hbonds

• graph
• hbtrie

Bindings for core::scoring::hbonds namespace

class pyrosetta.rosetta.core.scoring.hbonds.FadeInterval

Bases: pybind11_builtins.pybind11_object

Classic FadeInterval

stores an “fading interval” [a b c d] with a <= b <= c <= d and computes the fraction of containment for x, which is defined to be 0 if x is outside of (a,d), 1 if x is inside of [b,c], and a linear ramp otherwise.

___/—–___

i.e. (x-a)/(b-a) for x in (a,b), and (d-x)/(d-c) for x in (c,d) This is used to ensure that hbond scoring as a sum Er + ExH + ExD goes to zero at the edges.

Notes about discontinuities:

if x equals a, b, c, or d then deriv = 0 if x == a == b then value = 0 if x == c == d and a < c then value = 1 if x == c == d and a == c then value = 0 In particular if a == b == c == d then for all x, value == deriv == 0

Smooth FadeInteval

Rather than using a piecewise linear fading function, use a piecewise sigmoid function to have a continuous derivative.

Look for a canonical sigmoid function f(x) such that,

f(0) = 1 f(1) = 0 // goes through the the knots f’(0) = 0 f’(1) = 0 // is horizontal at the knots a continuous differative f(x-.5)-.5 is odd // symmetric

I claim, f(x) = 2x^3 - 3x^2 + 1, satisfies these constraints:

f(0) = 2(0)^3 - 3(x)^2 + 1 = 1 f(1) = 2(1)^3 - 3(1)^2 + 1 = 2 - 3 + 1 = 0

f’(x) = 6x^2 - 6x = 6x(x-1) f’(0) = 6(0)(0-1) = 0 f’(1) = 6(1)(1-1) = 0

a function g(x) is odd if g(-x) = -g(x) f((-x)-.5)-.5 = 2(-x-.5)^3 - 3(-x-.5)^2 + 1 - .5

= -2x^3 - 6x^2 - 4.5x - .5

-(f(x-.5)-.5) = -2(x-.5)^3 + 3(x-.5)^2 - 1 + .5

= -2x^3 - 6x^2 - 4.5x - .5

Given the knots –a-b—c-d– transform f(x) to fill a-b and c-d to connect the linear regions.

a-b region:

let z(x) = (x-a)/(b-a) and z’(x) = 1/(b-a) use g(x) = 1-f(-z(x)) = -2z^3 + 3z^2 and g’(x) = -6z(z-1)*z’(x)

c-d region:

let z(x) = (x-c)/(d-c) and z’(x) = 1/(d-c) use g(x) = f(z) = 2z^3 - 3z^2 + 1 and g’(x) = 6z(z-1)*z’(x)

get_fmax(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → float

C++: core::scoring::hbonds::FadeInterval::get_fmax() const –> double

get_fmin(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → float

C++: core::scoring::hbonds::FadeInterval::get_fmin() const –> double

get_max0(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → float

C++: core::scoring::hbonds::FadeInterval::get_max0() const –> double

get_min0(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → float

C++: core::scoring::hbonds::FadeInterval::get_min0() const –> double

get_name(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → str

C++: core::scoring::hbonds::FadeInterval::get_name() const –> std::string

get_smooth(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval) → bool

C++: core::scoring::hbonds::FadeInterval::get_smooth() const –> bool

show(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::hbonds::FadeInterval::show(class std::basic_ostream<char> &) const –> void

value(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval, x: float) → float

C++: core::scoring::hbonds::FadeInterval::value(const double) const –> double

value_deriv(self: pyrosetta.rosetta.core.scoring.hbonds.FadeInterval, x: float, val: float, deriv: float) → None

C++: core::scoring::hbonds::FadeInterval::value_deriv(const double, double &, double &) const –> void

class pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType

Bases: pybind11_builtins.pybind11_object

/// WARNING WARNING WARNING /// /// Changing the HBAccChemType or HBDonChemType will change the /// sort order in hbonds::hbtrie::HBAtom::operator<(…) and /// hbonds::hbtrie::HBAtom::operator==(…). Changing the sort /// order will __definitely__ cause trajectory changes. So make /// changes very carefully! /// ///////////////////////////////////////////////////////////////////////////

Members:

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

class pyrosetta.rosetta.core.scoring.hbonds.HBDerivType

Bases: pybind11_builtins.pybind11_object

Members:

hbderiv_NONE

hbderiv_ABE_GO

hbderiv_ABE_GO_GEOMSOL_OCC_ACC

hbderiv_ABE_GO_GEOMSOL_OCC_DON

hbderiv_MAX

class pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType

Bases: pybind11_builtins.pybind11_object

Members:

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

class pyrosetta.rosetta.core.scoring.hbonds.HBEvalType

Bases: pybind11_builtins.pybind11_object

Members:

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

class pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType

Bases: pybind11_builtins.pybind11_object

Members:

hbgd_NONE

hbgd_AHdist

hbgd_cosBAH

hbgd_cosAHD

hbgd_AHD

hbgd_chi

hbgd_MAX

class pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep

Bases: pybind11_builtins.pybind11_object

Members:

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

class pyrosetta.rosetta.core.scoring.hbonds.HBondSet

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

A class that holds Hbond objects and helps setup Hbonds for scoring

For general hydrogen bond information, either use the default or option constructor, then use the fill methods in hbonds.hh OR use the convenience constructors to detect all Hbonds. Use the copy constructors to fill HBondSets with the Hydrogen bonds you are interested in.

acc_bbg_in_bb_bb_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int) → bool

is the backbone bone acceptor group in a bb/bb hydrogen bond?

C++: core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond(const unsigned long) const –> bool

allow_hbond(*args, **kwargs)

Overloaded function.

1. allow_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, index: int) -> bool

Is this hbond allowed under the bb-bb exclusion scheme?

bb-bb exclusion scheme means that if the query hbond is a sc making a sc-bb hbond with a backbone already involved in a bb-bb hbond, return false This has been included by default when assessing pose Hbond energies due to Rosetta designing too many ser/thr bifricated hbonds in ss structures. Part of the reason is that Rosetta currently does NOT treat bifricated hbonds differently - so both hbonds are counted toward the score. Another reason is that the rotamer library itself favors local bb-sc hbonds. NOTE: This function is called while evaluating / setting up for energies (get_hbond_energies method in hbonds.hh).

