMIDAZOL_EPSILONaWATER = hbe_dIMEaH2O, hbe_dINDaH2O, hbe_dINDOLaWATER = hbe_dINDaH2O,
  hbe_dAMOaH2O, hbe_dAMINOaWATER = hbe_dAMOaH2O, hbe_dGDEaH2O, hbe_dGUANIDINIUM_EPSILONaWATER = hbe_dGDEaH2O,
  hbe_dGDHaH2O, hbe_dDIHYDRO_GUANIDINIUMaWATER = hbe_dGDHaH2O, hbe_dAHXaH2O, hbe_dAROMATIC_HYDROXYLaWATER = hbe_dAHXaH2O,
  hbe_dHXLaH2O, hbe_dHYDROXYLaWATER = hbe_dHXLaH2O, hbe_dH2OaH2O, hbe_dWATERaWATER = hbe_dH2OaH2O,
  hbe_GENERIC_SP2BB_SR, hbe_GENERIC_SP2BB_LR, hbe_GENERIC_SP3BB_SR, hbe_GENERIC_SP3BB_LR,
  hbe_GENERIC_RINGBB_SR, hbe_GENERIC_RINGBB_LR, hbe_GENERIC_SP2BSC_SR, hbe_GENERIC_SP2BSC_LR,
  hbe_GENERIC_SP3BSC_SR, hbe_GENERIC_SP3BSC_LR, hbe_GENERIC_RINGBSC_SR, hbe_GENERIC_RINGBSC_LR,
  hbe_GENERIC_SP2SCSC_SR, hbe_GENERIC_SP2SCSC_LR, hbe_GENERIC_SP3SCSC_SR, hbe_GENERIC_SP3SCSC_LR,
  hbe_GENERIC_RINGSCSC_SR, hbe_GENERIC_RINGSCSC_LR, hbe_MAX = hbe_GENERIC_RINGSCSC_LR
}
 
enum  HBSeqSep {
  seq_sep_other = 1, seq_sep_M4, seq_sep_M3, seq_sep_M2,
  seq_sep_PM1, seq_sep_P2, seq_sep_P3, seq_sep_P4,
  seq_sep_MAX = seq_sep_P4
}
 
enum  which_atom_in_hbond {
  which_hb_unassigned = 0, which_hb_hatm, which_hb_datm, which_last_donor_atm = which_hb_datm,
  which_hb_aatm, which_hb_abase, which_hb_abase_prime, which_hb_abase2,
  n_hb_atoms = which_hb_abase2
}
 If you have an atom that is involved in a hydrogen bond, this enumeration will help you keep track of the role that the atom plays. More...
 
enum  HBGeoDimType {
  hbgd_NONE = 1, hbgd_AHdist, hbgd_cosBAH, hbgd_cosAHD,
  hbgd_AHD, hbgd_chi, hbgd_MAX =hbgd_chi
}
 
enum  HBDerivType {
  hbderiv_NONE = 1, hbderiv_ABE_GO, hbderiv_ABE_GO_GEOMSOL_OCC_ACC, hbderiv_ABE_GO_GEOMSOL_OCC_DON,
  hbderiv_MAX = hbderiv_ABE_GO_GEOMSOL_OCC_DON
}
 

Functions

bool operator== (FadeInterval const &a, FadeInterval const &b)
 
bool operator!= (FadeInterval const &a, FadeInterval const &b)
 
ostream & operator<< (ostream &out, FadeInterval const &fade_interval)
 
bool operator== (HBEvalTuple const &a, HBEvalTuple const &b)
 
std::ostream & operator<< (std::ostream &out, HBEvalTuple const &hbt)
 
static Tracer tr ("core.scoring.hbonds.HBondDatabase")
 
static basic::Tracer tr ("core.scoring.hbonds.HbondEnergy")
 
void create_rotamer_descriptor (conformation::Residue const &res, hbonds::HBondOptions const &options, hbonds::HBondSet const &hbond_set, trie::RotamerDescriptor< hbtrie::HBAtom, hbtrie::HBCPData > &rotamer_descriptor, bool near_wat=false, bool is_wat=false)
 
bool operator== (HBondOptions const &a, HBondOptions const &b)
 
bool operator!= (HBondOptions const &a, HBondOptions const &b)
 
std::ostream & operator<< (std::ostream &out, const HBondOptions &options)
 
HBondOptionsOP deep_copy (HBondOptions const &source)
 Needed to allow this to be used with DeepCopyOPs. More...
 
static basic::Tracer tr ("core.scoring.hbonds.hbonds")
 
bool residue_near_water (pose::Pose const &pose, Size ii)
 Waters ///. More...
 
core::Size next_hb_res (core::scoring::hbonds::HBond const &c_hb, core::Size const res)
 Get the residue that this residue connects to through this particular hbond We treat hbonds as directed connections (we ignore donor/acceptor). More...
 
void find_hb_paths (HBondSet const &local_hb_set, utility::vector1< core::Size > const &bridge_residues, std::map< std::string, core::Size > &paths, core::Size const current_res, core::Size const max_depth, std::string const &current_path, core::Size const current_depth, HBondCOP prev_hb)
 Recursive function to find all unique HBond paths involving bridge_residues and ending with a residue that is not in our bridged_residue list. More...
 
void fill_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
 
void fill_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, SSWeightParameters const &sswt, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
 
bool calculate_intra_res_hbonds (conformation::Residue const &rsd, HBondOptions const &options)
 General Utilities ///. More...
 
void fill_intra_res_hbond_set (pose::Pose const &pose, bool const calculate_derivative, HBondSet &hbond_set, bool const exclude_bb=false, bool const exclude_bsc=false, bool const exclude_scb=false, bool const exclude_sc=false)
 HBondSet Filling (Deprecated in favor of direct hbset functions)///. More...
 
core::Real get_ssdep_weight (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, SSWeightParameters const &ssdep)
 
void fill_hbond_set_by_AHdist_threshold (pose::Pose const &pose, Real const AHdist_threshold, HBondSet &hbond_set)
 Fill HBondSet using the distance between the acceptor and hydrogen atoms as the definitional cutoff. Do not exclude any contacts and do not evaluate derivatives. More...
 
void identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_don_bb, bool const exclude_don_bsc, bool const exclude_acc_scb, bool const exclude_acc_sc,HBondSet &hbond_set, Real ssdep_weight_factor=1.0, bool bond_near_wat=false)
 HBond Database ///. More...
 
void identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, Real ssdep_weight_factor, bool bond_near_wat)
 
void identify_hbonds_1way (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, boost::unordered_map< core::Size, core::Size > &num_hbonds, Real ssdep_weight_factor, bool bond_near_wat)
 
Real hb_energy (HBondDatabase const &database, HBondOptions const &options, HBondSet const &hbset, conformation::Residue const &acc_rsd, Size aatm, conformation::Residue const &don_rsd, Size hatm)
 Returns the energy for the hydrogen bond between a given don/acceptor pair. More...
 
void identify_hbonds_1way_AHdist (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, Real const AHdist_threshold, HBondSet &hbond_set, bool bond_near_wat)
 
void identify_intra_res_hbonds (HBondDatabase const &database, conformation::Residue const &rsd, Size const rsd_nb, bool const evaluate_derivative, HBondSet &hbond_set, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc)
 
void identify_intra_res_hbonds (HBondDatabase const &database, conformation::Residue const &rsd, Size const rsd_nb, HBondOptions const &options, EnergyMap &emap)
 
void increment_hbond_energy (HBEvalType const &hbe_type, EnergyMap &emap, Real hbE)
 Scoring ///. More...
 
void increment_npd_hbond_energy (HBEvalType const &hbe_type, EnergyMap &emap, Real hbE, bool intra_res)
 Increment the appropriate places in the input energy map for a particular hydrogen bond. More...
 
void get_hbond_energies (HBondSet const &hbond_set, EnergyMap &emap)
 
Real hb_eval_type_weight (HBEvalType const &hbe_type, EnergyMap const &weights, bool const intra_res, bool const put_intra_into_total)
 
Real npd_hb_eval_type_weight (HBEvalType const &hbe_type, EnergyMap const &weights, bool const intra_res, bool const put_intra_into_total)
 
core::Real burial_weight (int const nb)
 
core::Real hb_env_dep_burial_lin (int const nb1, int const nb2)
 
void burial3class_weight_initializer (FArray2D_double &burial)
 
int get_burial_3 (int const neighbors, int const threshold_1, int const threshold_3)
 
core::Real hb_env_dep_burial_tk (int const nb1, int const nb2)
 
Real get_environment_dependent_weight (HBEvalTuple const &hbe_type, int const don_nb, int const acc_nb, HBondOptions const &options)
 
bool nonzero_hbond_weight (ScoreFunction const &scorefxn)
 
void identify_hbonds_1way_membrane (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_don_bb, bool const exclude_don_bsc, bool const exclude_acc_scb, bool const exclude_acc_sc, HBondSet &hbond_set, pose::Pose const &pose, bool bond_near_wat=false)
 Identify Membrane Hydrogen Bonds (Env) More...
 
void identify_hbonds_1way_membrane (HBondDatabase const &database, conformation::Residue const &don_rsd, conformation::Residue const &acc_rsd, Size const don_nb, Size const acc_nb, bool const evaluate_derivative, bool const exclude_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondOptions const &options, EnergyMap &emap, pose::Pose const &pose, bool bond_near_wat)
 
Real get_membrane_depth_dependent_weight (pose::Pose const &pose, int const don_nb, int const acc_nb, Vector const &Hxyz, Vector const &Axyz)
 
Real get_membrane_depth_dependent_weight (Vector const &normal, Vector const &center, Real const &thickness, Real const &steepness, int const don_nb, int const acc_nb, Vector const &Hxyz, Vector const &Axyz)
 
static basic::Tracer tr ("core.scoring.hbonds.hbonds_geom")
 
Real DUMMY_DERIV (0.0)
 
bool DUMMY_BOOL (false)
 
HBGeoDimType DUMMY_HBGEODIMTYPE (hbgd_NONE)
 
void fade_energy (Real &energy, Real &dE_dr, Real &dE_dxD, Real &dE_dxH, Real &dE_dxH2, Real &dE_dBAH, Real &dE_dchi)
 Fade the energy smoothly to zero over the energy range [-0.1, 0.1] Because of the additive functional form, in order to make derivative continuous at the boundary of definition, we fade the energy function smoothly to zero. More...
 
void bah_chi_compute_energy_sp2 (Real const d, Real const m, Real const l, Real const xH, Real const chi, Real const acc_don_scale, Real &energy, Real &dE_dBAH, Real &dE_dchi)
 Evaluate the Base-Acceptor-Hydrogen angle and Base-Acceptor torsion portion of the hydrogen bond energy and derivatives. More...
 
void bah_chi_compute_energy_sp3 (Real const xH, Real const chi, Real const acc_don_scale, Real &energy, Real &dE_dBAH, Real &dE_dchi)
 
HBDonChemType get_hb_don_chem_type (Size const datm, conformation::Residue const &don_rsd)
 
HBAccChemType get_hb_acc_chem_type (Size const aatm, conformation::Residue const &acc_rsd)
 
HBSeqSep get_seq_sep (HBDonChemType const &don_chem_type, HBAccChemType const &acc_chem_type, int const &sep)
 
hbonds::HBEvalTuple hbond_evaluation_type (hbtrie::HBAtom const &datm, Size const don_rsd, hbtrie::HBAtom const &aatm, Size const acc_rsd)
 
hbonds::HBEvalTuple hbond_evaluation_type (Size const datm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd)
 
void hbond_compute_energy (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Real const AHdis, Real const xD, Real const xH, Real const xH2, Real const chi, Real &energy, bool &apply_chi_torsion_penalty, HBGeoDimType &AHD_geometric_dimension, Real &dE_dr, Real &dE_dxD, Real &dE_dxH, Real &dE_dxH2, Real &dE_dBAH, Real &dE_dchi)
 
void hb_energy_deriv_u (HBondDatabase const &database, HBondOptions const &hbondoptions, hbonds::HBEvalTuple const &hbt, Vector const &Hxyz, Vector const &Dxyz, Vector const &HDunit, Vector const &Axyz, Vector const &Bxyz, Vector const &BAunit, Vector const &B2xyz, Vector const &B2Aunit, Real &energy, bool const evaluate_deriv, HBondDerivs &deriv)
 car Evaluate the energy and derivative components for a hydrogen bond More...
 
void hb_energy_deriv_u2 (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt,HBDerivType const deriv_type, Vector const &Hxyz,Vector const &Dxyz,Vector const &HDunit,Vector const &Axyz,Vector const &Bxyz,Vector const &BAunit,Vector const &B2xyz,Vector const &B2Aunit,Real &energy, HBondDerivs &deriv=DUMMY_DERIVS)
 Evaluate the hydrogen bond energy and derivatives after having first calculated the HD and BA *u*nit vectors; deriv type must have been chosen (why does this exist?) More...
 
void hb_energy_deriv (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Vector const &Dxyz, Vector const &Hxyz, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Real &energy, bool const evaluate_deriv, HBondDerivs &deriv)
 
void hb_energy_deriv (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Vector const &Dxyz, Vector const &Hxyz, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Real &energy, HBDerivType const deriv_type, HBondDerivs &deriv)
 
Vector create_acc_orientation_vector (HBondOptions const &hbondoptions, conformation::Residue const &residue, int atom_id)
 
void make_hbBasetoAcc_unitvector (HBondOptions const &hbondoptions, chemical::Hybridization const &acc_hybrid, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Vector &PBxyz, Vector &BAunit, Vector &B2Aunit)
 
void assign_abase_derivs (HBondOptions const &hbondoptions, conformation::Residue const &acc_rsd, Size acc_atom, chemical::Hybridization const &acc_hybrid, DerivVectorPair const &abase_deriv, Real weighted_energy, utility::vector1< DerivVectorPair > &acc_atom_derivs)
 
void assign_abase_derivs (HBondOptions const &hbondoptions, conformation::Residue const &acc_rsd, Size acc_atom, HBEvalTuple const &hbt, DerivVectorPair const &abase_deriv, Real weighted_energy, utility::vector1< DerivVectorPair > &acc_atom_derivs)
 
Vector create_don_orientation_vector (conformation::Residue const &residue, int atom_id)
 create a unit vector pointing from the hydrogen toward the donor The atom_id is the atom id of the hydrogen atom More...
 
static basic::Tracer t ("core.scoring.hbonds.HBondSet")
 
std::ostream & operator<< (std::ostream &out, const HBond &hbond)
 
bool operator== (HBond const &a, HBond const &b)
 
std::ostream & operator<< (std::ostream &out, const HBondSet &hbond_set)
 
bool operator== (HBondSet const &a, HBondSet const &b)
 
std::ostream & operator<< (std::ostream &out, const NPDHBondSet &hbond_set)
 
bool operator== (NPDHBondSet const &a, NPDHBondSet const &b)
 
void weights_for_hbonds (conformation::Residue const &res, Size atom, utility::vector1< Real > const &energies, utility::vector1< Real > &weights)
 depending on the hybridization type of the atom, compute the weights for its hydrogen bonds. No derivative evaluation. More...
 
