Namespaces
	hbtrie

Classes
class	FadeInterval
	Classic FadeInterval. More...

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	Polynomial_1d

struct	SSWeightParameters

Typedefs
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

typedef utility::pointer::shared_ptr < HBondResidueMinData >	HBondResidueMinDataOP

typedef utility::pointer::shared_ptr < HBondResidueMinData const >	HBondResidueMinDataCOP

typedef utility::pointer::shared_ptr < HBondResPairMinData >	HBondResPairMinDataOP

typedef utility::pointer::shared_ptr < HBondResPairMinData const >	HBondResPairMinDataCOP

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 < 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::owning_ptr < HBondTypeManager >	HBondTypeManagerOP

typedef utility::pointer::owning_ptr < HBondTypeManager const >	HBondTypeManagerCOP

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	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 THREAD_LOCAL 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	operator== (HBondOptions const &a, HBondOptions const &b)

bool	operator!= (HBondOptions const &a, HBondOptions const &b)

std::ostream &	operator<< (std::ostream &out, const HBondOptions &options)

static THREAD_LOCAL basic::Tracer	tr ("core.scoring.hbonds.hbonds")

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)

void	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)

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_bb, bool const exclude_bsc, bool const exclude_scb, bool const exclude_sc, HBondSet &hbond_set, Real ssdep_weight_factor)

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)

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)

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)

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	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)

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)

core::Real	hb_env_dep_burial_fd (int const nb1, int const nb2, core::Real low_scale, core::Real low_nb, core::Real high_nb)

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)
	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)

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 THREAD_LOCAL 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_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 (int const datm, conformation::Residue const &don_rsd)

HBAccChemType	get_hb_acc_chem_type (int 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, int const &don_rsd, hbtrie::HBAtom const &aatm, int const &acc_rsd)

hbonds::HBEvalTuple	hbond_evaluation_type (int const datm, conformation::Residue const &don_rsd, int const aatm, conformation::Residue const &acc_rsd)

void	hbond_compute_energy (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple hbt, Real const AHdis, Real const xD, Real const xH, 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_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, 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,Real &energy, HBondDerivs &deriv=DUMMY_DERIVS)
	Evaluate the hydrogen bond energy and derivatives after having first calculated the HD and BA unit 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)

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 THREAD_LOCAL 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)

ostream &	operator<< (ostream &out, const Polynomial_1d &poly)

static THREAD_LOCAL 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 }

static core::Real const	MAX_HB_ENERGY = { 0.0 }

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

typedef utility::pointer::shared_ptr< HBondResidueMinData const > core::scoring::hbonds::HBondResidueMinDataCOP

typedef utility::pointer::shared_ptr< HBondResidueMinData > core::scoring::hbonds::HBondResidueMinDataOP

typedef utility::pointer::shared_ptr< HBondResPairMinData const > core::scoring::hbonds::HBondResPairMinDataCOP

typedef utility::pointer::shared_ptr< HBondResPairMinData > core::scoring::hbonds::HBondResPairMinDataOP

typedef utility::pointer::shared_ptr< HBondSet const > core::scoring::hbonds::HBondSetCOP

typedef utility::pointer::shared_ptr< HBondSet > core::scoring::hbonds::HBondSetOP

typedef utility::pointer::owning_ptr< HBondTypeManager const > core::scoring::hbonds::HBondTypeManagerCOP

typedef utility::pointer::owning_ptr< HBondTypeManager > core::scoring::hbonds::HBondTypeManagerOP

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

enum core::scoring::hbonds::HBAccChemType

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

enum core::scoring::hbonds::HBDerivType

Enumerator
hbderiv_NONE
hbderiv_ABE_GO
hbderiv_ABE_GO_GEOMSOL_OCC_ACC
hbderiv_ABE_GO_GEOMSOL_OCC_DON
hbderiv_MAX

enum core::scoring::hbonds::HBDonChemType

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

enum core::scoring::hbonds::HBEvalType

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

enum core::scoring::hbonds::HBGeoDimType

Enumerator
hbgd_NONE
hbgd_AHdist
hbgd_cosBAH
hbgd_cosAHD
hbgd_AHD
hbgd_chi
hbgd_MAX

enum core::scoring::hbonds::HBondWeightType

Enumerator
hbw_NONE
hbw_SR_BB
hbw_LR_BB
hbw_SR_BB_SC
hbw_LR_BB_SC
hbw_SC
hbw_MAX

enum core::scoring::hbonds::HBSeqSep

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

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(), core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), and core::scoring::hbonds::HBondEnergy::hbond_derivs_1way().