C++: core::scoring::hbonds::HBondSet::allow_hbond(const unsigned long) const –> bool

2. allow_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> bool

C++: core::scoring::hbonds::HBondSet::allow_hbond(const class core::scoring::hbonds::HBond &) const –> bool

append_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, dhatm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, aatm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, hbe_tuple: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, energy: float, weight: float, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) → None

Add a new hbond to the list

updates the “hbchk” array as necessary

C++: core::scoring::hbonds::HBondSet::append_hbond(const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::hbonds::HBEvalTuple &, const double, const double, const struct core::scoring::hbonds::HBondDerivs &) –> void

assign(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → pyrosetta.rosetta.core.scoring.hbonds.HBondSet

C++: core::scoring::hbonds::HBondSet::operator=(const class core::scoring::hbonds::HBondSet &) –> class core::scoring::hbonds::HBondSet &

atom_hbonds(*args, **kwargs)

Overloaded function.

1. atom_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t
2. atom_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID, include_only_allowed: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a vector of the hbonds involving a particular atom

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::atom_hbonds(const class core::id::AtomID &, bool) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > >

atom_hbonds_all(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a reference to a vector of all the hbonds involving a particular atom; in

contrast to “atom_hbonds” (above), this function does not exclude sc/bb hydrogen bonds

C++: core::scoring::hbonds::HBondSet::atom_hbonds_all(const class core::id::AtomID &) const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > > &

clear(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

Delete all the data

C++: core::scoring::hbonds::HBondSet::clear() –> void

clone(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → pyrosetta.rosetta.basic.datacache.CacheableData

Clone this object

C++: core::scoring::hbonds::HBondSet::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

copy_bb_donor_acceptor_arrays(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, src: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

C++: core::scoring::hbonds::HBondSet::copy_bb_donor_acceptor_arrays(const class core::scoring::hbonds::HBondSet &) –> void

don_bbg_in_bb_bb_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int) → bool

is the backbone bone donor group in a bb/bb hydrogen bond?

C++: core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond(const unsigned long) const –> bool

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, number: int) → pyrosetta.rosetta.core.scoring.hbonds.HBond

Access hbond

C++: core::scoring::hbonds::HBondSet::hbond(const unsigned long) const –> const class core::scoring::hbonds::HBond &

hbond_cop(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, number: int) → pyrosetta.rosetta.core.scoring.hbonds.HBond

Access hbond

C++: core::scoring::hbonds::HBondSet::hbond_cop(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::HBond>

hbond_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → core::scoring::hbonds::HBondOptions

Read access to the stored hbond options

C++: core::scoring::hbonds::HBondSet::hbond_options() const –> const class core::scoring::hbonds::HBondOptions &

hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_hbonds_HBond_t

Return the vector of HBond pointers

C++: core::scoring::hbonds::HBondSet::hbonds() const –> const class utility::vector1<class std::shared_ptr<class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<class core::scoring::hbonds::HBond> > > &

nbrs(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) → int

general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies.

C++: core::scoring::hbonds::HBondSet::nbrs(const unsigned long) const –> int

nhbonds(*args, **kwargs)

Overloaded function.

1. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> int

Number of hbonds

C++: core::scoring::hbonds::HBondSet::nhbonds() const –> unsigned long

2. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) -> int
3. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, include_only_allowed: bool) -> int

Number of hbonds involving this residue

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::nhbonds(const unsigned long, bool) const –> unsigned long

4. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) -> int
5. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID, include_only_allowed: bool) -> int

Number of hbonds involving this atom

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::nhbonds(const class core::id::AtomID &, bool) const –> unsigned long

residue_hbonds(*args, **kwargs)

Overloaded function.

1. residue_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t
2. residue_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, include_only_allowed: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a vector of all the hbonds involving this residue

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::residue_hbonds(const unsigned long, bool) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > >

resize_bb_donor_acceptor_arrays(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, new_dimension: int) → None

Resize bb info arrays

C++: core::scoring::hbonds::HBondSet::resize_bb_donor_acceptor_arrays(const unsigned long) –> void

set_backbone_backbone_acceptor(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int, state: bool) → None

Manually set the state of backbone-backbone acceptor. Used for symmetry.

C++: core::scoring::hbonds::HBondSet::set_backbone_backbone_acceptor(const unsigned long, bool) –> void

set_backbone_backbone_donor(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int, state: bool) → None

Manually set the state of backbone-backbone donor. Used for symmetry.

C++: core::scoring::hbonds::HBondSet::set_backbone_backbone_donor(const unsigned long, bool) –> void

set_hbond_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, options: core::scoring::hbonds::HBondOptions) → None

set the hbond options for this hbond set; clears all hbonds already stored

C++: core::scoring::hbonds::HBondSet::set_hbond_options(const class core::scoring::hbonds::HBondOptions &) –> void

set_nbrs(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, value: int) → None

Used by SymmetricScorFunction. Not sure why. Not for general use.

C++: core::scoring::hbonds::HBondSet::set_nbrs(const unsigned long, unsigned long) –> void

setup_for_residue_pair_energies(*args, **kwargs)

Overloaded function.

1. setup_for_residue_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. setup_for_residue_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool) -> None
3. setup_for_residue_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, backbone_only: bool) -> None

C++: core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(const class core::pose::Pose &, const bool, const bool) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, out: pyrosetta.rosetta.std.ostream) -> None

Print just the information stored in each individual

hbond.

C++: core::scoring::hbonds::HBondSet::show(class std::basic_ostream<char> &) const –> void

2. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None

C++: core::scoring::hbonds::HBondSet::show() const –> void

3. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, print_header: bool, out: pyrosetta.rosetta.std.ostream) -> None

Print nicely formated summary of the hbonds and their geometry in the pose.