void weights_and_derivs_for_hbonds (conformation::Residue const &res, Size atom, utility::vector1< Real > const &energies, utility::vector1< Real > &weights, utility::vector1< utility::vector1< Real > > &dwt_dE)
 depending on the hybridization type of the atom, compute the weights for its hydrogen bonds. No derivative evaluation. More...
 
void get_weights_for_one_partner_hbonder (utility::vector1< Real > const &energies, utility::vector1< Real > &weights, utility::vector1< utility::vector1< Real > > &dwt_dE)
 
Real get_weights_for_one_partner_hbonder (utility::vector1< Real > const &energies, utility::vector1< Real > &weights)
 Helper function used by the weights_for_hbonds function above. More...
 
void get_weights_for_two_partner_hbonder (utility::vector1< Real > const &energies, utility::vector1< Real > &weights, utility::vector1< utility::vector1< Real > > &dwt_dE)
 
void get_weights_for_two_partner_hbonder (utility::vector1< Real > const &energies, utility::vector1< Real > &weights)
 Helper function used by the weights_for_hbonds function above. More...
 
ostream & operator<< (ostream &out, const Polynomial_1d &poly)
 
static basic::Tracer TR ("core.scoring.hbonds.types")
 
Size hb_eval_type (HBDonChemType don_chem_type, HBAccChemType acc_chem_type, HBSeqSep seq_sep_type)
 
HBEvalType string_to_hb_eval_type (std::string const &hbe_str)
 converts a string into an HBEvalType More...
 
void HBEval_lookup_initializer (ObjexxFCL::FArray3D< HBEvalType > &hbe)
 
void initialize_HBEval_lookup ()
 makes it explicit that the HBEval lookup table is initialized somewhere More...
 
chemical::Hybridization get_hbe_acc_hybrid (HBEvalType const &hbe)
 
bool hbe_is_BB_type (HBEvalType hbe)
 
bool hbe_is_SC_type (HBEvalType hbe)
 
HBondWeightType get_hbond_weight_type (HBEvalType const &hbe_type)
 

Variables

Size const HB_EVAL_TYPE_COUNT = { (hbdon_MAX-1)*(hbacc_MAX-1)*(seq_sep_MAX-1)}
 
static core::Real const MAX_R = { 3.0 }
 
static core::Real const MIN_R = { 0.0 }
 
static core::Real const MIN_xH = { -1.0 }
 
static core::Real const MIN_xD = { 0.0 }
 
static core::Real const MAX_xH = { 1.0 }
 
static core::Real const MAX_xD = { 1.0 }
 
static core::Real const MIN_R2 = { MIN_R * MIN_R }
 
static core::Real const MAX_R2 = { MAX_R * MAX_R }
 
HBEvalTuple DUMMY_HBE
 
HBondDerivs DUMMY_DERIVS
 
HBondDerivs const ZERO_DERIV2D = { DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair() }
 
Real DUMMY_DERIV
 
bool DUMMY_BOOL
 
HBGeoDimType DUMMY_HBGEODIMTYPE
 
utility::pointer::shared_ptr
< ObjexxFCL::FArray3D
< HBEvalType > const > 
HBEval_lookup
 

Typedef Documentation

typedef utility::pointer::shared_ptr< FadeInterval const > core::scoring::hbonds::FadeIntervalCOP
typedef utility::pointer::shared_ptr< FadeInterval > core::scoring::hbonds::FadeIntervalOP
typedef utility::pointer::shared_ptr< HBond const > core::scoring::hbonds::HBondCOP
typedef utility::pointer::shared_ptr< HBondDatabase const > core::scoring::hbonds::HBondDatabaseCOP
typedef utility::pointer::shared_ptr< HBondDatabase > core::scoring::hbonds::HBondDatabaseOP
typedef utility::pointer::shared_ptr< HBondEnergy const > core::scoring::hbonds::HBondEnergyCAP
typedef utility::pointer::shared_ptr< HBondEnergy const > core::scoring::hbonds::HBondEnergyCOP
typedef utility::pointer::shared_ptr< HBondEnergy > core::scoring::hbonds::HBondEnergyOP
typedef utility::pointer::shared_ptr< HBond > core::scoring::hbonds::HBondOP
typedef utility::pointer::shared_ptr< HBondOptions const > core::scoring::hbonds::HBondOptionsCOP
typedef utility::pointer::shared_ptr< HBondOptions > core::scoring::hbonds::HBondOptionsOP
using core::scoring::hbonds::HBondResidueMinDataCOP = typedef utility::pointer::shared_ptr<const HBondResidueMinData>
using core::scoring::hbonds::HBondResidueMinDataOP = typedef utility::pointer::shared_ptr<HBondResidueMinData>
using core::scoring::hbonds::HBondResPairMinDataCOP = typedef utility::pointer::shared_ptr<const HBondResPairMinData>
using core::scoring::hbonds::HBondResPairMinDataOP = typedef utility::pointer::shared_ptr<HBondResPairMinData>
typedef utility::pointer::shared_ptr< HBondSet const > core::scoring::hbonds::HBondSetCOP
typedef utility::pointer::shared_ptr< HBondSet > core::scoring::hbonds::HBondSetOP
typedef utility::pointer::shared_ptr< HBondTypeManager const > core::scoring::hbonds::HBondTypeManagerCOP
typedef utility::pointer::shared_ptr< HBondTypeManager > core::scoring::hbonds::HBondTypeManagerOP
typedef utility::pointer::shared_ptr< NPDHBondSet const > core::scoring::hbonds::NPDHBondSetCOP
typedef utility::pointer::shared_ptr< NPDHBondSet > core::scoring::hbonds::NPDHBondSetOP
typedef utility::pointer::shared_ptr< Polynomial_1d const > core::scoring::hbonds::Polynomial_1dCOP
typedef utility::pointer::shared_ptr< Polynomial_1d > core::scoring::hbonds::Polynomial_1dOP