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
	)

References core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), and core::conformation::Residue::is_RNA().

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), fill_intra_res_hbond_set(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), and identify_intra_res_hbonds().

Vector core::scoring::hbonds::create_acc_orientation_vector	(	HBondOptions const &	hbondoptions,
		conformation::Residue const &	residue,
		int	atom_id
	)

References core::conformation::Residue::abase2(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::chemical::AtomType::hybridization(), make_hbBasetoAcc_unitvector(), core::conformation::Atom::type(), protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

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

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
	)

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

bool core::scoring::hbonds::DUMMY_BOOL ( false )

Real core::scoring::hbonds::DUMMY_DERIV ( 0. 0 )

Referenced by bah_chi_compute_energy_sp2(), bah_chi_compute_energy_sp3(), fade_energy(), and hbond_compute_energy().

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_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
	)

This routine fills an hbond-set with hbonds. All hbonds are included, even ones which might be excluded later based on the backbone-hbond exclusion.

WARNING WARNING WARNING The pose must have an update energies object, eg it must be scored. WARNING WARNING WARNING

References fill_hbond_set().

Referenced by protocols::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), core::pose::rna::classify_base_pairs(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), protocols::stepwise::sampler::protein::generate_beta_database_test(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), core::scoring::rna::data::RNA_DMS_Potential::initialize(), protocols::dna::PDBOutput::output_hbond_info(), protocols::farna::print_hbonds(), protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), and core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies().

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
	)

References core::scoring::hbonds::HBondSet::clear(), core::pose::Pose::conformation(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::scoring::hbonds::HBondOptions::exclude_self_hbonds(), fill_intra_res_hbond_set(), core::graph::Edge::get_node(), core::graph::Graph::get_node(), get_ssdep_weight(), core::scoring::hbonds::HBondSet::hbond_options(), identify_hbonds_1way(), identify_hbonds_1way_membrane(), core::conformation::Conformation::is_membrane(), core::scoring::hbonds::HBondOptions::Mbhbond(), core::graph::Node::num_neighbors_counting_self_static(), core::scoring::hbonds::HBondOptions::params_database_tag(), core::pose::Pose::residue(), core::scoring::Energies::residue_neighbors_updated(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by fill_hbond_set().

void core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold	(	core::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.

References core::scoring::hbonds::HBondSet::clear(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::graph::Edge::get_node(), core::scoring::hbonds::HBondSet::hbond_options(), identify_hbonds_1way_AHdist(), core::scoring::hbonds::HBondOptions::params_database_tag(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by protocols::features::HBondFeatures::report_features().

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
	)

References calculate_intra_res_hbonds(), core::pose::Pose::energies(), core::scoring::hbonds::HBondSet::hbond_options(), identify_intra_res_hbonds(), core::scoring::hbonds::HBondOptions::params_database_tag(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by fill_hbond_set().

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
	)

References core::scoring::hbonds::HBEvalTuple::eval_type(), hb_env_dep_burial_fd(), hb_env_dep_burial_lin(), hb_env_dep_burial_tk(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_high_nneigh(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_low_nneigh(), core::scoring::hbonds::HBondOptions::hb_env_dep_new_low_scale(), hbe_is_SC_type(), core::scoring::hbonds::HBondOptions::smooth_hb_env_dep(), and core::scoring::hbonds::HBondOptions::use_hb_env_dep_new().

Referenced by core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), identify_hbonds_1way(), identify_hbonds_1way_AHdist(), identify_intra_res_hbonds(), and core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty().

HBAccChemType core::scoring::hbonds::get_hb_acc_chem_type	(	int const	aatm,
		conformation::Residue const &	acc_rsd
	)

Referenced by core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), create_rotamer_descriptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), hbond_evaluation_type(), and protocols::features::HBondFeatures::insert_site_row().