C++: core::scoring::hbonds::HBondSet::show(const class core::pose::Pose &, const bool, class std::basic_ostream<char> &) const –> void

4. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None
5. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, print_header: bool) -> None

C++: core::scoring::hbonds::HBondSet::show(const class core::pose::Pose &, const bool) const –> void

6. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int, print_header: bool, out: pyrosetta.rosetta.std.ostream) -> None

Print nicely formated summary of all the hbonds to a

specific residue

C++: core::scoring::hbonds::HBondSet::show(const class core::pose::Pose &, const unsigned long, const bool, class std::basic_ostream<char> &) const –> void

7. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int) -> None
8. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int, print_header: bool) -> None

C++: core::scoring::hbonds::HBondSet::show(const class core::pose::Pose &, const unsigned long, const bool) const –> void

sort_by_weighted_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

C++: core::scoring::hbonds::HBondSet::sort_by_weighted_energy() –> void

class pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType

Bases: pybind11_builtins.pybind11_object

//// if you modify the hbond types please update the strings name //// in ScoreTypeManager.cc //// //// WARNING WARNING WARNING //////////////////////////////////////////////////////////////////////////////

Members:

hbw_NONE

hbw_SR_BB

hbw_LR_BB

hbw_SR_BB_SC

hbw_LR_BB_SC

hbw_SC

hbw_MAX

class pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy

Bases: pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy

First pass implementation; somewhat ineffecient. The NPDHbondEnergy will cache a map of all hbonds by donor and acceptor in the Pose during setup_for_scoring, and will then retrieve these values during calls to residue_pair_energy. Doesn’t work properly for packing.

assign(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, : pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy) → pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy

C++: core::scoring::hbonds::NPDHBondEnergy::operator=(const class core::scoring::hbonds::NPDHBondEnergy &) –> class core::scoring::hbonds::NPDHBondEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy) → float

C++: core::scoring::hbonds::NPDHBondEnergy::atomic_interaction_cutoff() const –> double

backbone_backbone_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::backbone_backbone_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

backbone_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::backbone_sidechain_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::TwoBodyEnergy::bump_energy_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::methods::TwoBodyEnergy::bump_energy_full(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: core::scoring::hbonds::NPDHBondEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose) → bool

Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

defines_intrares_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, p: pyrosetta.rosetta.core.pose.Pose) → bool

Use the dof_derivative interface for this energy method when

calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_dof_derivatives(const class core::pose::Pose &) const –> bool

defines_intrares_energy(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, weights: pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::hbonds::NPDHBondEnergy::defines_intrares_energy(const class core::scoring::EMapVector &) const –> bool

defines_intrares_energy_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res: pyrosetta.rosetta.core.conformation.Residue) → bool

If a score function defines no intra-residue scores for a particular

residue, then it may opt-out of being asked during minimization to evaluate the score for this residue.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_energy_for_residue(const class core::conformation::Residue &) const –> bool

defines_score_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns “true” for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning “false” for residue pairs that do no move wrt each other.

C++: core::scoring::methods::TwoBodyEnergy::defines_score_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, bool) const –> bool

divides_backbone_and_sidechain_energetics(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) → bool

A derived class should return true for this function if it implements its own

versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are “provably distant” based on a pair of bounding spheres for a sidechains and backbones and this method’s atomic_interaction_cutoff energy method.

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : ObjexxFCL::FArray1D<int>, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

f1 and f2 are zeroed

C++: core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

C++: core::scoring::methods::TwoBodyEnergy::eval_intrares_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::hbonds::NPDHBondEnergy::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

eval_intrares_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

C++: core::scoring::methods::TwoBodyEnergy::eval_intrares_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

eval_intraresidue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::TwoBodyEnergy::eval_intraresidue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

eval_residue_pair_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, : pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect

to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.

C++: core::scoring::methods::TwoBodyEnergy::eval_residue_pair_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) → None

Batch computation of rotamer/background energies. Need not be overriden

in derived class – by default, iterates over all rotamers in the set, and calls derived class’s residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_background_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None

Batch computation of rotamer/background energies. Need not be overriden

in derived class – by default, iterates over all rotamers in the set, and calls derived class’s residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(const class core::conformation::RotamerSetBase &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

evaluate_rotamer_intrares_energies(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) → None

Batch computation of rotamer intrares energies. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

C++: core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_intrares_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None

Batch computation of rotamer intrares energy map. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

C++: core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

evaluate_rotamer_pair_energies(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: ObjexxFCL::FArray2D<float>) → None

Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class ObjexxFCL::FArray2D<float> &) const –> void

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose) → None

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::hbonds::NPDHBondEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy) → float

C++: core::scoring::hbonds::NPDHBondEnergy::hydrogen_interaction_cutoff2() const –> double

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None

HBondEnergy is context sensitive

C++: core::scoring::hbonds::NPDHBondEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::ContextDependentTwoBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::scoring::hbonds::NPDHBondEnergy::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

requires_a_setup_for_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_derivatives_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_derivatives_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

requires_a_setup_for_scoring_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → bool

Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

C++: core::scoring::methods::TwoBodyEnergy::requires_a_setup_for_scoring_for_residue_pair_opportunity(const class core::pose::Pose &) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::hbonds::NPDHBondEnergy::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

residue_pair_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

C++: core::scoring::methods::TwoBodyEnergy::residue_pair_energy_ext(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::hbonds::NPDHBondEnergy::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work necessary before evaluating the derivatives for this residue

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_derivatives_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) → None

Do any setup work necessary before evaluating the derivatives for this residue pair

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → None

Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

C++: core::scoring::methods::TwoBodyEnergy::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::hbonds::NPDHBondEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None
2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_scoring_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) → None

Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : bool) → None

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(class std::basic_ostream<char> &, class core::pose::Pose &, bool) const –> void

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

C++: core::scoring::methods::TwoBodyEnergy::sidechain_sidechain_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, resid: int) → None

If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) → bool

Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

during minimization routines should return “true” when this function is invoked on them. This class provides a default “return false” implementation so that classes not desiring to take advantage of this alternate interface need to do nothing.

C++: core::scoring::methods::TwoBodyEnergy::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) → bool

Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::use_extended_residue_pair_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → int

Return the version of the energy method

C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long

class pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet

Bases: pyrosetta.rosetta.core.scoring.hbonds.HBondSet

A class that holds Hbond objects and helps setup Hbonds for scoring

For general hydrogen bond information, either use the default or option constructor, then use the fill methods in hbonds.hh OR use the convenience constructors to detect all Hbonds. Use the copy constructors to fill NPDHBondSets with the Hydrogen bonds you are interested in.

acc_bbg_in_bb_bb_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int) → bool

is the backbone bone acceptor group in a bb/bb hydrogen bond?

C++: core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond(const unsigned long) const –> bool

allow_hbond(*args, **kwargs)

Overloaded function.

1. allow_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, index: int) -> bool

Is this hbond allowed under the bb-bb exclusion scheme?

bb-bb exclusion scheme means that if the query hbond is a sc making a sc-bb hbond with a backbone already involved in a bb-bb hbond, return false This has been included by default when assessing pose Hbond energies due to Rosetta designing too many ser/thr bifricated hbonds in ss structures. Part of the reason is that Rosetta currently does NOT treat bifricated hbonds differently - so both hbonds are counted toward the score. Another reason is that the rotamer library itself favors local bb-sc hbonds. NOTE: This function is called while evaluating / setting up for energies (get_hbond_energies method in hbonds.hh).

C++: core::scoring::hbonds::HBondSet::allow_hbond(const unsigned long) const –> bool

2. allow_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, hbond: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> bool

C++: core::scoring::hbonds::HBondSet::allow_hbond(const class core::scoring::hbonds::HBond &) const –> bool

append_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, dhatm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, aatm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, hbe_tuple: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, energy: float, weight: float, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) → None

Add a new hbond to the list

updates the “hbchk” array as necessary

C++: core::scoring::hbonds::HBondSet::append_hbond(const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::hbonds::HBEvalTuple &, const double, const double, const struct core::scoring::hbonds::HBondDerivs &) –> void

assign(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, : pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet) → pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet

C++: core::scoring::hbonds::NPDHBondSet::operator=(const class core::scoring::hbonds::NPDHBondSet &) –> class core::scoring::hbonds::NPDHBondSet &

atom_hbonds(*args, **kwargs)

Overloaded function.

1. atom_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t
2. atom_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID, include_only_allowed: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a vector of the hbonds involving a particular atom

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::atom_hbonds(const class core::id::AtomID &, bool) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > >

atom_hbonds_all(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a reference to a vector of all the hbonds involving a particular atom; in

contrast to “atom_hbonds” (above), this function does not exclude sc/bb hydrogen bonds

C++: core::scoring::hbonds::HBondSet::atom_hbonds_all(const class core::id::AtomID &) const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > > &

clear(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

Delete all the data

C++: core::scoring::hbonds::HBondSet::clear() –> void

clone(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet) → pyrosetta.rosetta.basic.datacache.CacheableData

Clone this object

C++: core::scoring::hbonds::NPDHBondSet::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

copy_bb_donor_acceptor_arrays(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, src: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

C++: core::scoring::hbonds::HBondSet::copy_bb_donor_acceptor_arrays(const class core::scoring::hbonds::HBondSet &) –> void

dEtot_dEhb(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, hbond_index: int) → float

Return the derivative for the system induced by a change in energy of a particular hbond

as caused by movement by its atoms

C++: core::scoring::hbonds::NPDHBondSet::dEtot_dEhb(unsigned long) const –> double

d_hbond_weight_dE(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, id: pyrosetta.rosetta.core.id.AtomID, hbond_fixed_index: int, hbond_changing_index: int) → float

Return the derivative of the non-pairwise-decomposable weight for a particular atom for a particular

hbond (by index for that atom ) as a function of the change in energy of another (possibly the same) hbond (by index) given the AtomID of the acceptor or the donor.

C++: core::scoring::hbonds::NPDHBondSet::d_hbond_weight_dE(const class core::id::AtomID &, unsigned long, unsigned long) const –> double

don_bbg_in_bb_bb_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int) → bool

is the backbone bone donor group in a bb/bb hydrogen bond?

C++: core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond(const unsigned long) const –> bool

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

hbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, number: int) → pyrosetta.rosetta.core.scoring.hbonds.HBond

Access hbond

C++: core::scoring::hbonds::HBondSet::hbond(const unsigned long) const –> const class core::scoring::hbonds::HBond &

hbond_cop(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, number: int) → pyrosetta.rosetta.core.scoring.hbonds.HBond

Access hbond

C++: core::scoring::hbonds::HBondSet::hbond_cop(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::HBond>

hbond_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → core::scoring::hbonds::HBondOptions

Read access to the stored hbond options

C++: core::scoring::hbonds::HBondSet::hbond_options() const –> const class core::scoring::hbonds::HBondOptions &

hbond_weight(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, id: pyrosetta.rosetta.core.id.AtomID, hbond_index: int) → float

Return the non-pairwise-decomposable weight for a particular atom for a particular

hbond (by index for that atom – stored in HBond::acc_index() or HBond::don_index())

C++: core::scoring::hbonds::NPDHBondSet::hbond_weight(const class core::id::AtomID &, unsigned long) const –> double

hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_hbonds_HBond_t

Return the vector of HBond pointers

C++: core::scoring::hbonds::HBondSet::hbonds() const –> const class utility::vector1<class std::shared_ptr<class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<class core::scoring::hbonds::HBond> > > &

nbrs(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) → int

general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies.

C++: core::scoring::hbonds::HBondSet::nbrs(const unsigned long) const –> int

nhbonds(*args, **kwargs)

Overloaded function.

1. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> int

Number of hbonds

C++: core::scoring::hbonds::HBondSet::nhbonds() const –> unsigned long

2. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) -> int
3. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, include_only_allowed: bool) -> int

Number of hbonds involving this residue

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::nhbonds(const unsigned long, bool) const –> unsigned long

4. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID) -> int
5. nhbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, atom: pyrosetta.rosetta.core.id.AtomID, include_only_allowed: bool) -> int

Number of hbonds involving this atom

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::nhbonds(const class core::id::AtomID &, bool) const –> unsigned long

residue_hbonds(*args, **kwargs)

Overloaded function.

1. residue_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t
2. residue_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, include_only_allowed: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t

Get a vector of all the hbonds involving this residue

Excludes ‘not allowed’ bonds by default. See hbond_allowed function for more info)

C++: core::scoring::hbonds::HBondSet::residue_hbonds(const unsigned long, bool) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > >

resize_bb_donor_acceptor_arrays(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, new_dimension: int) → None

Resize bb info arrays

C++: core::scoring::hbonds::HBondSet::resize_bb_donor_acceptor_arrays(const unsigned long) –> void

set_backbone_backbone_acceptor(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int, state: bool) → None

Manually set the state of backbone-backbone acceptor. Used for symmetry.

C++: core::scoring::hbonds::HBondSet::set_backbone_backbone_acceptor(const unsigned long, bool) –> void

set_backbone_backbone_donor(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, residue: int, state: bool) → None

Manually set the state of backbone-backbone donor. Used for symmetry.

C++: core::scoring::hbonds::HBondSet::set_backbone_backbone_donor(const unsigned long, bool) –> void

set_hbond_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, options: core::scoring::hbonds::HBondOptions) → None

set the hbond options for this hbond set; clears all hbonds already stored

C++: core::scoring::hbonds::HBondSet::set_hbond_options(const class core::scoring::hbonds::HBondOptions &) –> void

set_nbrs(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, seqpos: int, value: int) → None

Used by SymmetricScorFunction. Not sure why. Not for general use.

C++: core::scoring::hbonds::HBondSet::set_nbrs(const unsigned long, unsigned long) –> void

setup_for_residue_pair_energies(*args, **kwargs)

Overloaded function.

1. setup_for_residue_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. setup_for_residue_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool) -> None

C++: core::scoring::hbonds::NPDHBondSet::setup_for_residue_pair_energies(const class core::pose::Pose &, const bool) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, out: pyrosetta.rosetta.std.ostream) -> None

Print just the information stored in each individual

hbond.

C++: core::scoring::hbonds::NPDHBondSet::show(class std::basic_ostream<char> &) const –> void

2. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet) -> None

C++: core::scoring::hbonds::NPDHBondSet::show() const –> void

3. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, print_header: bool, out: pyrosetta.rosetta.std.ostream) -> None

Print nicely formated summary of the hbonds and their geometry in the pose.

C++: core::scoring::hbonds::NPDHBondSet::show(const class core::pose::Pose &, const bool, class std::basic_ostream<char> &) const –> void

4. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None
5. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, print_header: bool) -> None

C++: core::scoring::hbonds::NPDHBondSet::show(const class core::pose::Pose &, const bool) const –> void

6. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int, print_header: bool, out: pyrosetta.rosetta.std.ostream) -> None

Print nicely formated summary of all the hbonds to a

specific residue

C++: core::scoring::hbonds::NPDHBondSet::show(const class core::pose::Pose &, const unsigned long, const bool, class std::basic_ostream<char> &) const –> void

7. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int) -> None
8. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose, residue: int, print_header: bool) -> None

C++: core::scoring::hbonds::NPDHBondSet::show(const class core::pose::Pose &, const unsigned long, const bool) const –> void

sort_by_weighted_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

C++: core::scoring::hbonds::HBondSet::sort_by_weighted_energy() –> void

pyrosetta.rosetta.core.scoring.hbonds.assign_abase_derivs(*args, **kwargs)

Overloaded function.

1. assign_abase_derivs(hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_atom: int, acc_hybrid: pyrosetta.rosetta.core.chemical.Hybridization, abase_deriv: pyrosetta.rosetta.core.scoring.DerivVectorPair, weighted_energy: float, acc_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) -> None

C++: core::scoring::hbonds::assign_abase_derivs(const class core::scoring::hbonds::HBondOptions &, const class core::conformation::Residue &, unsigned long, const enum core::chemical::Hybridization &, const class core::scoring::DerivVectorPair &, double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) –> void

2. assign_abase_derivs(hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_atom: int, hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, abase_deriv: pyrosetta.rosetta.core.scoring.DerivVectorPair, weighted_energy: float, acc_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) -> None

C++: core::scoring::hbonds::assign_abase_derivs(const class core::scoring::hbonds::HBondOptions &, const class core::conformation::Residue &, unsigned long, const class core::scoring::hbonds::HBEvalTuple &, const class core::scoring::DerivVectorPair &, double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) –> void

pyrosetta.rosetta.core.scoring.hbonds.calculate_intra_res_hbonds(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) → bool

C++: core::scoring::hbonds::calculate_intra_res_hbonds(const class core::conformation::Residue &, const class core::scoring::hbonds::HBondOptions &) –> bool

pyrosetta.rosetta.core.scoring.hbonds.create_acc_orientation_vector(hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, residue: pyrosetta.rosetta.core.conformation.Residue, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::hbonds::create_acc_orientation_vector(const class core::scoring::hbonds::HBondOptions &, const class core::conformation::Residue &, int) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.hbonds.create_don_orientation_vector(residue: pyrosetta.rosetta.core.conformation.Residue, atom_id: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::hbonds::create_don_orientation_vector(const class core::conformation::Residue &, int) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.hbonds.fade_energy(*args, **kwargs)

Overloaded function.

1. fade_energy(energy: float) -> None
2. fade_energy(energy: float, dE_dr: float) -> None
3. fade_energy(energy: float, dE_dr: float, dE_dxD: float) -> None
4. fade_energy(energy: float, dE_dr: float, dE_dxD: float, dE_dxH: float) -> None
5. fade_energy(energy: float, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float) -> None
6. fade_energy(energy: float, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float, dE_dBAH: float) -> None
7. fade_energy(energy: float, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float, dE_dBAH: float, dE_dchi: float) -> None

C++: core::scoring::hbonds::fade_energy(double &, double &, double &, double &, double &, double &, double &) –> void

pyrosetta.rosetta.core.scoring.hbonds.fill_hbond_set(*args, **kwargs)

Overloaded function.

1. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None
2. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool) -> None
3. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool) -> None
4. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool) -> None
5. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool, exclude_sc: bool) -> None

C++: core::scoring::hbonds::fill_hbond_set(const class core::pose::Pose &, const bool, class core::scoring::hbonds::HBondSet &, const bool, const bool, const bool, const bool) –> void

6. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters) -> None
7. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters, exclude_bb: bool) -> None
8. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters, exclude_bb: bool, exclude_bsc: bool) -> None
9. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool) -> None
10. fill_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, : pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool, exclude_sc: bool) -> None

C++: core::scoring::hbonds::fill_hbond_set(const class core::pose::Pose &, const bool, class core::scoring::hbonds::HBondSet &, const struct core::scoring::hbonds::SSWeightParameters &, const bool, const bool, const bool, const bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.fill_hbond_set_by_AHdist_threshold(pose: pyrosetta.rosetta.core.pose.Pose, AHdist_threshold: float, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) → None

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.

C++: core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(const class core::pose::Pose &, const double, class core::scoring::hbonds::HBondSet &) –> void

pyrosetta.rosetta.core.scoring.hbonds.fill_intra_res_hbond_set(*args, **kwargs)

Overloaded function.

1. fill_intra_res_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None
2. fill_intra_res_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool) -> None
3. fill_intra_res_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool) -> None
4. fill_intra_res_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool) -> None
5. fill_intra_res_hbond_set(pose: pyrosetta.rosetta.core.pose.Pose, calculate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool, exclude_sc: bool) -> None

C++: core::scoring::hbonds::fill_intra_res_hbond_set(const class core::pose::Pose &, const bool, class core::scoring::hbonds::HBondSet &, const bool, const bool, const bool, const bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.get_environment_dependent_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, don_nb: int, acc_nb: int, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) → float

C++: core::scoring::hbonds::get_environment_dependent_weight(const class core::scoring::hbonds::HBEvalTuple &, const int, const int, const class core::scoring::hbonds::HBondOptions &) –> double

pyrosetta.rosetta.core.scoring.hbonds.get_hb_acc_chem_type(aatm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType

C++: core::scoring::hbonds::get_hb_acc_chem_type(const unsigned long, const class core::conformation::Residue &) –> enum core::scoring::hbonds::HBAccChemType

pyrosetta.rosetta.core.scoring.hbonds.get_hb_don_chem_type(datm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType

C++: core::scoring::hbonds::get_hb_don_chem_type(const unsigned long, const class core::conformation::Residue &) –> enum core::scoring::hbonds::HBDonChemType

pyrosetta.rosetta.core.scoring.hbonds.get_hbe_acc_hybrid(hbe: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType) → pyrosetta.rosetta.core.chemical.Hybridization

C++: core::scoring::hbonds::get_hbe_acc_hybrid(const enum core::scoring::hbonds::HBEvalType &) –> enum core::chemical::Hybridization

pyrosetta.rosetta.core.scoring.hbonds.get_hbond_energies(hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::hbonds::get_hbond_energies(const class core::scoring::hbonds::HBondSet &, class core::scoring::EMapVector &) –> void

pyrosetta.rosetta.core.scoring.hbonds.get_hbond_weight_type(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType) → pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType

C++: core::scoring::hbonds::get_hbond_weight_type(const enum core::scoring::hbonds::HBEvalType &) –> enum core::scoring::hbonds::HBondWeightType

pyrosetta.rosetta.core.scoring.hbonds.get_membrane_depth_dependent_weight(*args, **kwargs)

Overloaded function.

1. get_membrane_depth_dependent_weight(pose: pyrosetta.rosetta.core.pose.Pose, don_nb: int, acc_nb: int, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: core::scoring::hbonds::get_membrane_depth_dependent_weight(const class core::pose::Pose &, const int, const int, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

2. get_membrane_depth_dependent_weight(normal: pyrosetta.rosetta.numeric.xyzVector_double_t, center: pyrosetta.rosetta.numeric.xyzVector_double_t, thickness: float, steepness: float, don_nb: int, acc_nb: int, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

C++: core::scoring::hbonds::get_membrane_depth_dependent_weight(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double &, const double &, const int, const int, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.core.scoring.hbonds.get_seq_sep(don_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType, acc_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType, sep: int) → pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep

C++: core::scoring::hbonds::get_seq_sep(const enum core::scoring::hbonds::HBDonChemType &, const enum core::scoring::hbonds::HBAccChemType &, const int &) –> enum core::scoring::hbonds::HBSeqSep

pyrosetta.rosetta.core.scoring.hbonds.get_ssdep_weight(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, ssdep: pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters) → float

C++: core::scoring::hbonds::get_ssdep_weight(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const struct core::scoring::hbonds::SSWeightParameters &) –> double

pyrosetta.rosetta.core.scoring.hbonds.get_weights_for_one_partner_hbonder(*args, **kwargs)

Overloaded function.

1. get_weights_for_one_partner_hbonder(energies: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double, dwt_dE: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None

C++: core::scoring::hbonds::get_weights_for_one_partner_hbonder(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

2. get_weights_for_one_partner_hbonder(energies: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) -> float

Helper function used by the weights_for_hbonds function above.

C++: core::scoring::hbonds::get_weights_for_one_partner_hbonder(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> double

pyrosetta.rosetta.core.scoring.hbonds.get_weights_for_two_partner_hbonder(*args, **kwargs)

Overloaded function.

1. get_weights_for_two_partner_hbonder(energies: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double, dwt_dE: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None

C++: core::scoring::hbonds::get_weights_for_two_partner_hbonder(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

2. get_weights_for_two_partner_hbonder(energies: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) -> None

Helper function used by the weights_for_hbonds function above.

C++: core::scoring::hbonds::get_weights_for_two_partner_hbonder(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.hbonds.hb_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbset: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, acc: pyrosetta.rosetta.core.conformation.Residue, acc_atm: int, don: pyrosetta.rosetta.core.conformation.Residue, don_atm: int) → float

Returns the energy for the hydrogen bond between a given don/acceptor

pair

C++: core::scoring::hbonds::hb_energy(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBondSet &, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, unsigned long) –> double

pyrosetta.rosetta.core.scoring.hbonds.hb_energy_deriv(*args, **kwargs)

Overloaded function.

1. hb_energy_deriv(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float) -> None
2. hb_energy_deriv(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, calculate_derivative: bool) -> None
3. hb_energy_deriv(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, calculate_derivative: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

C++: core::scoring::hbonds::hb_energy_deriv(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, const bool, struct core::scoring::hbonds::HBondDerivs &) –> void

4. hb_energy_deriv(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, deriv_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType) -> None
5. hb_energy_deriv(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, deriv_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

C++: core::scoring::hbonds::hb_energy_deriv(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, const enum core::scoring::hbonds::HBDerivType, struct core::scoring::hbonds::HBondDerivs &) –> void

pyrosetta.rosetta.core.scoring.hbonds.hb_energy_deriv_u(*args, **kwargs)

Overloaded function.

1. hb_energy_deriv_u(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, HDunit: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float) -> None
2. hb_energy_deriv_u(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, HDunit: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, calculate_derivative: bool) -> None
3. hb_energy_deriv_u(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, HDunit: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, calculate_derivative: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

Evaluate the hydrogen bond energy and derivatives after having first calculated

the HD and BA *u*nit vectors

C++: core::scoring::hbonds::hb_energy_deriv_u(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, const bool, struct core::scoring::hbonds::HBondDerivs &) –> void

pyrosetta.rosetta.core.scoring.hbonds.hb_energy_deriv_u2(*args, **kwargs)

Overloaded function.

1. hb_energy_deriv_u2(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, deriv_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, HDunit: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float) -> None
2. hb_energy_deriv_u2(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, deriv_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType, Hxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Dxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, HDunit: pyrosetta.rosetta.numeric.xyzVector_double_t, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t, energy: float, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

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?)

C++: core::scoring::hbonds::hb_energy_deriv_u2(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const enum core::scoring::hbonds::HBDerivType, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, struct core::scoring::hbonds::HBondDerivs &) –> void

pyrosetta.rosetta.core.scoring.hbonds.hb_eval_type(don_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType, acc_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType, seq_sep_type: pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep) → int

C++: core::scoring::hbonds::hb_eval_type(enum core::scoring::hbonds::HBDonChemType, enum core::scoring::hbonds::HBAccChemType, enum core::scoring::hbonds::HBSeqSep) –> unsigned long

pyrosetta.rosetta.core.scoring.hbonds.hb_eval_type_weight(*args, **kwargs)

Overloaded function.

1. hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> float
2. hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, intra_res: bool) -> float
3. hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, intra_res: bool, put_intra_into_total: bool) -> float

C++: core::scoring::hbonds::hb_eval_type_weight(const enum core::scoring::hbonds::HBEvalType &, const class core::scoring::EMapVector &, const bool, const bool) –> double

pyrosetta.rosetta.core.scoring.hbonds.hbe_is_BB_type(hbe: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType) → bool

C++: core::scoring::hbonds::hbe_is_BB_type(enum core::scoring::hbonds::HBEvalType) –> bool

pyrosetta.rosetta.core.scoring.hbonds.hbe_is_SC_type(hbe: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType) → bool

C++: core::scoring::hbonds::hbe_is_SC_type(enum core::scoring::hbonds::HBEvalType) –> bool

pyrosetta.rosetta.core.scoring.hbonds.hbond_compute_energy(*args, **kwargs)

Overloaded function.

1. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float) -> None
2. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool) -> None
3. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType) -> None
4. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float) -> None
5. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float, dE_dxD: float) -> None
6. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float, dE_dxD: float, dE_dxH: float) -> None
7. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float) -> None
8. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float, dchipen_dBAH: float) -> None
9. hbond_compute_energy(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, AHdis: float, xD: float, xH: float, xH2: float, chi: float, energy: float, apply_chi_torsion_penalty: bool, AHD_geometric_dimension: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType, dE_dr: float, dE_dxD: float, dE_dxH: float, dE_dxH2: float, dchipen_dBAH: float, dchipen_dchi: float) -> None

C++: core::scoring::hbonds::hbond_compute_energy(const class core::scoring::hbonds::HBondDatabase &, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const double, const double, const double, const double, const double, double &, bool &, enum core::scoring::hbonds::HBGeoDimType &, double &, double &, double &, double &, double &, double &) –> void

pyrosetta.rosetta.core.scoring.hbonds.hbond_evaluation_type(*args, **kwargs)

Overloaded function.

1. hbond_evaluation_type(datm: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, don_rsd: int, aatm: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, acc_rsd: int) -> pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple

C++: core::scoring::hbonds::hbond_evaluation_type(const class core::scoring::hbonds::hbtrie::HBAtom &, const unsigned long, const class core::scoring::hbonds::hbtrie::HBAtom &, const unsigned long) –> class core::scoring::hbonds::HBEvalTuple

2. hbond_evaluation_type(datm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, aatm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple

C++: core::scoring::hbonds::hbond_evaluation_type(const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &) –> class core::scoring::hbonds::HBEvalTuple

pyrosetta.rosetta.core.scoring.hbonds.identify_hbonds_1way(*args, **kwargs)

Overloaded function.

1. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None
2. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, ssdep_weight_factor: float) -> None
3. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, ssdep_weight_factor: float, bond_near_wat: bool) -> None

C++: core::scoring::hbonds::identify_hbonds_1way(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const bool, const bool, const bool, const bool, const bool, class core::scoring::hbonds::HBondSet &, double, bool) –> void

4. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None
5. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, ssdep_weight_factor: float) -> None
6. identify_hbonds_1way(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, ssdep_weight_factor: float, bond_near_wat: bool) -> None

C++: core::scoring::hbonds::identify_hbonds_1way(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const bool, const bool, const bool, const bool, const bool, const class core::scoring::hbonds::HBondOptions &, class core::scoring::EMapVector &, double, bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.identify_hbonds_1way_AHdist(*args, **kwargs)

Overloaded function.

1. identify_hbonds_1way_AHdist(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, AHdist_threshold: float, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None
2. identify_hbonds_1way_AHdist(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, AHdist_threshold: float, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bond_near_wat: bool) -> None

C++: core::scoring::hbonds::identify_hbonds_1way_AHdist(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const double, class core::scoring::hbonds::HBondSet &, bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.identify_hbonds_1way_membrane(*args, **kwargs)

Overloaded function.

1. identify_hbonds_1way_membrane(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. identify_hbonds_1way_membrane(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose, bond_near_wat: bool) -> None

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).

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

C++: core::scoring::hbonds::identify_hbonds_1way_membrane(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const bool, const bool, const bool, const bool, const bool, class core::scoring::hbonds::HBondSet &, const class core::pose::Pose &, bool) –> void

3. identify_hbonds_1way_membrane(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, pose: pyrosetta.rosetta.core.pose.Pose) -> None
4. identify_hbonds_1way_membrane(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, evaluate_derivative: bool, exclude_don_bb: bool, exclude_don_bsc: bool, exclude_acc_scb: bool, exclude_acc_sc: bool, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, pose: pyrosetta.rosetta.core.pose.Pose, bond_near_wat: bool) -> None

C++: core::scoring::hbonds::identify_hbonds_1way_membrane(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const bool, const bool, const bool, const bool, const bool, const class core::scoring::hbonds::HBondOptions &, class core::scoring::EMapVector &, const class core::pose::Pose &, bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.identify_intra_res_hbonds(*args, **kwargs)

Overloaded function.

1. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, evaluate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet) -> None
2. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, evaluate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool) -> None
3. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, evaluate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool) -> None
4. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, evaluate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool) -> None
5. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, evaluate_derivative: bool, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, exclude_bb: bool, exclude_bsc: bool, exclude_scb: bool, exclude_sc: bool) -> None

C++: core::scoring::hbonds::identify_intra_res_hbonds(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const unsigned long, const bool, class core::scoring::hbonds::HBondSet &, const bool, const bool, const bool, const bool) –> void

6. identify_intra_res_hbonds(database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, rsd: pyrosetta.rosetta.core.conformation.Residue, rsd_nb: int, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::hbonds::identify_intra_res_hbonds(const class core::scoring::hbonds::HBondDatabase &, const class core::conformation::Residue &, const unsigned long, const class core::scoring::hbonds::HBondOptions &, class core::scoring::EMapVector &) –> void

pyrosetta.rosetta.core.scoring.hbonds.increment_hbond_energy(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, hbE: float) → None

Increment the appropriate places in the input energy map for a particular hydrogen bond

C++: core::scoring::hbonds::increment_hbond_energy(const enum core::scoring::hbonds::HBEvalType &, class core::scoring::EMapVector &, double) –> void

pyrosetta.rosetta.core.scoring.hbonds.increment_npd_hbond_energy(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, hbE: float, intra_res: bool) → None

Increment the appropriate places in the input energy map for a particular hydrogen bond

C++: core::scoring::hbonds::increment_npd_hbond_energy(const enum core::scoring::hbonds::HBEvalType &, class core::scoring::EMapVector &, double, bool) –> void

pyrosetta.rosetta.core.scoring.hbonds.initialize_HBEval_lookup() → None

C++: core::scoring::hbonds::initialize_HBEval_lookup() –> void

pyrosetta.rosetta.core.scoring.hbonds.make_hbBasetoAcc_unitvector(hbondoptions: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, acc_hybrid: pyrosetta.rosetta.core.chemical.Hybridization, Axyz: pyrosetta.rosetta.numeric.xyzVector_double_t, Bxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, B2xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, PBxyz: pyrosetta.rosetta.numeric.xyzVector_double_t, BAunit: pyrosetta.rosetta.numeric.xyzVector_double_t, B2Aunit: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: core::scoring::hbonds::make_hbBasetoAcc_unitvector(const class core::scoring::hbonds::HBondOptions &, const enum core::chemical::Hybridization &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.core.scoring.hbonds.nonzero_hbond_weight(scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → bool

C++: core::scoring::hbonds::nonzero_hbond_weight(const class core::scoring::ScoreFunction &) –> bool

pyrosetta.rosetta.core.scoring.hbonds.npd_hb_eval_type_weight(*args, **kwargs)

Overloaded function.

1. npd_hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> float
2. npd_hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, intra_res: bool) -> float
3. npd_hb_eval_type_weight(hbe_type: pyrosetta.rosetta.core.scoring.hbonds.HBEvalType, emap: pyrosetta.rosetta.core.scoring.EMapVector, intra_res: bool, put_intra_into_total: bool) -> float

C++: core::scoring::hbonds::npd_hb_eval_type_weight(const enum core::scoring::hbonds::HBEvalType &, const class core::scoring::EMapVector &, const bool, const bool) –> double

pyrosetta.rosetta.core.scoring.hbonds.residue_near_water(pose: pyrosetta.rosetta.core.pose.Pose, ii: int) → bool

C++: core::scoring::hbonds::residue_near_water(const class core::pose::Pose &, unsigned long) –> bool

pyrosetta.rosetta.core.scoring.hbonds.string_to_hb_eval_type(hbe_str: str) → pyrosetta.rosetta.core.scoring.hbonds.HBEvalType

converts a string into an HBEvalType

C++: core::scoring::hbonds::string_to_hb_eval_type(const class std::basic_string<char> &) –> enum core::scoring::hbonds::HBEvalType

pyrosetta.rosetta.core.scoring.hbonds.weights_for_hbonds(res: pyrosetta.rosetta.core.conformation.Residue, atom: int, energies: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) → None

Given a vector of energies for hydrogen bonds for a particular atom, compute the weights

assigned to them. The residue need not have been seen by the NPDHBondSet prior to this function evaluation.

C++: core::scoring::hbonds::weights_for_hbonds(const class core::conformation::Residue &, unsigned long, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond

Bases: pybind11_builtins.pybind11_object

If you have an atom that is involved in a hydrogen bond, this enumeration

will help you keep track of the role that the atom plays.

Members:

which_hb_unassigned

which_hb_hatm

which_hb_datm

which_last_donor_atm

which_hb_aatm

which_hb_abase

which_hb_abase_prime

which_hb_abase2

n_hb_atoms