Enumeration Type Documentation

Enumerator
hbacc_NONE 
hbacc_PBA 
hbacc_CXA 
hbacc_CXL 
hbacc_IMD 
hbacc_IME 
hbacc_AHX 
hbacc_HXL 
hbacc_PCA_DNA 
hbacc_PES_DNA 
hbacc_RRI_DNA 
hbacc_PCA_RNA 
hbacc_PES_RNA 
hbacc_RRI_RNA 
hbacc_H2O 
hbacc_GENERIC_SP2BB 
hbacc_GENERIC_SP2SC 
hbacc_GENERIC_SP3BB 
hbacc_GENERIC_SP3SC 
hbacc_GENERIC_RINGBB 
hbacc_GENERIC_RINGSC 
hbacc_MAX 
Enumerator
hbderiv_NONE 
hbderiv_ABE_GO 
hbderiv_ABE_GO_GEOMSOL_OCC_ACC 
hbderiv_ABE_GO_GEOMSOL_OCC_DON 
hbderiv_MAX 
Enumerator
hbdon_NONE 
hbdon_PBA 
hbdon_CXA 
hbdon_IMD 
hbdon_IME 
hbdon_IND 
hbdon_AMO 
hbdon_GDE 
hbdon_GDH 
hbdon_AHX 
hbdon_HXL 
hbdon_H2O 
hbdon_GENERIC_BB 
hbdon_GENERIC_SC 
hbdon_MAX 
Enumerator
hbe_UNKNOWN 
hbe_NONE 
hbe_dPBAaPBAsepM4helix 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM4helix 
hbe_dPBAaPBAsepM3turn 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM3turn 
hbe_dPBAaPBAsepM2turn 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM2turn 
hbe_dPBAaPBAsepPM1 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepPM1 
hbe_dPBAaPBAsepP2turn 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP2turn 
hbe_dPBAaPBAsepP3turn 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP3turn 
hbe_dPBAaPBAsepP4helix 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP4helix 
hbe_dPBAaPBAsepother 
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepother 
hbe_dCXAaPBAsepPM1 
hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepPM1 
hbe_dIMDaPBAsepPM1 
hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepPM1 
hbe_dIMEaPBAsepPM1 
hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepPM1 
hbe_dINDaPBAsepPM1 
hbe_dINDOLaPROTEIN_BB_AMIDEsepPM1 
hbe_dAMOaPBAsepPM1 
hbe_dAMINOaPROTEIN_BB_AMIDEsepPM1 
hbe_dGDEaPBAsepPM1 
hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepPM1 
hbe_dGDHaPBAsepPM1 
hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepPM1 
hbe_dAHXaPBAsepPM1 
hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepPM1 
hbe_dHXLaPBAsepPM1 
hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepPM1 
hbe_dCXAaPBAsepother 
hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepother 
hbe_dIMDaPBAsepother 
hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepother 
hbe_dIMEaPBAsepother 
hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepother 
hbe_dINDaPBAsepother 
hbe_dINDOLaPROTEIN_BB_AMIDEsepother 
hbe_dAMOaPBAsepother 
hbe_dAMINOaPROTEIN_BB_AMIDEsepother 
hbe_dGDEaPBAsepother 
hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepother 
hbe_dGDHaPBAsepother 
hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepother 
hbe_dAHXaPBAsepother 
hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepother 
hbe_dHXLaPBAsepother 
hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepother 
hbe_dH2OaPBA 
hbe_WATERaPROTEIN_BB_AMIDE 
hbe_dPBAaCXAsepPM1 
hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepPM1 
hbe_dPBAaCXAsepother 
hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepother 
hbe_dCXAaCXA 
hbe_dCARBOXAMIDEaCARBOXAMIDE 
hbe_dIMDaCXA 
hbe_dIMIDAZOL_DELTAaCARBOXAMIDE 
hbe_dIMEaCXA 
hbe_dIMIDAZOL_EPSILONaCARBOXAMIDE 
hbe_dINDaCXA 
hbe_dINDOLaCARBOXAMIDE 
hbe_dAMOaCXA 
hbe_dAMINOaCARBOXAMIDE 
hbe_dGDEaCXA 
hbe_dGUANIDINIUM_EPSILONaCARBOXAMIDE 
hbe_dGDHaCXA 
hbe_dDIHYDRO_GUANIDINIUMaCARBOXAMIDE 
hbe_dAHXaCXA 
hbe_dAROMATIC_HYDROXYLaCARBOXAMIDE 
hbe_dHXLaCXA 
hbe_dHYDROXYLaCARBOXAMIDE 
hbe_dH2OaCXA 
hbe_dWATERaCARBOXAMIDE 
hbe_dPBAaCXLsepPM1 
hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepPM1 
hbe_dPBAaCXLsepother 
hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepother 
hbe_dCXAaCXL 
hbe_dCARBOXAMIDEaCARBOXYL 
hbe_dIMDaCXL 
hbe_dIMIDAZOL_DELTAaCARBOXYL 
hbe_dIMEaCXL 
hbe_dIMIDAZOL_EPSILONaCARBOXYL 
hbe_dINDaCXL 
hbe_dINDOLaCARBOXYL 
hbe_dAMOaCXL 
hbe_dAMINOaCARBOXYL 
hbe_dGDEaCXL 
hbe_dGUANIDINIUM_EPSILONaCARBOXYL 
hbe_dGDHaCXL 
hbe_dDIHYDRO_GUANIDINIUMaCARBOXYL 
hbe_dAHXaCXL 
hbe_dAROMATIC_HYDROXYLaCARBOXYL 
hbe_dHXLaCXL 
hbe_dHYDROXYLaCARBOXYL 
hbe_dH2OaCXL 
hbe_dWATERaCARBOXYL 
hbe_dPBAaIMDsepPM1 
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepPM1 
hbe_dPBAaIMDsepother 
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepother 
hbe_dCXAaIMD 
hbe_dCARBOXAMIDEaIMIDAZOL_DELTA 
hbe_dIMDaIMD 
hbe_dIMIDAZOL_DELTAaIMIDAZOL_DELTA 
hbe_dIMEaIMD 
hbe_dIMIDAZOL_EPSILONaIMIDAZOL_DELTA 
hbe_dINDaIMD 
hbe_dINDOLaIMIDAZOL_DELTA 
hbe_dAMOaIMD 
hbe_dAMINOaIMIDAZOL_DELTA 
hbe_dGDEaIMD 
hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_DELTA 
hbe_dGDHaIMD 
hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_DELTA 
hbe_dAHXaIMD 
hbe_dAROMATIC_HYDROXYLaIMIDAZOL_DELTA 
hbe_dHXLaIMD 
hbe_dHYDROXYLaIMIDAZOL_DELTA 
hbe_dH2OaIMD 
hbe_dWATERaIMIDAZOL_DELTA 
hbe_dPBAaIMEsepPM1 
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepPM1 
hbe_dPBAaIMEsepother 
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepother 
hbe_dCXAaIME 
hbe_dCARBOXAMIDEaIMIDAZOL_EPSILON 
hbe_dIMDaIME 
hbe_dIMIDAZOL_DELTAaIMIDAZOL_EPSILON 
hbe_dIMEaIME 
hbe_dIMIDAZOL_EPSILONaIMIDAZOL_EPSILON 
hbe_dINDaIME 
hbe_dINDOLaIMIDAZOL_EPSILON 
hbe_dAMOaIME 
hbe_dAMINOaIMIDAZOL_EPSILON 
hbe_dGDEaIME 
hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_EPSILON 
hbe_dGDHaIME 
hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_EPSILON 
hbe_dAHXaIME 
hbe_dAROMATIC_HYDROXYLaIMIDAZOL_EPSILON 
hbe_dHXLaIME 
hbe_dHYDROXYLaIMIDAZOL_EPSILON 
hbe_dH2OaIME 
hbe_dWATERaIMIDAZOL_EPSILON 
hbe_dPBAaAHXsepPM1 
hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepPM1 
hbe_dPBAaAHXsepother 
hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepother 
hbe_dCXAaAHX 
hbe_dCARBOXAMIDEaAROMATIC_HYDROXYL 
hbe_dIMDaAHX 
hbe_dIMIDAZOL_DELTAaAROMATIC_HYDROXYL 
hbe_dIMEaAHX 
hbe_dIMIDAZOL_EPSILONaAROMATIC_HYDROXYL 
hbe_dINDaAHX 
hbe_dINDOLaAROMATIC_HYDROXYL 
hbe_dAMOaAHX 
hbe_dAMINOaAROMATIC_HYDROXYL 
hbe_dGDEaAHX 
hbe_dGUANIDINIUM_EPSILONaAROMATIC_HYDROXYL 
hbe_dGDHaAHX 
hbe_dDIHYDRO_GUANIDINIUMaAROMATIC_HYDROXYL 
hbe_dAHXaAHX 
hbe_dAROMATIC_HYDROXYLaAROMATIC_HYDROXYL 
hbe_dHXLaAHX 
hbe_dHYDROXYLaAROMATIC_HYDROXYL 
hbe_dH2OaAHX 
hbe_dWATERaAROMATIC_HYDROXYL 
hbe_dPBAaHXLsepPM1 
hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepPM1 
hbe_dPBAaHXLsepother 
hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepother 
hbe_dCXAaHXL 
hbe_dCARBOXAMIDEaHYDROXYL 
hbe_dIMDaHXL 
hbe_dIMIDAZOL_DELTAaHYDROXYL 
hbe_dIMEaHXL 
hbe_dIMIDAZOL_EPSILONaHYDXROXYL 
hbe_dINDaHXL 
hbe_dINDOLaHYDROXYL 
hbe_dAMOaHXL 
hbe_dAMINOaHYDROXYL 
hbe_dGDEaHXL 
hbe_dGUANIDINIUM_EPSILONaHYDROXYL 
hbe_dGDHaHXL 
hbe_dDIHYDRO_GUANIDINIUMaHYDROXYL 
hbe_dAHXaHXL 
hbe_dAROMATIC_HYDROXYLaHYDROXYL 
hbe_dHXLaHXL 
hbe_dHYDROXYLaHYDROXYL 
hbe_dH2OaHXL 
hbe_dWATERaHYDROXYL 
hbe_dPBAaPCA_DNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepPM1 
hbe_dPBAaPCA_DNAsepother 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepother 
hbe_dCXAaPCA_DNA 
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_DNA 
hbe_dIMDaPCA_DNA 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_DNA 
hbe_dIMEaPCA_DNA 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_DNA 
hbe_dINDaPCA_DNA 
hbe_dINDOLaPHOSPHATE_CARBONYL_DNA 
hbe_dAMOaPCA_DNA 
hbe_dAMINOaPHOSPHATE_CARBONYL_DNA 
hbe_dGDEaPCA_DNA 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_DNA 
hbe_dGDHaPCA_DNA 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_DNA 
hbe_dAHXaPCA_DNA 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_DNA 
hbe_dHXLaPCA_DNA 
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_DNA 
hbe_dH2OaPCA_DNA 
hbe_dWATERaPHOSPHATE_CARBONYL_DNA 
hbe_dPBAaPCA_RNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dPBAaPCA_RNAsepother 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dCXAaPCA_RNAsepPM1 
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dCXAaPCA_RNAsepother 
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dIMDaPCA_RNAsepPM1 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dIMDaPCA_RNAsepother 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dIMEaPCA_RNAsepPM1 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dIMEaPCA_RNAsepother 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dINDaPCA_RNAsepPM1 
hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dINDaPCA_RNAsepother 
hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dAMOaPCA_RNAsepPM1 
hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dAMOaPCA_RNAsepother 
hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dGDEaPCA_RNAsepPM1 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dGDEaPCA_RNAsepother 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dGDHaPCA_RNAsepPM1 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepPM1 
hbe_dGDHaPCA_RNAsepother 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepother 
hbe_dAHXaPCA_RNAsepPM1 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dAHXaPCA_RNAsepother 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dHXLaPCA_RNAsepPM1 
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 
hbe_dHXLaPCA_RNAsepother 
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepother 
hbe_dH2OaPCA_RNA 
hbe_dWATERaPHOSPHATE_CARBONYL_RNA 
hbe_dPBAaPES_DNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepPM1 
hbe_dPBAaPES_DNAsepother 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepother 
hbe_dCXAaPES_DNA 
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_DNA 
hbe_dIMDaPES_DNA 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_DNA 
hbe_dIMEaPES_DNA 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_DNA 
hbe_dINDaPES_DNA 
hbe_dINDOLaPHOSPHATE_ESTER_DNA 
hbe_dAMOaPES_DNA 
hbe_dAMINOaPHOSPHATE_ESTER_DNA 
hbe_dGDEaPES_DNA 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_DNA 
hbe_dGDHaPES_DNA 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_DNA 
hbe_dAHXaPES_DNA 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_DNA 
hbe_dHXLaPES_DNA 
hbe_dHYDROXYLaPHOSPHATE_ESTER_DNA 
hbe_dH2OaPES_DNA 
hbe_dWATERaPHOSPHATE_ESTER_DNA 
hbe_dPBAaPES_RNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dPBAaPES_RNAsepother 
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepother 
hbe_dCXAaPES_RNAsepPM1 
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dCXAaPES_RNAsepother 
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepother 
hbe_dIMDaPES_RNAsepPM1 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dIMDaPES_RNAsepother 
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepother 
hbe_dIMEaPES_RNAsepPM1 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dIMEaPES_RNAsepother 
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepother 
hbe_dINDaPES_RNAsepPM1 
hbe_dINDOLaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dINDaPES_RNAsepother 
hbe_dINDOLaPHOSPHATE_ESTER_RNAsepother 
hbe_dAMOaPES_RNAsepPM1 
hbe_dAMINOaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dAMOaPES_RNAsepother 
hbe_dAMINOaPHOSPHATE_ESTER_RNAsepother 
hbe_dGDEaPES_RNAsepPM1 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dGDEaPES_RNAsepother 
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepother 
hbe_dGDHaPES_RNAsepPM1 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dGDHaPES_RNAsepother 
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepother 
hbe_dAHXaPES_RNAsepPM1 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dAHXaPES_RNAsepother 
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepother 
hbe_dHXLaPES_RNAsepPM1 
hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 
hbe_dHXLaPES_RNAsepother 
hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepother 
hbe_dH2OaPES_RNA 
hbe_dWATERaPHOSPHATE_ESTER_RNAsepother 
hbe_dPBAaRRI_DNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepPM1 
hbe_dPBAaRRI_DNAsepother 
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepother 
hbe_dCXAaRRI_DNA 
hbe_dCARBOXAMIDEaRIBOSE_RING_DNA 
hbe_dIMDaRRI_DNA 
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_DNA 
hbe_dIMEaRRI_DNA 
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_DNA 
hbe_dINDaRRI_DNA 
hbe_dINDOLaRIBOSE_RING_DNA 
hbe_dAMOaRRI_DNA 
hbe_dAMINOaRIBOSE_RING_DNA 
hbe_dGDEaRRI_DNA 
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_DNA 
hbe_dGDHaRRI_DNA 
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_DNA 
hbe_dAHXaRRI_DNA 
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_DNA 
hbe_dHXLaRRI_DNA 
hbe_dHYDROXYLaRIBOSE_RING_DNA 
hbe_dH2OaRRI_DNA 
hbe_dWATERaRIBOSE_RING_DNA 
hbe_dPBAaRRI_RNAsepPM1 
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepPM1 
hbe_dPBAaRRI_RNAsepother 
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepother 
hbe_dCXAaRRI_RNAsepPM1 
hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepPM1 
hbe_dCXAaRRI_RNAsepother 
hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepother 
hbe_dIMDaRRI_RNAsepPM1 
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepPM1 
hbe_dIMDaRRI_RNAsepother 
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepother 
hbe_dIMEaRRI_RNAsepPM1 
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepPM1 
hbe_dIMEaRRI_RNAsepother 
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepother 
hbe_dINDaRRI_RNAsepPM1 
hbe_dINDOLaRIBOSE_RING_RNAsepPM1 
hbe_dINDaRRI_RNAsepother 
hbe_dINDOLaRIBOSE_RING_RNAsepother 
hbe_dAMOaRRI_RNAsepPM1 
hbe_dAMINOaRIBOSE_RING_RNAsepPM1 
hbe_dAMOaRRI_RNAsepother 
hbe_dAMINOaRIBOSE_RING_RNAsepother 
hbe_dGDEaRRI_RNAsepPM1 
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepPM1 
hbe_dGDEaRRI_RNAsepother 
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepother 
hbe_dGDHaRRI_RNAsepPM1 
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepPM1 
hbe_dGDHaRRI_RNAsepother 
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepother 
hbe_dAHXaRRI_RNAsepPM1 
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepPM1 
hbe_dAHXaRRI_RNAsepother 
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepother 
hbe_dHXLaRRI_RNAsepPM1 
hbe_dHYDROXYLaRIBOSE_RING_RNAsepPM1 
hbe_dHXLaRRI_RNAsepother 
hbe_dHYDROXYLaRIBOSE_RING_RNAsepother 
hbe_dH2OaRRI_RNA 
hbe_dWATERaRIBOSE_RING_RNAsepother 
hbe_dPBAaH2O 
hbe_dPROTEIN_BB_AMIDEaWATER 
hbe_dCXAaH2O 
hbe_dCARBOXAMIDEaWATER 
hbe_dIMDaH2O 
hbe_dIMIDAZOL_DELTAaWATER 
hbe_dIMEaH2O 
hbe_dIMIDAZOL_EPSILONaWATER 
hbe_dINDaH2O 
hbe_dINDOLaWATER 
hbe_dAMOaH2O 
hbe_dAMINOaWATER 
hbe_dGDEaH2O 
hbe_dGUANIDINIUM_EPSILONaWATER 
hbe_dGDHaH2O 
hbe_dDIHYDRO_GUANIDINIUMaWATER 
hbe_dAHXaH2O 
hbe_dAROMATIC_HYDROXYLaWATER 
hbe_dHXLaH2O 
hbe_dHYDROXYLaWATER 
hbe_dH2OaH2O 
hbe_dWATERaWATER 
hbe_GENERIC_SP2BB_SR 
hbe_GENERIC_SP2BB_LR 
hbe_GENERIC_SP3BB_SR 
hbe_GENERIC_SP3BB_LR 
hbe_GENERIC_RINGBB_SR 
hbe_GENERIC_RINGBB_LR 
hbe_GENERIC_SP2BSC_SR 
hbe_GENERIC_SP2BSC_LR 
hbe_GENERIC_SP3BSC_SR 
hbe_GENERIC_SP3BSC_LR 
hbe_GENERIC_RINGBSC_SR 
hbe_GENERIC_RINGBSC_LR 
hbe_GENERIC_SP2SCSC_SR 
hbe_GENERIC_SP2SCSC_LR 
hbe_GENERIC_SP3SCSC_SR 
hbe_GENERIC_SP3SCSC_LR 
hbe_GENERIC_RINGSCSC_SR 
hbe_GENERIC_RINGSCSC_LR 
hbe_MAX 
Enumerator
hbgd_NONE 
hbgd_AHdist 
hbgd_cosBAH 
hbgd_cosAHD 
hbgd_AHD 
hbgd_chi 
hbgd_MAX 
Enumerator
hbw_NONE 
hbw_SR_BB 
hbw_LR_BB 
hbw_SR_BB_SC 
hbw_LR_BB_SC 
hbw_SC 
hbw_MAX 
Enumerator
seq_sep_other 
seq_sep_M4 
seq_sep_M3 
seq_sep_M2 
seq_sep_PM1 
seq_sep_P2 
seq_sep_P3 
seq_sep_P4 
seq_sep_MAX 

If you have an atom that is involved in a hydrogen bond, this enumeration will help you keep track of the role that the atom plays.

Enumerator
which_hb_unassigned 
which_hb_hatm 
which_hb_datm 
which_last_donor_atm 
which_hb_aatm 
which_hb_abase 
which_hb_abase_prime 
which_hb_abase2 
n_hb_atoms 

Function Documentation

void core::scoring::hbonds::assign_abase_derivs ( HBondOptions const &  hbondoptions,
conformation::Residue const &  acc_rsd,
Size  acc_atom,
chemical::Hybridization const &  acc_hybrid,
DerivVectorPair const &  abase_deriv,
Real  weighted_energy,
utility::vector1< DerivVectorPair > &  acc_atom_derivs 
)

Divide up the f1/f2 contributions calculated for the PBxyz coordinate among the atom(s) that define the location of the PBxyz coordinate. In the base of ring-hybridized acceptors, half of the derivative goes to the abase, and half of hte derivative goes to the abase2. This code mirrors the logic in the make_hbBasetoAcc_unitvector code above.

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, and tr().

Referenced by core::scoring::magnesium::MgEnergy::eval_mg_interaction(), and core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor().

void core::scoring::hbonds::assign_abase_derivs ( HBondOptions const &  hbondoptions,
conformation::Residue const &  acc_rsd,
Size  acc_atom,
HBEvalTuple const &  hbt,
DerivVectorPair const &  abase_deriv,
Real  weighted_energy,
utility::vector1< DerivVectorPair > &  acc_atom_derivs 
)

Divide up the f1/f2 contributions calculated for the PBxyz coordinate among the atom(s) that define the location of the PBxyz coordinate. In the base of ring-hybridized acceptors, half of the derivative goes to the abase, and half of hte derivative goes to the abase2. This code mirrors the logic in the make_hbBasetoAcc_unitvector code above.

References core::scoring::hbonds::HBEvalTuple::eval_type(), and get_hbe_acc_hybrid().

void core::scoring::hbonds::bah_chi_compute_energy_sp2 ( Real const  d,
Real const  m,
Real const  l,
Real const  xH,
Real const  chi,
Real const  acc_don_scale,
Real &  energy,
Real &  dE_dBAH,
Real &  dE_dchi 
)
inline

Evaluate the Base-Acceptor-Hydrogen angle and Base-Acceptor torsion portion of the hydrogen bond energy and derivatives.

Formula #11

F (chi=0 or chi=pi) | G (chi=pi/2 or chi=3*pi/2) | ---—\ /-----—|--—_ _/---—|- m - 0.5 | \ / | _ _/ |- 1 m \ / | _ _/ | | \ /-\ / —| ----/ |- d - 0.5 |_ | ___/ ___/ d| |_ -0.5 |<-l->| | | | |<-BAH=2pi/3 | |<-BAh=2pi/3 - l

BAH := Base-Acceptor-Hydrogen interior Angle BAH=pi when linear and BAH=pi/2 when perpendicular

chi : Torsion angle defined by ABase2-Base-Acceptor-Hydrogen The Sp2 orbials are in the ABase2-Base-Acceptor plane For Backbone acceptors ABase2=C-alpha

d := distance from minimum value of -0.5 at BAH=120 to BAH=180 in f defined by HBondOptions::sp2_BAH180_rise() which is set by -corrections:score:hb_sp2_BAH180_rise flag and defaults to 0.75

m := distance from minimum to maximum values of f must rise high enough so that E_fade_max = maxBAH_CHI + minAHD + minAHdist (0.1) = m + (minBAH_CHI) + (-0.5) + (-0.5) m = 1.6 l := period/2 of the BAH=120 to BAH=60 piece of F emperically fit to be 0.357

F := d/2 * cos(3(pi-BAH) + d/2 - 0.5 BAH > 2pi/3 m/2 * cos(pi - (2pi/3 - BAH)/l) + m/2 - 0.5 2pi/3 > BAH > pi(2/3 - l) m-0.5 pi(2/3 - l) > BAH

G := d - 0.5 BAH > 2pi/3 (m-d)/2 * cos(pi - (2pi/3 - BAH)/l) + (m-d)/2 + d + 0.5 2pi/3 > BAH > pi(2/3 - l) m-0.5 pi(2/3 - l) > BAH

H := inteprolate smoothly betwen F and G going around chi (cos(2*chi) + 1)/2

E := Energy for BAH/CHI term H*F + (1-H)*G

dE/dchi := dH/dchi*f - dH/dchi*g = -sin(2*chi)*F + sin(2*chi)*G

dE/dBAH := H*dF/dBAH + (1-H)*dG/dBAH

dF/dBAH := 3 * d/2 * sin(3(pi-BAH)) BAH > 2pi/3 m/2 * -1/l * sin(pi - (2pi/3 - BAH)/l) 2pi/3 > BAH > pi(2/3 - l) 0 pi(2/3 - l) > BAH

dG/dBAH := 0 BAH > 2pi/3 (m-d)/2 * -1/l * sin(pi - (2pi/3 - BAH)/) 2pi/3 > BAH > pi(2/3 - l) 0 pi(2/3 - l) > BAH

References DUMMY_DERIV(), core::chemical::element::F, protocols::comparative_modeling::features::G, and core::chemical::element::H.