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

Referenced by core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), create_rotamer_descriptor(), 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 )

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 )

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), get_hbond_energies(), hb_eval_type_weight(), protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), identify_hbonds_1way(), identify_hbonds_1way_membrane(), and core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy().

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
	)

References core::conformation::membrane::center, core::scoring::MembraneEmbed::center(), core::pose::Pose::conformation(), hb_env_dep_burial_lin(), core::conformation::Conformation::is_membrane(), core::scoring::Membrane_FAEmbed_from_pose(), core::conformation::Conformation::membrane_info(), core::scoring::MembraneEmbed_from_pose(), core::conformation::membrane::normal, core::scoring::MembraneEmbed::normal(), core::scoring::Membrane_FAEmbed::steepness(), core::conformation::membrane::thickness, and core::scoring::Membrane_FAEmbed::thickness().

Referenced by core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(), and core::scoring::hbonds::HBondEnergy::hbond_derivs_1way().

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
	)

References hb_env_dep_burial_lin(), and core::conformation::membrane::thickness.

Referenced by identify_hbonds_1way_membrane().

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
	)

References protocols::match::upstream::b, core::scoring::hbonds::SSWeightParameters::h_, core::scoring::hbonds::SSWeightParameters::l_, core::scoring::hbonds::SSWeightParameters::len_h_, core::scoring::hbonds::SSWeightParameters::len_l_, core::pose::Pose::secstruct(), core::conformation::Residue::seqpos(), core::scoring::hbonds::SSWeightParameters::ssdep_, and core::pose::Pose::total_residue().

Referenced by core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), fill_hbond_set(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), and core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext().

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
	)

Remarks: See comments on helper function above.

References hb_energy_deriv(), hbderiv_ABE_GO, and hbderiv_NONE.

Referenced by core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::check_hbond_score(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), identify_hbonds_1way(), identify_hbonds_1way_AHdist(), identify_hbonds_1way_membrane(), identify_intra_res_hbonds(), and core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty().

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
	)

References core::scoring::hbonds::HBEvalTuple::eval_type(), get_hbe_acc_hybrid(), hb_energy_deriv_u2(), hbe_UNKNOWN, make_hbBasetoAcc_unitvector(), tr(), and ZERO_DERIV2D.

Referenced by hb_energy_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,
		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

energy acceptor 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,
		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

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

Referenced by hb_energy_deriv(), and hb_energy_deriv_u().

core::Real core::scoring::hbonds::hb_env_dep_burial_fd	(	int const	nb1,
		int const	nb2,
		core::Real	low_scale,
		core::Real	low_nb,
		core::Real	high_nb
	)

core::Real core::scoring::hbonds::hb_env_dep_burial_lin	(	int const	nb1,
		int const	nb2
	)

References burial_weight().

Referenced by get_environment_dependent_weight(), and get_membrane_depth_dependent_weight().

core::Real core::scoring::hbonds::hb_env_dep_burial_tk	(	int const	nb1,
		int const	nb2
	)

References burial3class_weight_initializer(), and get_burial_3().

Referenced by get_environment_dependent_weight().

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 )

Referenced by hbe_is_SC_type().

bool core::scoring::hbonds::hbe_is_SC_type ( HBEvalType hbe )

References hbe_is_BB_type().

Referenced by get_environment_dependent_weight().

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	hbt,
		Real const	AHdis,
		Real const	xD,
		Real const	xH,
		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_dBAH,
		Real &	dE_dchi
	)

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::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

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

References get_hb_acc_chem_type(), get_hb_don_chem_type(), get_seq_sep(), and core::conformation::Residue::polymeric_oriented_sequence_distance().

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
	)

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.

Referenced by core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), hbonded(), hbonded_atom(), 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
	)

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
	)

Referenced by fill_hbond_set().

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
	)

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(), DUMMY_DERIVS, get_environment_dependent_weight(), hb_energy_deriv(), core::scoring::hbonds::HBondSet::hbond_options(), core::conformation::Residue::Hpos_polar(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by fill_hbond_set_by_AHdist_threshold().

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
	)

Identify Membrane Hydrogen Bonds (Env)

Corrects for strength of hydrogen bonding in the membrane (depth-dependent). This version of the method switches between the previous membrane code (MembraneEmbed cached to the pose) and updated RosettaMP Framework (2015).

Note: This code still preserves duplicated hbond interface for membranes TODO: REMOVE THE CODE DUPLICATION!!!!

Referenced by core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), 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_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
	)

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
	)

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

void core::scoring::hbonds::identify_intra_res_hbonds	(	HBondDatabase const &	database,
		conformation::Residue const &	rsd,
		Size const	rsd_nb,
		HBondOptions const &	options,
		EnergyMap &	emap
	)

References calculate_intra_res_hbonds(), core::scoring::hbonds::HBond::energy(), core::scoring::hbond, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbond_intra, core::scoring::hbonds::HBondSet::nhbonds(), core::scoring::hbonds::HBondOptions::put_intra_into_total(), and core::scoring::hbonds::HBond::weight().

Referenced by fill_intra_res_hbond_set().

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
	)

Parameters

BAunit the coordinate for the pseudo-acceptor-base atom, used in derivative evaluation

References 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 create_acc_orientation_vector(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::magnesium::get_cos_theta(), hb_energy_deriv(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and protocols::dna::PDBOutput::output_hbond_info().

bool core::scoring::hbonds::nonzero_hbond_weight ( ScoreFunction const & scorefxn )

References core::scoring::ScoreFunction::has_nonzero_weight(), core::scoring::hbond, core::scoring::hbond_bb_sc, core::scoring::hbond_intra, core::scoring::hbond_lr_bb, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, and core::scoring::hbond_sr_bb_sc.

bool core::scoring::hbonds::operator!=	(	FadeInterval const &	a,
		FadeInterval const &	b
	)

References protocols::match::upstream::b.

bool core::scoring::hbonds::operator!=	(	HBondOptions const &	a,
		HBondOptions const &	b
	)

References protocols::match::upstream::b.

std::ostream & core::scoring::hbonds::operator<<	(	ostream &	out,
		const Polynomial_1d &	poly
	)

References core::scoring::hbonds::Polynomial_1d::show().

std::ostream& core::scoring::hbonds::operator<<	(	std::ostream &	out,
		HBEvalTuple const &	hbt
	)

inline

References core::scoring::hbonds::HBEvalTuple::show().

ostream& core::scoring::hbonds::operator<<	(	std::ostream &	out,
		FadeInterval const &	fade_interval
	)

References core::scoring::hbonds::FadeInterval::show().

std::ostream& core::scoring::hbonds::operator<<	(	std::ostream &	out,
		const HBond &	hbond
	)

References core::scoring::hbonds::HBond::show().

std::ostream& core::scoring::hbonds::operator<<	(	std::ostream &	out,
		const HBondOptions &	options
	)

References core::scoring::hbonds::HBondOptions::show().

std::ostream& core::scoring::hbonds::operator<<	(	std::ostream &	out,
		const HBondSet &	hbond_set
	)

References core::scoring::hbonds::HBondSet::show().

bool core::scoring::hbonds::operator==	(	HBEvalTuple const &	a,
		HBEvalTuple const &	b
	)

References core::scoring::hbonds::HBEvalTuple::acc_type_, core::scoring::hbonds::HBEvalTuple::don_type_, core::scoring::hbonds::HBEvalTuple::eval_type_, and core::scoring::hbonds::HBEvalTuple::seq_sep_.

bool core::scoring::hbonds::operator==	(	FadeInterval const &	a,
		FadeInterval const &	b
	)

References core::scoring::hbonds::FadeInterval::fmax_, core::scoring::hbonds::FadeInterval::fmin_, core::scoring::hbonds::FadeInterval::max0_, core::scoring::hbonds::FadeInterval::min0_, and core::scoring::hbonds::FadeInterval::smooth_.

bool core::scoring::hbonds::operator==	(	HBond const &	a,
		HBond const &	b
	)

bool core::scoring::hbonds::operator==	(	HBondOptions const &	a,
		HBondOptions const &	b
	)

bool core::scoring::hbonds::operator==	(	HBondSet const &	a,
		HBondSet const &	b
	)

References core::scoring::hbonds::HBondSet::atom_map_, core::scoring::hbonds::HBondSet::atom_map_init_, core::scoring::hbonds::HBondSet::backbone_backbone_acceptor_, core::scoring::hbonds::HBondSet::backbone_backbone_donor_, core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), core::scoring::hbonds::HBondSet::options_, and t().