Referenced by hbond_compute_energy().

void core::scoring::hbonds::bah_chi_compute_energy_sp3 ( Real const  xH,
Real const  chi,
Real const  acc_don_scale,
Real &  energy,
Real &  dE_dBAH,
Real &  dE_dchi 
)
inline

References DUMMY_DERIV().

Referenced by hbond_compute_energy().

void core::scoring::hbonds::burial3class_weight_initializer ( FArray2D_double &  burial)

References core::scoring::burial.

Referenced by hb_env_dep_burial_tk().

core::Real core::scoring::hbonds::burial_weight ( int const  nb)
inline

Referenced by hb_env_dep_burial_lin().

bool core::scoring::hbonds::calculate_intra_res_hbonds ( conformation::Residue const &  rsd,
HBondOptions const &  options 
)
Vector core::scoring::hbonds::create_acc_orientation_vector ( HBondOptions const &  hbondoptions,
conformation::Residue const &  residue,
int  atom_id 
)
Vector core::scoring::hbonds::create_don_orientation_vector ( conformation::Residue const &  residue,
int  atom_id 
)

create a unit vector pointing from the hydrogen toward the donor The atom_id is the atom id of the hydrogen atom

References core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type_set(), protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

void core::scoring::hbonds::create_rotamer_descriptor ( conformation::Residue const &  res,
hbonds::HBondOptions const &  options,
hbonds::HBondSet const &  hbond_set,
trie::RotamerDescriptor< hbtrie::HBAtom, hbtrie::HBCPData > &  rotamer_descriptor,
bool  near_wat = false,
bool  is_wat = false 
)
HBondOptionsOP core::scoring::hbonds::deep_copy ( HBondOptions const &  source)

Needed to allow this to be used with DeepCopyOPs.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org).
bool core::scoring::hbonds::DUMMY_BOOL ( false  )
Real core::scoring::hbonds::DUMMY_DERIV ( 0.  0)
HBGeoDimType core::scoring::hbonds::DUMMY_HBGEODIMTYPE ( hbgd_NONE  )
void core::scoring::hbonds::fade_energy ( Real &  energy,
Real &  dE_dr,
Real &  dE_dxD,
Real &  dE_dxH,
Real &  dE_dxH2,
Real &  dE_dBAH,
Real &  dE_dchi 
)

Fade the energy smoothly to zero over the energy range [-0.1, 0.1] Because of the additive functional form, in order to make derivative continuous at the boundary of definition, we fade the energy function smoothly to zero.

Check that f(x) = -0.025 + 0.5x - 2.5x^2 satisfies f(-.1) = -0.025 + 0.5*(-.1) - 2.5*(-.1)^2 = -.1 f( .1) = -0.025 + 0.5*(.1) - 2.5*(.1)^2 = 0 f'(-.1) = 0.5 - 2.5*2*(-.1) = 1 f'(.1) = 0.5 - 2.5*2*(.1) = 0

References DUMMY_DERIV(), and protocols::features::L.

Referenced by hbond_compute_energy().

void core::scoring::hbonds::fill_hbond_set ( pose::Pose const &  pose,
bool const  calculate_derivative,
HBondSet &  hbond_set,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc 
)
void core::scoring::hbonds::fill_hbond_set ( pose::Pose const &  pose,
bool const  calculate_derivative,
HBondSet &  hbond_set,
SSWeightParameters const &  sswt,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc 
)
void core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold ( core::pose::Pose const &  pose,
Real const  AHdist_threshold,
HBondSet &  hbond_set 
)
void core::scoring::hbonds::fill_intra_res_hbond_set ( pose::Pose const &  pose,
bool const  calculate_derivative,
HBondSet &  hbond_set,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc 
)
void core::scoring::hbonds::find_hb_paths ( HBondSet const &  local_hb_set,
utility::vector1< core::Size > const &  bridge_residues,
std::map< std::string, core::Size > &  paths,
core::Size const  current_res,
core::Size const  max_depth,
std::string const &  current_path,
core::Size const  current_depth,
HBondCOP  prev_hb 
)

Recursive function to find all unique HBond paths involving bridge_residues and ending with a residue that is not in our bridged_residue list.

Recursive function to find all unique HBond paths involving bridge_residue and ending with a residue that is not in our bridged list.

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

Used in WaterMediatedHbondMetric where bridge_residues are waters

Populates paths as the non-const reference through recursion. Path is a splittable string of the connections. ex: 191-221-333 where residue 221 is a bridge_residue in our list.

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References next_hb_res(), core::scoring::hbonds::HBondSet::residue_hbonds(), and core::id::to_string().

Referenced by core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::find_hb_paths().

int core::scoring::hbonds::get_burial_3 ( int const  neighbors,
int const  threshold_1,
int const  threshold_3 
)
inline

Referenced by hb_env_dep_burial_tk().

Real core::scoring::hbonds::get_environment_dependent_weight ( HBEvalTuple const &  hbe_type,
int const  don_nb,
int const  acc_nb,
HBondOptions const &  options 
)
HBAccChemType core::scoring::hbonds::get_hb_acc_chem_type ( Size const  aatm,
conformation::Residue const &  acc_rsd 
)

References protocols::comparative_modeling::features::A, protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_b3a, core::chemical::aa_b3c, core::chemical::aa_b3cisACHC, core::chemical::aa_b3cisACPC, core::chemical::aa_b3d, core::chemical::aa_b3e, core::chemical::aa_b3f, core::chemical::aa_b3g, core::chemical::aa_b3h, core::chemical::aa_b3i, core::chemical::aa_b3k, core::chemical::aa_b3l, core::chemical::aa_b3m, core::chemical::aa_b3n, core::chemical::aa_b3p, core::chemical::aa_b3q, core::chemical::aa_b3r, core::chemical::aa_b3s, core::chemical::aa_b3t, core::chemical::aa_b3transACPC, core::chemical::aa_b3v, core::chemical::aa_b3w, core::chemical::aa_b3y, core::chemical::aa_cys, core::chemical::aa_dal, core::chemical::aa_dan, core::chemical::aa_dar, core::chemical::aa_das, core::chemical::aa_dcs, core::chemical::aa_dgn, core::chemical::aa_dgu, core::chemical::aa_dhi, core::chemical::aa_dil, core::chemical::aa_dle, core::chemical::aa_dly, core::chemical::aa_dme, core::chemical::aa_dph, core::chemical::aa_dpr, core::chemical::aa_dse, core::chemical::aa_dth, core::chemical::aa_dtr, core::chemical::aa_dty, core::chemical::aa_dva, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_h2o, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_none, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_unk, core::chemical::aa_unp, core::chemical::aa_val, core::chemical::aa_vrt, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::has_variant_type(), hbacc_AHX, hbacc_CXA, hbacc_CXL, hbacc_GENERIC_RINGBB, hbacc_GENERIC_RINGSC, hbacc_GENERIC_SP2BB, hbacc_GENERIC_SP2SC, hbacc_GENERIC_SP3BB, hbacc_GENERIC_SP3SC, hbacc_H2O, hbacc_HXL, hbacc_IMD, hbacc_IME, hbacc_NONE, hbacc_PBA, hbacc_PCA_DNA, hbacc_PCA_RNA, hbacc_PES_DNA, hbacc_PES_RNA, hbacc_RRI_DNA, hbacc_RRI_RNA, core::chemical::AtomType::hybridization(), core::chemical::element::I, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_upper_terminus(), core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_lra, core::chemical::na_lrc, core::chemical::na_lrg, core::chemical::na_lur, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, core::chemical::na_ura, core::conformation::Residue::name(), core::chemical::rna::RNA_Info::o2prime_index(), core::chemical::rna::RNA_Info::o3prime_atom_index(), core::chemical::rna::RNA_Info::o4prime_atom_index(), core::chemical::rna::RNA_Info::o5prime_atom_index(), core::chemical::rna::RNA_Info::op1_atom_index(), core::chemical::rna::RNA_Info::op2_atom_index(), core::chemical::ou3_aib, core::chemical::ou3_ala, core::chemical::ou3_arg, core::chemical::ou3_asn, core::chemical::ou3_asp, core::chemical::ou3_cys, core::chemical::ou3_gln, core::chemical::ou3_glu, core::chemical::ou3_gly, core::chemical::ou3_his, core::chemical::ou3_ile, core::chemical::ou3_leu, core::chemical::ou3_lys, core::chemical::ou3_met, core::chemical::ou3_phe, core::chemical::ou3_pro, core::chemical::ou3_ser, core::chemical::ou3_thr, core::chemical::ou3_trp, core::chemical::ou3_tyr, core::chemical::ou3_val, core::chemical::PROTONATED_N1, core::chemical::PROTONATED_N3, core::chemical::RING_HYBRID, core::chemical::ResidueType::RNA_info(), core::conformation::Residue::seqpos(), core::chemical::ResidueType::show(), core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, tr(), core::conformation::Residue::type(), and core::chemical::UNKNOWN_HYBRID.

Referenced by core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::hbonds::NPDHBondSet::derive_per_hbond_donor_and_acceptor_weights(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), hbond_evaluation_type(), protocols::features::HBondFeatures::insert_site_row(), weights_and_derivs_for_hbonds(), and weights_for_hbonds().

HBDonChemType core::scoring::hbonds::get_hb_don_chem_type ( Size const  datm,
conformation::Residue const &  don_rsd 
)

References protocols::comparative_modeling::features::A, protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_b3a, core::chemical::aa_b3c, core::chemical::aa_b3cisACHC, core::chemical::aa_b3cisACPC, core::chemical::aa_b3d, core::chemical::aa_b3e, core::chemical::aa_b3f, core::chemical::aa_b3g, core::chemical::aa_b3h, core::chemical::aa_b3i, core::chemical::aa_b3k, core::chemical::aa_b3l, core::chemical::aa_b3m, core::chemical::aa_b3n, core::chemical::aa_b3p, core::chemical::aa_b3q, core::chemical::aa_b3r, core::chemical::aa_b3s, core::chemical::aa_b3t, core::chemical::aa_b3transACPC, core::chemical::aa_b3v, core::chemical::aa_b3w, core::chemical::aa_b3y, core::chemical::aa_cys, core::chemical::aa_dal, core::chemical::aa_dan, core::chemical::aa_dar, core::chemical::aa_das, core::chemical::aa_dcs, core::chemical::aa_dgn, core::chemical::aa_dgu, core::chemical::aa_dhi, core::chemical::aa_dil, core::chemical::aa_dle, core::chemical::aa_dly, core::chemical::aa_dme, core::chemical::aa_dph, core::chemical::aa_dpr, core::chemical::aa_dse, core::chemical::aa_dth, core::chemical::aa_dtr, core::chemical::aa_dty, core::chemical::aa_dva, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_h2o, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_none, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_unk, core::chemical::aa_unp, core::chemical::aa_val, core::chemical::aa_vrt, core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::conformation::Residue::has_variant_type(), hbdon_AHX, hbdon_AMO, hbdon_CXA, hbdon_GDE, hbdon_GDH, hbdon_GENERIC_BB, hbdon_GENERIC_SC, hbdon_H2O, hbdon_HXL, hbdon_IMD, hbdon_IME, hbdon_IND, hbdon_NONE, hbdon_PBA, core::chemical::element::I, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_lra, core::chemical::na_lrc, core::chemical::na_lrg, core::chemical::na_lur, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, core::chemical::na_ura, core::conformation::Residue::name1(), core::chemical::ou3_aib, core::chemical::ou3_ala, core::chemical::ou3_arg, core::chemical::ou3_asn, core::chemical::ou3_asp, core::chemical::ou3_cys, core::chemical::ou3_gln, core::chemical::ou3_glu, core::chemical::ou3_gly, core::chemical::ou3_his, core::chemical::ou3_ile, core::chemical::ou3_leu, core::chemical::ou3_lys, core::chemical::ou3_met, core::chemical::ou3_phe, core::chemical::ou3_pro, core::chemical::ou3_ser, core::chemical::ou3_thr, core::chemical::ou3_trp, core::chemical::ou3_tyr, core::chemical::ou3_val, core::chemical::PROTONATED_N1, core::chemical::PROTONATED_N3, core::conformation::Residue::seqpos(), and core::conformation::Residue::type().

Referenced by core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), hbond_evaluation_type(), and protocols::features::HBondFeatures::insert_site_row().

chemical::Hybridization core::scoring::hbonds::get_hbe_acc_hybrid ( HBEvalType const &  hbe)

References hbe_dAHXaAHX, hbe_dAHXaCXA, hbe_dAHXaCXL, hbe_dAHXaH2O, hbe_dAHXaHXL, hbe_dAHXaIMD, hbe_dAHXaIME, hbe_dAHXaPBAsepother, hbe_dAHXaPBAsepPM1, hbe_dAHXaPCA_DNA, hbe_dAHXaPCA_RNAsepother, hbe_dAHXaPCA_RNAsepPM1, hbe_dAHXaPES_DNA, hbe_dAHXaPES_RNAsepother, hbe_dAHXaPES_RNAsepPM1, hbe_dAHXaRRI_DNA, hbe_dAHXaRRI_RNAsepother, hbe_dAHXaRRI_RNAsepPM1, hbe_dAMOaAHX, hbe_dAMOaCXA, hbe_dAMOaCXL, hbe_dAMOaH2O, hbe_dAMOaHXL, hbe_dAMOaIMD, hbe_dAMOaIME, hbe_dAMOaPBAsepother, hbe_dAMOaPBAsepPM1, hbe_dAMOaPCA_DNA, hbe_dAMOaPCA_RNAsepother, hbe_dAMOaPCA_RNAsepPM1, hbe_dAMOaPES_DNA, hbe_dAMOaPES_RNAsepother, hbe_dAMOaPES_RNAsepPM1, hbe_dAMOaRRI_DNA, hbe_dAMOaRRI_RNAsepother, hbe_dAMOaRRI_RNAsepPM1, hbe_dCXAaAHX, hbe_dCXAaCXA, hbe_dCXAaCXL, hbe_dCXAaH2O, hbe_dCXAaHXL, hbe_dCXAaIMD, hbe_dCXAaIME, hbe_dCXAaPBAsepother, hbe_dCXAaPBAsepPM1, hbe_dCXAaPCA_DNA, hbe_dCXAaPCA_RNAsepother, hbe_dCXAaPCA_RNAsepPM1, hbe_dCXAaPES_DNA, hbe_dCXAaPES_RNAsepother, hbe_dCXAaPES_RNAsepPM1, hbe_dCXAaRRI_DNA, hbe_dCXAaRRI_RNAsepother, hbe_dCXAaRRI_RNAsepPM1, hbe_dGDEaAHX, hbe_dGDEaCXA, hbe_dGDEaCXL, hbe_dGDEaH2O, hbe_dGDEaHXL, hbe_dGDEaIMD, hbe_dGDEaIME, hbe_dGDEaPBAsepother, hbe_dGDEaPBAsepPM1, hbe_dGDEaPCA_DNA, hbe_dGDEaPCA_RNAsepother, hbe_dGDEaPCA_RNAsepPM1, hbe_dGDEaPES_DNA, hbe_dGDEaPES_RNAsepother, hbe_dGDEaPES_RNAsepPM1, hbe_dGDEaRRI_DNA, hbe_dGDEaRRI_RNAsepother, hbe_dGDEaRRI_RNAsepPM1, hbe_dGDHaAHX, hbe_dGDHaCXA, hbe_dGDHaCXL, hbe_dGDHaH2O, hbe_dGDHaHXL, hbe_dGDHaIMD, hbe_dGDHaIME, hbe_dGDHaPBAsepother, hbe_dGDHaPBAsepPM1, hbe_dGDHaPCA_DNA, hbe_dGDHaPCA_RNAsepother, hbe_dGDHaPCA_RNAsepPM1, hbe_dGDHaPES_DNA, hbe_dGDHaPES_RNAsepother, hbe_dGDHaPES_RNAsepPM1, hbe_dGDHaRRI_DNA, hbe_dGDHaRRI_RNAsepother, hbe_dGDHaRRI_RNAsepPM1, hbe_dH2OaAHX, hbe_dH2OaCXA, hbe_dH2OaCXL, hbe_dH2OaH2O, hbe_dH2OaHXL, hbe_dH2OaIMD, hbe_dH2OaIME, hbe_dH2OaPBA, hbe_dH2OaPCA_DNA, hbe_dH2OaPCA_RNA, hbe_dH2OaPES_DNA, hbe_dH2OaPES_RNA, hbe_dH2OaRRI_DNA, hbe_dH2OaRRI_RNA, hbe_dHXLaAHX, hbe_dHXLaCXA, hbe_dHXLaCXL, hbe_dHXLaH2O, hbe_dHXLaHXL, hbe_dHXLaIMD, hbe_dHXLaIME, hbe_dHXLaPBAsepother, hbe_dHXLaPBAsepPM1, hbe_dHXLaPCA_DNA, hbe_dHXLaPCA_RNAsepother, hbe_dHXLaPCA_RNAsepPM1, hbe_dHXLaPES_DNA, hbe_dHXLaPES_RNAsepother, hbe_dHXLaPES_RNAsepPM1, hbe_dHXLaRRI_DNA, hbe_dHXLaRRI_RNAsepother, hbe_dHXLaRRI_RNAsepPM1, hbe_dIMDaAHX, hbe_dIMDaCXA, hbe_dIMDaCXL, hbe_dIMDaH2O, hbe_dIMDaHXL, hbe_dIMDaIMD, hbe_dIMDaIME, hbe_dIMDaPBAsepother, hbe_dIMDaPBAsepPM1, hbe_dIMDaPCA_DNA, hbe_dIMDaPCA_RNAsepother, hbe_dIMDaPCA_RNAsepPM1, hbe_dIMDaPES_DNA, hbe_dIMDaPES_RNAsepother, hbe_dIMDaPES_RNAsepPM1, hbe_dIMDaRRI_DNA, hbe_dIMDaRRI_RNAsepother, hbe_dIMDaRRI_RNAsepPM1, hbe_dIMEaAHX, hbe_dIMEaCXA, hbe_dIMEaCXL, hbe_dIMEaH2O, hbe_dIMEaHXL, hbe_dIMEaIMD, hbe_dIMEaIME, hbe_dIMEaPBAsepother, hbe_dIMEaPBAsepPM1, hbe_dIMEaPCA_DNA, hbe_dIMEaPCA_RNAsepother, hbe_dIMEaPCA_RNAsepPM1, hbe_dIMEaPES_DNA, hbe_dIMEaPES_RNAsepother, hbe_dIMEaPES_RNAsepPM1, hbe_dIMEaRRI_DNA, hbe_dIMEaRRI_RNAsepother, hbe_dIMEaRRI_RNAsepPM1, hbe_dINDaAHX, hbe_dINDaCXA, hbe_dINDaCXL, hbe_dINDaH2O, hbe_dINDaHXL, hbe_dINDaIMD, hbe_dINDaIME, hbe_dINDaPBAsepother, hbe_dINDaPBAsepPM1, hbe_dINDaPCA_DNA, hbe_dINDaPCA_RNAsepother, hbe_dINDaPCA_RNAsepPM1, hbe_dINDaPES_DNA, hbe_dINDaPES_RNAsepother, hbe_dINDaPES_RNAsepPM1, hbe_dINDaRRI_DNA, hbe_dINDaRRI_RNAsepother, hbe_dINDaRRI_RNAsepPM1, hbe_dPBAaAHXsepother, hbe_dPBAaAHXsepPM1, hbe_dPBAaCXAsepother, hbe_dPBAaCXAsepPM1, hbe_dPBAaCXLsepother, hbe_dPBAaCXLsepPM1, hbe_dPBAaH2O, hbe_dPBAaHXLsepother, hbe_dPBAaHXLsepPM1, hbe_dPBAaIMDsepother, hbe_dPBAaIMDsepPM1, hbe_dPBAaIMEsepother, hbe_dPBAaIMEsepPM1, hbe_dPBAaPBAsepM2turn, hbe_dPBAaPBAsepM3turn, hbe_dPBAaPBAsepM4helix, hbe_dPBAaPBAsepother, hbe_dPBAaPBAsepP2turn, hbe_dPBAaPBAsepP3turn, hbe_dPBAaPBAsepP4helix, hbe_dPBAaPBAsepPM1, hbe_dPBAaPCA_DNAsepother, hbe_dPBAaPCA_DNAsepPM1, hbe_dPBAaPCA_RNAsepother, hbe_dPBAaPCA_RNAsepPM1, hbe_dPBAaPES_DNAsepother, hbe_dPBAaPES_DNAsepPM1, hbe_dPBAaPES_RNAsepother, hbe_dPBAaPES_RNAsepPM1, hbe_dPBAaRRI_DNAsepother, hbe_dPBAaRRI_DNAsepPM1, hbe_dPBAaRRI_RNAsepother, hbe_dPBAaRRI_RNAsepPM1, hbe_GENERIC_RINGBB_LR, hbe_GENERIC_RINGBB_SR, hbe_GENERIC_RINGBSC_LR, hbe_GENERIC_RINGBSC_SR, hbe_GENERIC_RINGSCSC_LR, hbe_GENERIC_RINGSCSC_SR, hbe_GENERIC_SP2BB_LR, hbe_GENERIC_SP2BB_SR, hbe_GENERIC_SP2BSC_LR, hbe_GENERIC_SP2BSC_SR, hbe_GENERIC_SP2SCSC_LR, hbe_GENERIC_SP2SCSC_SR, hbe_GENERIC_SP3BB_LR, hbe_GENERIC_SP3BB_SR, hbe_GENERIC_SP3BSC_LR, hbe_GENERIC_SP3BSC_SR, hbe_GENERIC_SP3SCSC_LR, hbe_GENERIC_SP3SCSC_SR, hbe_NONE, hbe_UNKNOWN, core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, TR(), and core::chemical::UNKNOWN_HYBRID.

Referenced by assign_abase_derivs(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), hb_energy_deriv(), hb_energy_deriv_u2(), hbond_compute_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and protocols::dna::PDBOutput::output_hbond_info().

void core::scoring::hbonds::get_hbond_energies ( HBondSet const &  hbond_set,
EnergyMap &  emap 
)
HBondWeightType core::scoring::hbonds::get_hbond_weight_type ( HBEvalType const &  hbe_type)

References hbe_dAHXaAHX, hbe_dAHXaCXA, hbe_dAHXaCXL, hbe_dAHXaH2O, hbe_dAHXaHXL, hbe_dAHXaIMD, hbe_dAHXaIME, hbe_dAHXaPBAsepother, hbe_dAHXaPBAsepPM1, hbe_dAHXaPCA_DNA, hbe_dAHXaPCA_RNAsepother, hbe_dAHXaPCA_RNAsepPM1, hbe_dAHXaPES_DNA, hbe_dAHXaPES_RNAsepother, hbe_dAHXaPES_RNAsepPM1, hbe_dAHXaRRI_DNA, hbe_dAHXaRRI_RNAsepother, hbe_dAHXaRRI_RNAsepPM1, hbe_dAMOaAHX, hbe_dAMOaCXA, hbe_dAMOaCXL, hbe_dAMOaH2O, hbe_dAMOaHXL, hbe_dAMOaIMD, hbe_dAMOaIME, hbe_dAMOaPBAsepother, hbe_dAMOaPBAsepPM1, hbe_dAMOaPCA_DNA, hbe_dAMOaPCA_RNAsepother, hbe_dAMOaPCA_RNAsepPM1, hbe_dAMOaPES_DNA, hbe_dAMOaPES_RNAsepother, hbe_dAMOaPES_RNAsepPM1, hbe_dAMOaRRI_DNA, hbe_dAMOaRRI_RNAsepother, hbe_dAMOaRRI_RNAsepPM1, hbe_dCXAaAHX, hbe_dCXAaCXA, hbe_dCXAaCXL, hbe_dCXAaH2O, hbe_dCXAaHXL, hbe_dCXAaIMD, hbe_dCXAaIME, hbe_dCXAaPBAsepother, hbe_dCXAaPBAsepPM1, hbe_dCXAaPCA_DNA, hbe_dCXAaPCA_RNAsepother, hbe_dCXAaPCA_RNAsepPM1, hbe_dCXAaPES_DNA, hbe_dCXAaPES_RNAsepother, hbe_dCXAaPES_RNAsepPM1, hbe_dCXAaRRI_DNA, hbe_dCXAaRRI_RNAsepother, hbe_dCXAaRRI_RNAsepPM1, hbe_dGDEaAHX, hbe_dGDEaCXA, hbe_dGDEaCXL, hbe_dGDEaH2O, hbe_dGDEaHXL, hbe_dGDEaIMD, hbe_dGDEaIME, hbe_dGDEaPBAsepother, hbe_dGDEaPBAsepPM1, hbe_dGDEaPCA_DNA, hbe_dGDEaPCA_RNAsepother, hbe_dGDEaPCA_RNAsepPM1, hbe_dGDEaPES_DNA, hbe_dGDEaPES_RNAsepother, hbe_dGDEaPES_RNAsepPM1, hbe_dGDEaRRI_DNA, hbe_dGDEaRRI_RNAsepother, hbe_dGDEaRRI_RNAsepPM1, hbe_dGDHaAHX, hbe_dGDHaCXA, hbe_dGDHaCXL, hbe_dGDHaH2O, hbe_dGDHaHXL, hbe_dGDHaIMD, hbe_dGDHaIME, hbe_dGDHaPBAsepother, hbe_dGDHaPBAsepPM1, hbe_dGDHaPCA_DNA, hbe_dGDHaPCA_RNAsepother, hbe_dGDHaPCA_RNAsepPM1, hbe_dGDHaPES_DNA, hbe_dGDHaPES_RNAsepother, hbe_dGDHaPES_RNAsepPM1, hbe_dGDHaRRI_DNA, hbe_dGDHaRRI_RNAsepother, hbe_dGDHaRRI_RNAsepPM1, hbe_dH2OaAHX, hbe_dH2OaCXA, hbe_dH2OaCXL, hbe_dH2OaH2O, hbe_dH2OaHXL, hbe_dH2OaIMD, hbe_dH2OaIME, hbe_dH2OaPBA, hbe_dH2OaPCA_DNA, hbe_dH2OaPCA_RNA, hbe_dH2OaPES_DNA, hbe_dH2OaPES_RNA, hbe_dH2OaRRI_DNA, hbe_dH2OaRRI_RNA, hbe_dHXLaAHX, hbe_dHXLaCXA, hbe_dHXLaCXL, hbe_dHXLaH2O, hbe_dHXLaHXL, hbe_dHXLaIMD, hbe_dHXLaIME, hbe_dHXLaPBAsepother, hbe_dHXLaPBAsepPM1, hbe_dHXLaPCA_DNA, hbe_dHXLaPCA_RNAsepother, hbe_dHXLaPCA_RNAsepPM1, hbe_dHXLaPES_DNA, hbe_dHXLaPES_RNAsepother, hbe_dHXLaPES_RNAsepPM1, hbe_dHXLaRRI_DNA, hbe_dHXLaRRI_RNAsepother, hbe_dHXLaRRI_RNAsepPM1, hbe_dIMDaAHX, hbe_dIMDaCXA, hbe_dIMDaCXL, hbe_dIMDaH2O, hbe_dIMDaHXL, hbe_dIMDaIMD, hbe_dIMDaIME, hbe_dIMDaPBAsepother, hbe_dIMDaPBAsepPM1, hbe_dIMDaPCA_DNA, hbe_dIMDaPCA_RNAsepother, hbe_dIMDaPCA_RNAsepPM1, hbe_dIMDaPES_DNA, hbe_dIMDaPES_RNAsepother, hbe_dIMDaPES_RNAsepPM1, hbe_dIMDaRRI_DNA, hbe_dIMDaRRI_RNAsepother, hbe_dIMDaRRI_RNAsepPM1, hbe_dIMEaAHX, hbe_dIMEaCXA, hbe_dIMEaCXL, hbe_dIMEaH2O, hbe_dIMEaHXL, hbe_dIMEaIMD, hbe_dIMEaIME, hbe_dIMEaPBAsepother, hbe_dIMEaPBAsepPM1, hbe_dIMEaPCA_DNA, hbe_dIMEaPCA_RNAsepother, hbe_dIMEaPCA_RNAsepPM1, hbe_dIMEaPES_DNA, hbe_dIMEaPES_RNAsepother, hbe_dIMEaPES_RNAsepPM1, hbe_dIMEaRRI_DNA, hbe_dIMEaRRI_RNAsepother, hbe_dIMEaRRI_RNAsepPM1, hbe_dINDaAHX, hbe_dINDaCXA, hbe_dINDaCXL, hbe_dINDaH2O, hbe_dINDaHXL, hbe_dINDaIMD, hbe_dINDaIME, hbe_dINDaPBAsepother, hbe_dINDaPBAsepPM1, hbe_dINDaPCA_DNA, hbe_dINDaPCA_RNAsepother, hbe_dINDaPCA_RNAsepPM1, hbe_dINDaPES_DNA, hbe_dINDaPES_RNAsepother, hbe_dINDaPES_RNAsepPM1, hbe_dINDaRRI_DNA, hbe_dINDaRRI_RNAsepother, hbe_dINDaRRI_RNAsepPM1, hbe_dPBAaAHXsepother, hbe_dPBAaAHXsepPM1, hbe_dPBAaCXAsepother, hbe_dPBAaCXAsepPM1, hbe_dPBAaCXLsepother, hbe_dPBAaCXLsepPM1, hbe_dPBAaH2O, hbe_dPBAaHXLsepother, hbe_dPBAaHXLsepPM1, hbe_dPBAaIMDsepother, hbe_dPBAaIMDsepPM1, hbe_dPBAaIMEsepother, hbe_dPBAaIMEsepPM1, hbe_dPBAaPBAsepM2turn, hbe_dPBAaPBAsepM3turn, hbe_dPBAaPBAsepM4helix, hbe_dPBAaPBAsepother, hbe_dPBAaPBAsepP2turn, hbe_dPBAaPBAsepP3turn, hbe_dPBAaPBAsepP4helix, hbe_dPBAaPBAsepPM1, hbe_dPBAaPCA_DNAsepother, hbe_dPBAaPCA_DNAsepPM1, hbe_dPBAaPCA_RNAsepother, hbe_dPBAaPCA_RNAsepPM1, hbe_dPBAaPES_DNAsepother, hbe_dPBAaPES_DNAsepPM1, hbe_dPBAaPES_RNAsepother, hbe_dPBAaPES_RNAsepPM1, hbe_dPBAaRRI_DNAsepother, hbe_dPBAaRRI_DNAsepPM1, hbe_dPBAaRRI_RNAsepother, hbe_dPBAaRRI_RNAsepPM1, hbe_GENERIC_RINGBB_LR, hbe_GENERIC_RINGBB_SR, hbe_GENERIC_RINGBSC_LR, hbe_GENERIC_RINGBSC_SR, hbe_GENERIC_RINGSCSC_LR, hbe_GENERIC_RINGSCSC_SR, hbe_GENERIC_SP2BB_LR, hbe_GENERIC_SP2BB_SR, hbe_GENERIC_SP2BSC_LR, hbe_GENERIC_SP2BSC_SR, hbe_GENERIC_SP2SCSC_LR, hbe_GENERIC_SP2SCSC_SR, hbe_GENERIC_SP3BB_LR, hbe_GENERIC_SP3BB_SR, hbe_GENERIC_SP3BSC_LR, hbe_GENERIC_SP3BSC_SR, hbe_GENERIC_SP3SCSC_LR, hbe_GENERIC_SP3SCSC_SR, hbe_NONE, hbe_UNKNOWN, hbw_LR_BB, hbw_LR_BB_SC, hbw_NONE, hbw_SC, hbw_SR_BB, hbw_SR_BB_SC, and TR().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted(), hb_eval_type_weight(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), identify_hbonds_1way(), increment_hbond_energy(), increment_npd_hbond_energy(), core::scoring::ScoreFunction::intersubunit_hbond_energy(), and npd_hb_eval_type_weight().

Real core::scoring::hbonds::get_membrane_depth_dependent_weight ( pose::Pose const &  pose,
int const  don_nb,
int const  acc_nb,
Vector const &  Hxyz,
Vector const &  Axyz 
)
Real core::scoring::hbonds::get_membrane_depth_dependent_weight ( Vector const &  normal,
Vector const &  center,
Real const &  thickness,
Real const &  steepness,
int const  don_nb,
int const  acc_nb,
Vector const &  Hxyz,
Vector const &  Axyz 
)
HBSeqSep core::scoring::hbonds::get_seq_sep ( HBDonChemType const &  don_chem_type,
HBAccChemType const &  acc_chem_type,
int const &  sep 
)
core::Real core::scoring::hbonds::get_ssdep_weight ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
SSWeightParameters const &  ssdep 
)
void core::scoring::hbonds::get_weights_for_one_partner_hbonder ( utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights,
utility::vector1< utility::vector1< Real > > &  dwt_dE 
)
Real core::scoring::hbonds::get_weights_for_one_partner_hbonder ( utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights 
)

Helper function used by the weights_for_hbonds function above.

void core::scoring::hbonds::get_weights_for_two_partner_hbonder ( utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights,
utility::vector1< utility::vector1< Real > > &  dwt_dE 
)
void core::scoring::hbonds::get_weights_for_two_partner_hbonder ( utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights 
)

Helper function used by the weights_for_hbonds function above.

References get_weights_for_one_partner_hbonder().

Real core::scoring::hbonds::hb_energy ( HBondDatabase const &  database,
HBondOptions const &  options,
HBondSet const &  hbset,
conformation::Residue const &  acc_rsd,
Size  aatm,
conformation::Residue const &  don_rsd,
Size  hatm 
)
void core::scoring::hbonds::hb_energy_deriv ( HBondDatabase const &  database,
HBondOptions const &  hbondoptions,
HBEvalTuple const &  hbt,
Vector const &  Dxyz,
Vector const &  Hxyz,
Vector const &  Axyz,
Vector const &  Bxyz,
Vector const &  B2xyz,
Real &  energy,
bool const  evaluate_deriv,
HBondDerivs &  deriv 
)
void core::scoring::hbonds::hb_energy_deriv ( HBondDatabase const &  database,
HBondOptions const &  hbondoptions,
HBEvalTuple const &  hbt,
Vector const &  Dxyz,
Vector const &  Hxyz,
Vector const &  Axyz,
Vector const &  Bxyz,
Vector const &  B2xyz,
Real &  energy,
HBDerivType const  deriv_type,
HBondDerivs &  deriv 
)
void core::scoring::hbonds::hb_energy_deriv_u ( HBondDatabase const &  database,
HBondOptions const &  hbondoptions,
hbonds::HBEvalTuple const &  hbt,
Vector const &  Hxyz,
Vector const &  Dxyz,
Vector const &  HDunit,
Vector const &  Axyz,
Vector const &  Bxyz,
Vector const &  BAunit,
Vector const &  B2xyz,
Vector const &  B2Aunit,
Real &  energy,
bool const  evaluate_deriv,
HBondDerivs &  deriv 
)

car Evaluate the energy and derivative components for a hydrogen bond

Evaluate the hydrogen bond energy and derivatives after having first calculated the HD and BA *u*nit vectors.

car Energy is assumed to be a sum of independent functions of distance, car angle at the donor atom, and angle at the acceptor atom. This form car of the hydrogen bond potential was selected by Tanja Kortemme car The math for computing the derivative of the angular components of car the potential was derived by Bill Wedemeyer.

ora used also to calculate derivatives for RB movements if docking_flag T ora important NOTE: if in docking mode minimization is done NOT in tr space, this ora should be specified and the docking_specific part should be skipped

Parameters
hbe_type- [in] - hydrogen bond evaluation type from hbonds_ns.h
donor_res- [in] -
acceptor_res- [in] -
Dxyz- [in/out] - donor
Hxyz- [in/out] - proton
Axyz- [in/out] - acceptor
Bxyz- [in/out] - acceptor base
B2xyz- [in/out] - 2nd acceptor base for ring acceptors
energy- [out] -
deriv- [out (optional)] - xyz,f1/f2
deriv_type[in (optional)] - deriv is NORMAL(default), DOCK_ACC_DON, DOCK_DON_ACC
Global Read:
When docking derivatives are computed (DOCK_ACC_DON or DOCK_DON_ACC), center_of_rotation MUST BE DEFINED!
Global Write:
Remarks
References:
Author
Parameters
B2Aunitacceptor base 2 coords – will be needed for derivative evaluation when the torsional term comes online

References hb_energy_deriv_u2(), hbderiv_ABE_GO, and hbderiv_NONE.

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

void core::scoring::hbonds::hb_energy_deriv_u2 ( HBondDatabase const &  database,
HBondOptions const &  hbondoptions,
hbonds::HBEvalTuple const &  hbt,
HBDerivType const  deriv_type,
Vector const &  Hxyz,
Vector const &  Dxyz,
Vector const &  HDunit,
Vector const &  Axyz,
Vector const &  Bxyz,
Vector const &  BAunit,
Vector const &  B2xyz,
Vector const &  B2Aunit,
Real &  energy,
HBondDerivs &  deriv 
)

Evaluate the hydrogen bond energy and derivatives after having first calculated the HD and BA *u*nit vectors; deriv type must have been chosen (why does this exist?)

Innermost score/derivative evaluation logic in this function; "u" stands for "unit vector" and 2 stands for "the second u function" since the arguments to hbond_energy_deriv_u and the arguments to hbond_energy_deriv_u2 are interchangable (i.e. if we tried to overload the hbond_energy_deriv, we end up with infinite recursion as hbond_energy_deriv calls itself over and over again). In here, we have the logic for evaluating the hbond polynomials and, if deriv_type == hbderiv_ABE_GO, then it also computes the f1/f2 vectors for the 4 (eventually 5!) atoms involved in the hydrogen bond.

Parameters
B2Aunitacceptor base 2 coords – will be needed for derivative evaluation when the torsional term comes online

References core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::scoring::hbonds::HBEvalTuple::acc_type(), core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), get_hbe_acc_hybrid(), core::scoring::hbonds::HBondDerivs::h_deriv, hbacc_AHX, hbacc_HXL, hbderiv_ABE_GO_GEOMSOL_OCC_ACC, hbderiv_ABE_GO_GEOMSOL_OCC_DON, hbderiv_NONE, hbgd_AHD, hbgd_cosAHD, hbond_compute_energy(), core::scoring::hbonds::HBondOptions::max_hb_energy(), MAX_R2, MAX_xD, MAX_xH, core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(), protocols::mean_field::min(), MIN_R2, MIN_xD, MIN_xH, core::chemical::SP2_HYBRID, and core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty().

Referenced by hb_energy_deriv(), and hb_energy_deriv_u().

core::Real core::scoring::hbonds::hb_env_dep_burial_lin ( int const  nb1,
int const  nb2 
)
core::Real core::scoring::hbonds::hb_env_dep_burial_tk ( int const  nb1,
int const  nb2 
)
Size core::scoring::hbonds::hb_eval_type ( HBDonChemType  don_chem_type,
HBAccChemType  acc_chem_type,
HBSeqSep  seq_sep_type 
)

References hbacc_MAX, and seq_sep_MAX.

Real core::scoring::hbonds::hb_eval_type_weight ( HBEvalType const &  hbe_type,
EnergyMap const &  weights,
bool const  intra_res,
bool const  put_intra_into_total 
)
bool core::scoring::hbonds::hbe_is_BB_type ( HBEvalType  hbe)

References hbe_dAHXaAHX, hbe_dAHXaCXA, hbe_dAHXaCXL, hbe_dAHXaH2O, hbe_dAHXaHXL, hbe_dAHXaIMD, hbe_dAHXaIME, hbe_dAHXaPBAsepother, hbe_dAHXaPBAsepPM1, hbe_dAHXaPCA_DNA, hbe_dAHXaPCA_RNAsepother, hbe_dAHXaPCA_RNAsepPM1, hbe_dAHXaPES_DNA, hbe_dAHXaPES_RNAsepother, hbe_dAHXaPES_RNAsepPM1, hbe_dAHXaRRI_DNA, hbe_dAHXaRRI_RNAsepother, hbe_dAHXaRRI_RNAsepPM1, hbe_dAMOaAHX, hbe_dAMOaCXA, hbe_dAMOaCXL, hbe_dAMOaH2O, hbe_dAMOaHXL, hbe_dAMOaIMD, hbe_dAMOaIME, hbe_dAMOaPBAsepother, hbe_dAMOaPBAsepPM1, hbe_dAMOaPCA_DNA, hbe_dAMOaPCA_RNAsepother, hbe_dAMOaPCA_RNAsepPM1, hbe_dAMOaPES_DNA, hbe_dAMOaPES_RNAsepother, hbe_dAMOaPES_RNAsepPM1, hbe_dAMOaRRI_DNA, hbe_dAMOaRRI_RNAsepother, hbe_dAMOaRRI_RNAsepPM1, hbe_dCXAaAHX, hbe_dCXAaCXA, hbe_dCXAaCXL, hbe_dCXAaH2O, hbe_dCXAaHXL, hbe_dCXAaIMD, hbe_dCXAaIME, hbe_dCXAaPBAsepother, hbe_dCXAaPBAsepPM1, hbe_dCXAaPCA_DNA, hbe_dCXAaPCA_RNAsepother, hbe_dCXAaPCA_RNAsepPM1, hbe_dCXAaPES_DNA, hbe_dCXAaPES_RNAsepother, hbe_dCXAaPES_RNAsepPM1, hbe_dCXAaRRI_DNA, hbe_dCXAaRRI_RNAsepother, hbe_dCXAaRRI_RNAsepPM1, hbe_dGDEaAHX, hbe_dGDEaCXA, hbe_dGDEaCXL, hbe_dGDEaH2O, hbe_dGDEaHXL, hbe_dGDEaIMD, hbe_dGDEaIME, hbe_dGDEaPBAsepother, hbe_dGDEaPBAsepPM1, hbe_dGDEaPCA_DNA, hbe_dGDEaPCA_RNAsepother, hbe_dGDEaPCA_RNAsepPM1, hbe_dGDEaPES_DNA, hbe_dGDEaPES_RNAsepother, hbe_dGDEaPES_RNAsepPM1, hbe_dGDEaRRI_DNA, hbe_dGDEaRRI_RNAsepother, hbe_dGDEaRRI_RNAsepPM1, hbe_dGDHaAHX, hbe_dGDHaCXA, hbe_dGDHaCXL, hbe_dGDHaH2O, hbe_dGDHaHXL, hbe_dGDHaIMD, hbe_dGDHaIME, hbe_dGDHaPBAsepother, hbe_dGDHaPBAsepPM1, hbe_dGDHaPCA_DNA, hbe_dGDHaPCA_RNAsepother, hbe_dGDHaPCA_RNAsepPM1, hbe_dGDHaPES_DNA, hbe_dGDHaPES_RNAsepother, hbe_dGDHaPES_RNAsepPM1, hbe_dGDHaRRI_DNA, hbe_dGDHaRRI_RNAsepother, hbe_dGDHaRRI_RNAsepPM1, hbe_dH2OaAHX, hbe_dH2OaCXA, hbe_dH2OaCXL, hbe_dH2OaH2O, hbe_dH2OaHXL, hbe_dH2OaIMD, hbe_dH2OaIME, hbe_dH2OaPBA, hbe_dH2OaPCA_DNA, hbe_dH2OaPCA_RNA, hbe_dH2OaPES_DNA, hbe_dH2OaPES_RNA, hbe_dH2OaRRI_DNA, hbe_dH2OaRRI_RNA, hbe_dHXLaAHX, hbe_dHXLaCXA, hbe_dHXLaCXL, hbe_dHXLaH2O, hbe_dHXLaHXL, hbe_dHXLaIMD, hbe_dHXLaIME, hbe_dHXLaPBAsepother, hbe_dHXLaPBAsepPM1, hbe_dHXLaPCA_DNA, hbe_dHXLaPCA_RNAsepother, hbe_dHXLaPCA_RNAsepPM1, hbe_dHXLaPES_DNA, hbe_dHXLaPES_RNAsepother, hbe_dHXLaPES_RNAsepPM1, hbe_dHXLaRRI_DNA, hbe_dHXLaRRI_RNAsepother, hbe_dHXLaRRI_RNAsepPM1, hbe_dIMDaAHX, hbe_dIMDaCXA, hbe_dIMDaCXL, hbe_dIMDaH2O, hbe_dIMDaHXL, hbe_dIMDaIMD, hbe_dIMDaIME, hbe_dIMDaPBAsepother, hbe_dIMDaPBAsepPM1, hbe_dIMDaPCA_DNA, hbe_dIMDaPCA_RNAsepother, hbe_dIMDaPCA_RNAsepPM1, hbe_dIMDaPES_DNA, hbe_dIMDaPES_RNAsepother, hbe_dIMDaPES_RNAsepPM1, hbe_dIMDaRRI_DNA, hbe_dIMDaRRI_RNAsepother, hbe_dIMDaRRI_RNAsepPM1, hbe_dIMEaAHX, hbe_dIMEaCXA, hbe_dIMEaCXL, hbe_dIMEaH2O, hbe_dIMEaHXL, hbe_dIMEaIMD, hbe_dIMEaIME, hbe_dIMEaPBAsepother, hbe_dIMEaPBAsepPM1, hbe_dIMEaPCA_DNA, hbe_dIMEaPCA_RNAsepother, hbe_dIMEaPCA_RNAsepPM1, hbe_dIMEaPES_DNA, hbe_dIMEaPES_RNAsepother, hbe_dIMEaPES_RNAsepPM1, hbe_dIMEaRRI_DNA, hbe_dIMEaRRI_RNAsepother, hbe_dIMEaRRI_RNAsepPM1, hbe_dINDaAHX, hbe_dINDaCXA, hbe_dINDaCXL, hbe_dINDaH2O, hbe_dINDaHXL, hbe_dINDaIMD, hbe_dINDaIME, hbe_dINDaPBAsepother, hbe_dINDaPBAsepPM1, hbe_dINDaPCA_DNA, hbe_dINDaPCA_RNAsepother, hbe_dINDaPCA_RNAsepPM1, hbe_dINDaPES_DNA, hbe_dINDaPES_RNAsepother, hbe_dINDaPES_RNAsepPM1, hbe_dINDaRRI_DNA, hbe_dINDaRRI_RNAsepother, hbe_dINDaRRI_RNAsepPM1, hbe_dPBAaAHXsepother, hbe_dPBAaAHXsepPM1, hbe_dPBAaCXAsepother, hbe_dPBAaCXAsepPM1, hbe_dPBAaCXLsepother, hbe_dPBAaCXLsepPM1, hbe_dPBAaH2O, hbe_dPBAaHXLsepother, hbe_dPBAaHXLsepPM1, hbe_dPBAaIMDsepother, hbe_dPBAaIMDsepPM1, hbe_dPBAaIMEsepother, hbe_dPBAaIMEsepPM1, hbe_dPBAaPBAsepM2turn, hbe_dPBAaPBAsepM3turn, hbe_dPBAaPBAsepM4helix, hbe_dPBAaPBAsepother, hbe_dPBAaPBAsepP2turn, hbe_dPBAaPBAsepP3turn, hbe_dPBAaPBAsepP4helix, hbe_dPBAaPBAsepPM1, hbe_dPBAaPCA_DNAsepother, hbe_dPBAaPCA_DNAsepPM1, hbe_dPBAaPCA_RNAsepother, hbe_dPBAaPCA_RNAsepPM1, hbe_dPBAaPES_DNAsepother, hbe_dPBAaPES_DNAsepPM1, hbe_dPBAaPES_RNAsepother, hbe_dPBAaPES_RNAsepPM1, hbe_dPBAaRRI_DNAsepother, hbe_dPBAaRRI_DNAsepPM1, hbe_dPBAaRRI_RNAsepother, hbe_dPBAaRRI_RNAsepPM1, hbe_GENERIC_RINGBB_LR, hbe_GENERIC_RINGBB_SR, hbe_GENERIC_RINGBSC_LR, hbe_GENERIC_RINGBSC_SR, hbe_GENERIC_RINGSCSC_LR, hbe_GENERIC_RINGSCSC_SR, hbe_GENERIC_SP2BB_LR, hbe_GENERIC_SP2BB_SR, hbe_GENERIC_SP2BSC_LR, hbe_GENERIC_SP2BSC_SR, hbe_GENERIC_SP2SCSC_LR, hbe_GENERIC_SP2SCSC_SR, hbe_GENERIC_SP3BB_LR, hbe_GENERIC_SP3BB_SR, hbe_GENERIC_SP3BSC_LR, hbe_GENERIC_SP3BSC_SR, hbe_GENERIC_SP3SCSC_LR, hbe_GENERIC_SP3SCSC_SR, hbe_NONE, hbe_UNKNOWN, and TR().

Referenced by hbe_is_SC_type().

bool core::scoring::hbonds::hbe_is_SC_type ( HBEvalType  hbe)
void core::scoring::hbonds::HBEval_lookup_initializer ( ObjexxFCL::FArray3D< HBEvalType > &  hbe)

References hbacc_AHX, hbacc_CXA, hbacc_CXL, hbacc_GENERIC_RINGBB, hbacc_GENERIC_RINGSC, hbacc_GENERIC_SP2BB, hbacc_GENERIC_SP2SC, hbacc_GENERIC_SP3BB, hbacc_GENERIC_SP3SC, hbacc_H2O, hbacc_HXL, hbacc_IMD, hbacc_IME, hbacc_NONE, hbacc_PBA, hbacc_PCA_DNA, hbacc_PCA_RNA, hbacc_PES_DNA, hbacc_PES_RNA, hbacc_RRI_DNA, hbacc_RRI_RNA, hbdon_AHX, hbdon_AMO, hbdon_CXA, hbdon_GDE, hbdon_GDH, hbdon_GENERIC_BB, hbdon_GENERIC_SC, hbdon_H2O, hbdon_HXL, hbdon_IMD, hbdon_IME, hbdon_IND, hbdon_NONE, hbdon_PBA, hbe_dAHXaAHX, hbe_dAHXaCXA, hbe_dAHXaCXL, hbe_dAHXaH2O, hbe_dAHXaHXL, hbe_dAHXaIMD, hbe_dAHXaIME, hbe_dAHXaPBAsepother, hbe_dAHXaPBAsepPM1, hbe_dAHXaPCA_DNA, hbe_dAHXaPCA_RNAsepother, hbe_dAHXaPCA_RNAsepPM1, hbe_dAHXaPES_DNA, hbe_dAHXaPES_RNAsepother, hbe_dAHXaPES_RNAsepPM1, hbe_dAHXaRRI_DNA, hbe_dAHXaRRI_RNAsepother, hbe_dAHXaRRI_RNAsepPM1, hbe_dAMOaAHX, hbe_dAMOaCXA, hbe_dAMOaCXL, hbe_dAMOaH2O, hbe_dAMOaHXL, hbe_dAMOaIMD, hbe_dAMOaIME, hbe_dAMOaPBAsepother, hbe_dAMOaPBAsepPM1, hbe_dAMOaPCA_DNA, hbe_dAMOaPCA_RNAsepother, hbe_dAMOaPCA_RNAsepPM1, hbe_dAMOaPES_DNA, hbe_dAMOaPES_RNAsepother, hbe_dAMOaPES_RNAsepPM1, hbe_dAMOaRRI_DNA, hbe_dAMOaRRI_RNAsepother, hbe_dAMOaRRI_RNAsepPM1, hbe_dCXAaAHX, hbe_dCXAaCXA, hbe_dCXAaCXL, hbe_dCXAaH2O, hbe_dCXAaHXL, hbe_dCXAaIMD, hbe_dCXAaIME, hbe_dCXAaPBAsepother, hbe_dCXAaPBAsepPM1, hbe_dCXAaPCA_DNA, hbe_dCXAaPCA_RNAsepother, hbe_dCXAaPCA_RNAsepPM1, hbe_dCXAaPES_DNA, hbe_dCXAaPES_RNAsepother, hbe_dCXAaPES_RNAsepPM1, hbe_dCXAaRRI_DNA, hbe_dCXAaRRI_RNAsepother, hbe_dCXAaRRI_RNAsepPM1, hbe_dGDEaAHX, hbe_dGDEaCXA, hbe_dGDEaCXL, hbe_dGDEaH2O, hbe_dGDEaHXL, hbe_dGDEaIMD, hbe_dGDEaIME, hbe_dGDEaPBAsepother, hbe_dGDEaPBAsepPM1, hbe_dGDEaPCA_DNA, hbe_dGDEaPCA_RNAsepother, hbe_dGDEaPCA_RNAsepPM1, hbe_dGDEaPES_DNA, hbe_dGDEaPES_RNAsepother, hbe_dGDEaPES_RNAsepPM1, hbe_dGDEaRRI_DNA, hbe_dGDEaRRI_RNAsepother, hbe_dGDEaRRI_RNAsepPM1, hbe_dGDHaAHX, hbe_dGDHaCXA, hbe_dGDHaCXL, hbe_dGDHaH2O, hbe_dGDHaHXL, hbe_dGDHaIMD, hbe_dGDHaIME, hbe_dGDHaPBAsepother, hbe_dGDHaPBAsepPM1, hbe_dGDHaPCA_DNA, hbe_dGDHaPCA_RNAsepother, hbe_dGDHaPCA_RNAsepPM1, hbe_dGDHaPES_DNA, hbe_dGDHaPES_RNAsepother, hbe_dGDHaPES_RNAsepPM1, hbe_dGDHaRRI_DNA, hbe_dGDHaRRI_RNAsepother, hbe_dGDHaRRI_RNAsepPM1, hbe_dH2OaAHX, hbe_dH2OaCXA, hbe_dH2OaCXL, hbe_dH2OaH2O, hbe_dH2OaHXL, hbe_dH2OaIMD, hbe_dH2OaIME, hbe_dH2OaPBA, hbe_dH2OaPCA_DNA, hbe_dH2OaPCA_RNA, hbe_dH2OaPES_DNA, hbe_dH2OaPES_RNA, hbe_dH2OaRRI_DNA, hbe_dH2OaRRI_RNA, hbe_dHXLaAHX, hbe_dHXLaCXA, hbe_dHXLaCXL, hbe_dHXLaH2O, hbe_dHXLaHXL, hbe_dHXLaIMD, hbe_dHXLaIME, hbe_dHXLaPBAsepother, hbe_dHXLaPBAsepPM1, hbe_dHXLaPCA_DNA, hbe_dHXLaPCA_RNAsepother, hbe_dHXLaPCA_RNAsepPM1, hbe_dHXLaPES_DNA, hbe_dHXLaPES_RNAsepother, hbe_dHXLaPES_RNAsepPM1, hbe_dHXLaRRI_DNA, hbe_dHXLaRRI_RNAsepother, hbe_dHXLaRRI_RNAsepPM1, hbe_dIMDaAHX, hbe_dIMDaCXA, hbe_dIMDaCXL, hbe_dIMDaH2O, hbe_dIMDaHXL, hbe_dIMDaIMD, hbe_dIMDaIME, hbe_dIMDaPBAsepother, hbe_dIMDaPBAsepPM1, hbe_dIMDaPCA_DNA, hbe_dIMDaPCA_RNAsepother, hbe_dIMDaPCA_RNAsepPM1, hbe_dIMDaPES_DNA, hbe_dIMDaPES_RNAsepother, hbe_dIMDaPES_RNAsepPM1, hbe_dIMDaRRI_DNA, hbe_dIMDaRRI_RNAsepother, hbe_dIMDaRRI_RNAsepPM1, hbe_dIMEaAHX, hbe_dIMEaCXA, hbe_dIMEaCXL, hbe_dIMEaH2O, hbe_dIMEaHXL, hbe_dIMEaIMD, hbe_dIMEaIME, hbe_dIMEaPBAsepother, hbe_dIMEaPBAsepPM1, hbe_dIMEaPCA_DNA, hbe_dIMEaPCA_RNAsepother, hbe_dIMEaPCA_RNAsepPM1, hbe_dIMEaPES_DNA, hbe_dIMEaPES_RNAsepother, hbe_dIMEaPES_RNAsepPM1, hbe_dIMEaRRI_DNA, hbe_dIMEaRRI_RNAsepother, hbe_dIMEaRRI_RNAsepPM1, hbe_dINDaAHX, hbe_dINDaCXA, hbe_dINDaCXL, hbe_dINDaH2O, hbe_dINDaHXL, hbe_dINDaIMD, hbe_dINDaIME, hbe_dINDaPBAsepother, hbe_dINDaPBAsepPM1, hbe_dINDaPCA_DNA, hbe_dINDaPCA_RNAsepother, hbe_dINDaPCA_RNAsepPM1, hbe_dINDaPES_DNA, hbe_dINDaPES_RNAsepother, hbe_dINDaPES_RNAsepPM1, hbe_dINDaRRI_DNA, hbe_dINDaRRI_RNAsepother, hbe_dINDaRRI_RNAsepPM1, hbe_dPBAaAHXsepother, hbe_dPBAaAHXsepPM1, hbe_dPBAaCXAsepother, hbe_dPBAaCXAsepPM1, hbe_dPBAaCXLsepother, hbe_dPBAaCXLsepPM1, hbe_dPBAaH2O, hbe_dPBAaHXLsepother, hbe_dPBAaHXLsepPM1, hbe_dPBAaIMDsepother, hbe_dPBAaIMDsepPM1, hbe_dPBAaIMEsepother, hbe_dPBAaIMEsepPM1, hbe_dPBAaPBAsepM2turn, hbe_dPBAaPBAsepM3turn, hbe_dPBAaPBAsepM4helix, hbe_dPBAaPBAsepother, hbe_dPBAaPBAsepP2turn, hbe_dPBAaPBAsepP3turn, hbe_dPBAaPBAsepP4helix, hbe_dPBAaPBAsepPM1, hbe_dPBAaPCA_DNAsepother, hbe_dPBAaPCA_DNAsepPM1, hbe_dPBAaPCA_RNAsepother, hbe_dPBAaPCA_RNAsepPM1, hbe_dPBAaPES_DNAsepother, hbe_dPBAaPES_DNAsepPM1, hbe_dPBAaPES_RNAsepother, hbe_dPBAaPES_RNAsepPM1, hbe_dPBAaRRI_DNAsepother, hbe_dPBAaRRI_DNAsepPM1, hbe_dPBAaRRI_RNAsepother, hbe_dPBAaRRI_RNAsepPM1, hbe_GENERIC_RINGBB_LR, hbe_GENERIC_RINGBB_SR, hbe_GENERIC_RINGBSC_LR, hbe_GENERIC_RINGBSC_SR, hbe_GENERIC_RINGSCSC_LR, hbe_GENERIC_RINGSCSC_SR, hbe_GENERIC_SP2BB_LR, hbe_GENERIC_SP2BB_SR, hbe_GENERIC_SP2BSC_LR, hbe_GENERIC_SP2BSC_SR, hbe_GENERIC_SP2SCSC_LR, hbe_GENERIC_SP2SCSC_SR, hbe_GENERIC_SP3BB_LR, hbe_GENERIC_SP3BB_SR, hbe_GENERIC_SP3BSC_LR, hbe_GENERIC_SP3BSC_SR, hbe_GENERIC_SP3SCSC_LR, hbe_GENERIC_SP3SCSC_SR, hbe_NONE, hbe_UNKNOWN, seq_sep_M2, seq_sep_M3, seq_sep_M4, seq_sep_other, seq_sep_P2, seq_sep_P3, seq_sep_P4, seq_sep_PM1, and string_to_hb_eval_type().

Referenced by initialize_HBEval_lookup().

void core::scoring::hbonds::hbond_compute_energy ( HBondDatabase const &  database,
HBondOptions const &  hbondoptions,
HBEvalTuple const &  hbt,
Real const  AHdis,
Real const  xD,
Real const  xH,
Real const  xH2,
Real const  chi,
Real &  energy,
bool apply_chi_torsion_penalty,
HBGeoDimType &  AHD_geometric_dimension,
Real &  dE_dr,
Real &  dE_dxD,
Real &  dE_dxH,
Real &  dE_dxH2,
Real &  dE_dBAH,
Real &  dE_dchi 
)

References core::scoring::hbonds::HBondDatabase::acc_strength(), core::scoring::hbonds::HBEvalTuple::acc_type(), core::scoring::hbonds::HBondDatabase::AHdist_long_fade_lookup(), core::scoring::hbonds::HBondDatabase::AHdist_poly_lookup(), core::scoring::hbonds::HBondDatabase::AHdist_short_fade_lookup(), bah_chi_compute_energy_sp2(), bah_chi_compute_energy_sp3(), core::scoring::hbonds::HBondDatabase::cosAHD_fade_lookup(), core::scoring::hbonds::HBondDatabase::cosAHD_long_poly_lookup(), core::scoring::hbonds::HBondDatabase::cosAHD_short_poly_lookup(), core::scoring::hbonds::HBondDatabase::cosBAH2_fade_lookup(), core::scoring::hbonds::HBondDatabase::cosBAH2_poly_lookup(), core::scoring::hbonds::HBondDatabase::cosBAH_fade_lookup(), core::scoring::hbonds::HBondDatabase::cosBAH_long_poly_lookup(), core::scoring::hbonds::HBondDatabase::cosBAH_short_poly_lookup(), core::scoring::hbonds::HBondDatabase::don_strength(), core::scoring::hbonds::HBEvalTuple::don_type(), DUMMY_DERIV(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::HBondOptions::exclude_ether_oxygens(), fade_energy(), core::scoring::hbonds::HBondOptions::fade_energy(), get_hbe_acc_hybrid(), hbacc_AHX, hbacc_H2O, hbacc_HXL, hbacc_PES_DNA, hbacc_PES_RNA, hbacc_RRI_DNA, hbacc_RRI_RNA, hbe_UNKNOWN, hbgd_AHD, hbgd_cosAHD, core::scoring::hbonds::HBondOptions::hbond_energy_shift(), core::scoring::hbonds::HBondOptions::max_hb_energy(), MAX_R, MAX_xD, MAX_xH, core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(), MIN_R, MIN_xD, MIN_xH, core::chemical::element::Pr, core::scoring::hbonds::HBondOptions::sp2_BAH180_rise(), core::chemical::SP2_HYBRID, core::scoring::hbonds::HBondOptions::sp2_outer_width(), core::chemical::SP3_HYBRID, tr(), and core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty().

Referenced by core::scoring::geometric_solvation::WaterWeightGridSet::fill_water_grid(), hb_energy_deriv_u2(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

HBEvalTuple core::scoring::hbonds::hbond_evaluation_type ( hbtrie::HBAtom const &  datm,
Size const  don_rsd,
hbtrie::HBAtom const &  aatm,
Size const  acc_rsd 
)

Warning if you use this interface you are responsible for testing if the residues are on different chains!

References get_seq_sep(), core::scoring::hbonds::hbtrie::HBAtom::hb_acc_chem_type(), and core::scoring::hbonds::hbtrie::HBAtom::hb_don_chem_type().

Referenced by core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy().

HBEvalTuple core::scoring::hbonds::hbond_evaluation_type ( Size const  datm,
conformation::Residue const &  don_rsd,
Size const  aatm,
conformation::Residue const &  acc_rsd 
)
void core::scoring::hbonds::identify_hbonds_1way ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
bool const  evaluate_derivative,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc,
HBondSet &  hbond_set,
Real  ssdep_weight_factor,
bool  bond_near_wat 
)

HBond Database ///.

identify_hbonds_1way is overloaded to either add HBond objects to an HBondSet or to accumulate energy into a EnergyMap object. This is done for performance reasons. The allocation of the temporary HBondSet on the heap causes a substatial slow down.

References core::conformation::Residue::abase2(), core::conformation::Residue::accpt_pos(), core::scoring::hbonds::HBondSet::append_hbond(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::scoring::hbonds::HBEvalTuple::eval_type(), get_environment_dependent_weight(), get_hbond_weight_type(), hb_energy_deriv(), core::scoring::hbonds::HBondSet::hbond_options(), hbw_SR_BB, core::conformation::Residue::Hpos_polar(), core::scoring::hbonds::HBondOptions::max_hb_energy(), MAX_R2, core::conformation::Residue::seqpos(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), core::scoring::hbonds::HBondOptions::water_hybrid_sf(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::hbnet::UnsatSelector::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), fill_hbond_set(), core::pack::hbonds::find_hbonds_in_residue_pair(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), core::scoring::hbonds::HBondSet::HBondSet(), protocols::constel::HBondCommon::is_rmoi_hbonded(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), and core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy().

void core::scoring::hbonds::identify_hbonds_1way ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
bool const  evaluate_derivative,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc,
HBondOptions const &  options,
EnergyMap &  emap,
Real  ssdep_weight_factor,
bool  bond_near_wat 
)
void core::scoring::hbonds::identify_hbonds_1way ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
bool const  evaluate_derivative,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc,
HBondOptions const &  options,
EnergyMap &  emap,
boost::unordered_map< core::Size, core::Size > &  num_hbonds,
Real  ssdep_weight_factor,
bool  bond_near_wat 
)
void core::scoring::hbonds::identify_hbonds_1way_AHdist ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
Real const  AHdist_threshold,
HBondSet &  hbond_set,
bool  bond_near_wat 
)
void core::scoring::hbonds::identify_hbonds_1way_membrane ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
bool const  evaluate_derivative,
bool const  exclude_don_bb,
bool const  exclude_don_bsc,
bool const  exclude_acc_scb,
bool const  exclude_acc_sc,
HBondSet &  hbond_set,
pose::Pose const &  pose,
bool  bond_near_wat = false 
)
void core::scoring::hbonds::identify_hbonds_1way_membrane ( HBondDatabase const &  database,
conformation::Residue const &  don_rsd,
conformation::Residue const &  acc_rsd,
Size const  don_nb,
Size const  acc_nb,
bool const  evaluate_derivative,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc,
HBondOptions const &  options,
EnergyMap &  emap,
pose::Pose const &  pose,
bool  bond_near_wat 
)
void core::scoring::hbonds::identify_intra_res_hbonds ( HBondDatabase const &  database,
conformation::Residue const &  rsd,
Size const  rsd_nb,
bool const  evaluate_derivative,
HBondSet &  hbond_set,
bool const  exclude_bb,
bool const  exclude_bsc,
bool const  exclude_scb,
bool const  exclude_sc 
)
void core::scoring::hbonds::identify_intra_res_hbonds ( HBondDatabase const &  database,
conformation::Residue const &  rsd,
Size const  rsd_nb,
HBondOptions const &  options,
EnergyMap &  emap 
)
void core::scoring::hbonds::increment_hbond_energy ( HBEvalType const &  hbe_type,
EnergyMap &  emap,
Real  hbE 
)
void core::scoring::hbonds::increment_npd_hbond_energy ( HBEvalType const &  hbe_type,
EnergyMap &  emap,
Real  hbE,
bool  intra_res 
)
void core::scoring::hbonds::initialize_HBEval_lookup ( )

makes it explicit that the HBEval lookup table is initialized somewhere

References hbacc_MAX, hbdon_MAX, HBEval_lookup, HBEval_lookup_initializer(), and seq_sep_MAX.

Referenced by core::scoring::hbonds::HBondDatabase::initialize_HBEval().

void core::scoring::hbonds::make_hbBasetoAcc_unitvector ( HBondOptions const &  hbondoptions,
chemical::Hybridization const &  acc_hybrid,
Vector const &  Axyz,
Vector const &  Bxyz,
Vector const &  B2xyz,
Vector PBxyz,
Vector BAunit,
Vector B2Aunit 
)
core::Size core::scoring::hbonds::next_hb_res ( HBond const &  c_hb,
core::Size const  res 
)

Get the residue that this residue connects to through this particular hbond We treat hbonds as directed connections (we ignore donor/acceptor).

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::scoring::hbonds::HBond::acc_res(), and core::scoring::hbonds::HBond::don_res().

Referenced by core::simple_metrics::per_residue_metrics::HbondMetric::calculate(), and find_hb_paths().

bool core::scoring::hbonds::nonzero_hbond_weight ( ScoreFunction const &  scorefxn)
Real core::scoring::hbonds::npd_hb_eval_type_weight ( HBEvalType const &  hbe_type,
EnergyMap const &  weights,
bool const  intra_res,
bool const  put_intra_into_total 
)
bool core::scoring::hbonds::operator!= ( FadeInterval const &  a,
FadeInterval const &  b 
)
bool core::scoring::hbonds::operator!= ( HBondOptions const &  a,
HBondOptions const &  b 
)
std::ostream & core::scoring::hbonds::operator<< ( ostream &  out,
const Polynomial_1d &  poly 
)
std::ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
HBEvalTuple const &  hbt 
)
inline
ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
FadeInterval const &  fade_interval 
)
std::ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
const NPDHBondSet &  hbond_set 
)
std::ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
const HBond &  hbond 
)
std::ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
const HBondOptions &  options 
)
std::ostream& core::scoring::hbonds::operator<< ( std::ostream &  out,
const HBondSet &  hbond_set 
)
bool core::scoring::hbonds::operator== ( HBEvalTuple const &  a,
HBEvalTuple const &  b 
)
bool core::scoring::hbonds::operator== ( FadeInterval const &  a,
FadeInterval const &  b 
)
bool core::scoring::hbonds::operator== ( NPDHBondSet const &  a,
NPDHBondSet const &  b 
)
bool core::scoring::hbonds::operator== ( HBond const &  a,
HBond const &  b 
)
bool core::scoring::hbonds::operator== ( HBondOptions const &  a,
HBondOptions const &  b 
)

References core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check_, core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies_, core::scoring::hbonds::HBondOptions::exclude_DNA_DNA_, core::scoring::hbonds::HBondOptions::exclude_ether_oxygens_, core::scoring::hbonds::HBondOptions::exclude_intra_res_protein_, core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA_, core::scoring::hbonds::HBondOptions::exclude_self_hbonds_, core::scoring::hbonds::HBondOptions::fade_energy_, core::scoring::hbonds::HBondOptions::hbond_energy_shift_, core::scoring::hbonds::HBondOptions::ldsrbb_high_scale_, core::scoring::hbonds::HBondOptions::ldsrbb_low_scale_, core::scoring::hbonds::HBondOptions::ldsrbb_maxlength_, core::scoring::hbonds::HBondOptions::ldsrbb_minlength_, core::scoring::hbonds::HBondOptions::length_dependent_srbb_, core::scoring::hbonds::HBondOptions::max_hb_energy_, core::scoring::hbonds::HBondOptions::Mbhbond_, core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy_, core::scoring::hbonds::HBondOptions::mphbond_, core::scoring::hbonds::HBondOptions::params_database_tag_, core::scoring::hbonds::HBondOptions::put_intra_into_total_, core::scoring::hbonds::HBondOptions::smooth_hb_env_dep_, core::scoring::hbonds::HBondOptions::sp2_BAH180_rise_, core::scoring::hbonds::HBondOptions::sp2_outer_width_, core::scoring::hbonds::HBondOptions::use_hb_env_dep_, core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA_, core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty_, and core::scoring::hbonds::HBondOptions::water_hybrid_sf_.

bool core::scoring::hbonds::operator== ( HBondSet const &  a,
HBondSet const &  b 
)
bool core::scoring::hbonds::residue_near_water ( pose::Pose const &  pose,
Size  ii 
)
HBEvalType core::scoring::hbonds::string_to_hb_eval_type ( std::string const &  hbe_str)

converts a string into an HBEvalType

References hbe_dH2OaHXL, and hbe_GENERIC_SP3SCSC_LR.

Referenced by HBEval_lookup_initializer().

static basic::Tracer core::scoring::hbonds::t ( "core.scoring.hbonds.HBondSet"  )
static
static basic::Tracer core::scoring::hbonds::TR ( "core.scoring.hbonds.types"  )
static
static Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.HBondDatabase"  )
static
static basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.hbonds"  )
static
static basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.hbonds_geom"  )
static
static basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.HbondEnergy"  )
static
void core::scoring::hbonds::weights_and_derivs_for_hbonds ( conformation::Residue const &  res,
Size  atom,
utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights,
utility::vector1< utility::vector1< Real > > &  dwt_dE 
)

depending on the hybridization type of the atom, compute the weights for its hydrogen bonds. No derivative evaluation.

References core::conformation::Residue::atom_is_polar_hydrogen(), get_hb_acc_chem_type(), get_weights_for_one_partner_hbonder(), get_weights_for_two_partner_hbonder(), hbacc_GENERIC_RINGBB, hbacc_GENERIC_RINGSC, hbacc_IMD, and hbacc_IME.

void core::scoring::hbonds::weights_for_hbonds ( conformation::Residue const &  res,
Size  atom,
utility::vector1< Real > const &  energies,
utility::vector1< Real > &  weights 
)

depending on the hybridization type of the atom, compute the weights for its hydrogen bonds. No derivative evaluation.

Given a vector of energies for hydrogen bonds for a particular atom, compute the weights assigned to them. The residue need not have been seen by the NPDHBondSet prior to this function evaluation.

References core::conformation::Residue::atom_is_polar_hydrogen(), get_hb_acc_chem_type(), get_weights_for_one_partner_hbonder(), get_weights_for_two_partner_hbonder(), hbacc_GENERIC_RINGBB, hbacc_GENERIC_RINGSC, hbacc_IMD, and hbacc_IME.

Referenced by core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds().

Variable Documentation

bool core::scoring::hbonds::DUMMY_BOOL
Real core::scoring::hbonds::DUMMY_DERIV
HBondDerivs core::scoring::hbonds::DUMMY_DERIVS
HBEvalTuple core::scoring::hbonds::DUMMY_HBE
HBGeoDimType core::scoring::hbonds::DUMMY_HBGEODIMTYPE
Size const core::scoring::hbonds::HB_EVAL_TYPE_COUNT = { (hbdon_MAX-1)*(hbacc_MAX-1)*(seq_sep_MAX-1)}
utility::pointer::shared_ptr< ObjexxFCL::FArray3D< HBEvalType > const > core::scoring::hbonds::HBEval_lookup
core::Real const core::scoring::hbonds::MAX_R = { 3.0 }
static
core::Real const core::scoring::hbonds::MAX_R2 = { MAX_R * MAX_R }
static
core::Real const core::scoring::hbonds::MAX_xD = { 1.0 }
static
core::Real const core::scoring::hbonds::MAX_xH = { 1.0 }
static
core::Real const core::scoring::hbonds::MIN_R = { 0.0 }
static
core::Real const core::scoring::hbonds::MIN_R2 = { MIN_R * MIN_R }
static
core::Real const core::scoring::hbonds::MIN_xD = { 0.0 }
static
core::Real const core::scoring::hbonds::MIN_xH = { -1.0 }
static
HBondDerivs const core::scoring::hbonds::ZERO_DERIV2D = { DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair() }