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 THREAD_LOCAL basic::Tracer core::scoring::hbonds::t ( "core.scoring.hbonds.HBondSet" )

static

Referenced by operator==().

static THREAD_LOCAL basic::Tracer core::scoring::hbonds::TR ( "core.scoring.hbonds.types" )

static

Referenced by get_hbe_acc_hybrid(), get_hbond_weight_type(), and hbe_is_BB_type().

static THREAD_LOCAL basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.hbonds" )

static

Referenced by get_hbond_energies(), hb_eval_type_weight(), identify_hbonds_1way(), and identify_hbonds_1way_membrane().

static THREAD_LOCAL basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.hbonds_geom" )

static

Referenced by assign_abase_derivs(), hb_energy_deriv(), hbond_compute_energy(), and make_hbBasetoAcc_unitvector().

static Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.HBondDatabase" )

static

Referenced by core::scoring::hbonds::HBondDatabase::initialize(), core::scoring::hbonds::HBondDatabase::initialize_acc_strength(), core::scoring::hbonds::HBondDatabase::initialize_don_strength(), and core::scoring::hbonds::HBondDatabase::initialize_HBEval().

static THREAD_LOCAL basic::Tracer core::scoring::hbonds::tr ( "core.scoring.hbonds.HbondEnergy" )

static

Variable Documentation

bool core::scoring::hbonds::DUMMY_BOOL

Real core::scoring::hbonds::DUMMY_DERIV

HBondDerivs core::scoring::hbonds::DUMMY_DERIVS

Referenced by core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(), identify_hbonds_1way_AHdist(), and protocols::dna::RotamerDNAHBondFilter::operator()().

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

Referenced by initialize_HBEval_lookup(), and core::scoring::hbonds::HBondDatabase::report_parameter_features().

core::Real const core::scoring::hbonds::MAX_HB_ENERGY = { 0.0 }

static

Referenced by core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(), hb_energy_deriv_u2(), hbond_compute_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), identify_hbonds_1way(), identify_hbonds_1way_membrane(), and identify_intra_res_hbonds().

core::Real const core::scoring::hbonds::MAX_R = { 3.0 }

static

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atomic_interaction_cutoff(), core::scoring::hbonds::HBondEnergy::atomic_interaction_cutoff(), core::scoring::geometric_solvation::WaterWeightGridSet::fill_water_grid(), hbond_compute_energy(), core::scoring::hbonds::HBondEnergy::hydrogen_interaction_cutoff2(), and protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

core::Real const core::scoring::hbonds::MAX_R2 = { MAX_R * MAX_R }

static

Referenced by core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), hb_energy_deriv_u2(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::HBondEnergy::heavyatom_hydrogenatom_energy(), identify_hbonds_1way(), identify_hbonds_1way_membrane(), identify_intra_res_hbonds(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and protocols::dna::RotamerDNAHBondFilter::operator()().

core::Real const core::scoring::hbonds::MAX_xD = { 1.0 }

static

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

core::Real const core::scoring::hbonds::MAX_xH = { 1.0 }

static

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

core::Real const core::scoring::hbonds::MIN_R = { 0.0 }

static

Referenced by core::scoring::geometric_solvation::WaterWeightGridSet::fill_water_grid(), hbond_compute_energy(), and protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

core::Real const core::scoring::hbonds::MIN_R2 = { MIN_R * MIN_R }

static

Referenced by hb_energy_deriv_u2(), core::scoring::hbonds::HBondEnergy::heavyatom_hydrogenatom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and protocols::dna::RotamerDNAHBondFilter::operator()().

core::Real const core::scoring::hbonds::MIN_xD = { 0.0 }

static

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

core::Real const core::scoring::hbonds::MIN_xH = { -1.0 }

static

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

HBondDerivs const core::scoring::hbonds::ZERO_DERIV2D = { DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair() }

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), hb_energy_deriv(), and core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation