hbonds

Bindings for core::scoring::hbonds namespace

class pyrosetta.rosetta.core.scoring.hbonds.AssignmentScaleAndDerivVectID

Bases: pybind11_object

Classes (that probably shouldn’t be in here!!! ) ///

property dvect_id_
property scale_
class pyrosetta.rosetta.core.scoring.hbonds.FadeInterval

Bases: 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(std::ostream &) 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_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

hbacc_AHX = <HBAccChemType.hbacc_AHX: 7>
hbacc_CXA = <HBAccChemType.hbacc_CXA: 3>
hbacc_CXL = <HBAccChemType.hbacc_CXL: 4>
hbacc_GENERIC_RINGBB = <HBAccChemType.hbacc_GENERIC_RINGBB: 20>
hbacc_GENERIC_RINGSC = <HBAccChemType.hbacc_GENERIC_RINGSC: 21>
hbacc_GENERIC_SP2BB = <HBAccChemType.hbacc_GENERIC_SP2BB: 16>
hbacc_GENERIC_SP2SC = <HBAccChemType.hbacc_GENERIC_SP2SC: 17>
hbacc_GENERIC_SP3BB = <HBAccChemType.hbacc_GENERIC_SP3BB: 18>
hbacc_GENERIC_SP3SC = <HBAccChemType.hbacc_GENERIC_SP3SC: 19>
hbacc_H2O = <HBAccChemType.hbacc_H2O: 15>
hbacc_HXL = <HBAccChemType.hbacc_HXL: 8>
hbacc_IMD = <HBAccChemType.hbacc_IMD: 5>
hbacc_IME = <HBAccChemType.hbacc_IME: 6>
hbacc_MAX = <HBAccChemType.hbacc_GENERIC_RINGSC: 21>
hbacc_NONE = <HBAccChemType.hbacc_NONE: 1>
hbacc_PBA = <HBAccChemType.hbacc_PBA: 2>
hbacc_PCA_DNA = <HBAccChemType.hbacc_PCA_DNA: 9>
hbacc_PCA_RNA = <HBAccChemType.hbacc_PCA_RNA: 12>
hbacc_PES_DNA = <HBAccChemType.hbacc_PES_DNA: 10>
hbacc_PES_RNA = <HBAccChemType.hbacc_PES_RNA: 13>
hbacc_RRI_DNA = <HBAccChemType.hbacc_RRI_DNA: 11>
hbacc_RRI_RNA = <HBAccChemType.hbacc_RRI_RNA: 14>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner

Bases: pybind11_object

a_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::a_ind() const –> unsigned long

abase2_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::abase2_ind() const –> unsigned long

abase_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::abase_ind() const –> unsigned long

abase_prime_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::abase_prime_ind() const –> unsigned long

assignment(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner, which: pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond) → pyrosetta.rosetta.core.scoring.hbonds.AssignmentScaleAndDerivVectID
For a given role in the hbond, return the scale factor and the entry

in the HBondDerivs struct so that the derivative can be properly assigned to that atom.

C++: core::scoring::hbonds::HBDerivAssigner::assignment(enum core::scoring::hbonds::which_atom_in_hbond) –> struct core::scoring::hbonds::AssignmentScaleAndDerivVectID

d_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::d_ind() const –> unsigned long

h_ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner) → int

C++: core::scoring::hbonds::HBDerivAssigner::h_ind() const –> unsigned long

ind(self: pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner, which: pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond) → int

C++: core::scoring::hbonds::HBDerivAssigner::ind(enum core::scoring::hbonds::which_atom_in_hbond) –> unsigned long

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

Bases: pybind11_object

Members:

hbderiv_NONE

hbderiv_ABE_GO

hbderiv_ABE_GO_GEOMSOL_OCC_ACC

hbderiv_ABE_GO_GEOMSOL_OCC_DON

hbderiv_MAX

hbderiv_ABE_GO = <HBDerivType.hbderiv_ABE_GO: 2>
hbderiv_ABE_GO_GEOMSOL_OCC_ACC = <HBDerivType.hbderiv_ABE_GO_GEOMSOL_OCC_ACC: 3>
hbderiv_ABE_GO_GEOMSOL_OCC_DON = <HBDerivType.hbderiv_ABE_GO_GEOMSOL_OCC_DON: 4>
hbderiv_MAX = <HBDerivType.hbderiv_ABE_GO_GEOMSOL_OCC_DON: 4>
hbderiv_NONE = <HBDerivType.hbderiv_NONE: 1>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType

Bases: 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

hbdon_AHX = <HBDonChemType.hbdon_AHX: 10>
hbdon_AMO = <HBDonChemType.hbdon_AMO: 7>
hbdon_CXA = <HBDonChemType.hbdon_CXA: 3>
hbdon_GDE = <HBDonChemType.hbdon_GDE: 8>
hbdon_GDH = <HBDonChemType.hbdon_GDH: 9>
hbdon_GENERIC_BB = <HBDonChemType.hbdon_GENERIC_BB: 13>
hbdon_GENERIC_SC = <HBDonChemType.hbdon_GENERIC_SC: 14>
hbdon_H2O = <HBDonChemType.hbdon_H2O: 12>
hbdon_HXL = <HBDonChemType.hbdon_HXL: 11>
hbdon_IMD = <HBDonChemType.hbdon_IMD: 4>
hbdon_IME = <HBDonChemType.hbdon_IME: 5>
hbdon_IND = <HBDonChemType.hbdon_IND: 6>
hbdon_MAX = <HBDonChemType.hbdon_GENERIC_SC: 14>
hbdon_NONE = <HBDonChemType.hbdon_NONE: 1>
hbdon_PBA = <HBDonChemType.hbdon_PBA: 2>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple

Bases: pybind11_object

acc_type(*args, **kwargs)

Overloaded function.

  1. acc_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, acc: pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType) -> None

C++: core::scoring::hbonds::HBEvalTuple::acc_type(enum core::scoring::hbonds::HBAccChemType) –> void

  1. acc_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) -> pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType

C++: core::scoring::hbonds::HBEvalTuple::acc_type() const –> enum core::scoring::hbonds::HBAccChemType

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

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

don_type(*args, **kwargs)

Overloaded function.

  1. don_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, don: pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType) -> None

C++: core::scoring::hbonds::HBEvalTuple::don_type(enum core::scoring::hbonds::HBDonChemType) –> void

  1. don_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) -> pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType

C++: core::scoring::hbonds::HBEvalTuple::don_type() const –> enum core::scoring::hbonds::HBDonChemType

eval_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) → pyrosetta.rosetta.core.scoring.hbonds.HBEvalType

C++: core::scoring::hbonds::HBEvalTuple::eval_type() const –> enum core::scoring::hbonds::HBEvalType

sequence_sep(*args, **kwargs)

Overloaded function.

  1. sequence_sep(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, seqsep: pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep) -> None

C++: core::scoring::hbonds::HBEvalTuple::sequence_sep(enum core::scoring::hbonds::HBSeqSep) –> void

  1. sequence_sep(self: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) -> pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep

C++: core::scoring::hbonds::HBEvalTuple::sequence_sep() const –> enum core::scoring::hbonds::HBSeqSep

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

C++: core::scoring::hbonds::HBEvalTuple::show(std::ostream &) const –> void

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

Bases: 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

hbe_GENERIC_RINGBB_LR = <HBEvalType.hbe_GENERIC_RINGBB_LR: 216>
hbe_GENERIC_RINGBB_SR = <HBEvalType.hbe_GENERIC_RINGBB_SR: 215>
hbe_GENERIC_RINGBSC_LR = <HBEvalType.hbe_GENERIC_RINGBSC_LR: 222>
hbe_GENERIC_RINGBSC_SR = <HBEvalType.hbe_GENERIC_RINGBSC_SR: 221>
hbe_GENERIC_RINGSCSC_LR = <HBEvalType.hbe_GENERIC_RINGSCSC_LR: 228>
hbe_GENERIC_RINGSCSC_SR = <HBEvalType.hbe_GENERIC_RINGSCSC_SR: 227>
hbe_GENERIC_SP2BB_LR = <HBEvalType.hbe_GENERIC_SP2BB_LR: 212>
hbe_GENERIC_SP2BB_SR = <HBEvalType.hbe_GENERIC_SP2BB_SR: 211>
hbe_GENERIC_SP2BSC_LR = <HBEvalType.hbe_GENERIC_SP2BSC_LR: 218>
hbe_GENERIC_SP2BSC_SR = <HBEvalType.hbe_GENERIC_SP2BSC_SR: 217>
hbe_GENERIC_SP2SCSC_LR = <HBEvalType.hbe_GENERIC_SP2SCSC_LR: 224>
hbe_GENERIC_SP2SCSC_SR = <HBEvalType.hbe_GENERIC_SP2SCSC_SR: 223>
hbe_GENERIC_SP3BB_LR = <HBEvalType.hbe_GENERIC_SP3BB_LR: 214>
hbe_GENERIC_SP3BB_SR = <HBEvalType.hbe_GENERIC_SP3BB_SR: 213>
hbe_GENERIC_SP3BSC_LR = <HBEvalType.hbe_GENERIC_SP3BSC_LR: 220>
hbe_GENERIC_SP3BSC_SR = <HBEvalType.hbe_GENERIC_SP3BSC_SR: 219>
hbe_GENERIC_SP3SCSC_LR = <HBEvalType.hbe_GENERIC_SP3SCSC_LR: 226>
hbe_GENERIC_SP3SCSC_SR = <HBEvalType.hbe_GENERIC_SP3SCSC_SR: 225>
hbe_MAX = <HBEvalType.hbe_GENERIC_RINGSCSC_LR: 228>
hbe_NONE = <HBEvalType.hbe_NONE: 1>
hbe_UNKNOWN = <HBEvalType.hbe_UNKNOWN: 0>
hbe_WATERaPROTEIN_BB_AMIDE = <HBEvalType.hbe_dH2OaPBA: 28>
hbe_dAHXaAHX = <HBEvalType.hbe_dAHXaAHX: 86>
hbe_dAHXaCXA = <HBEvalType.hbe_dAHXaCXA: 38>
hbe_dAHXaCXL = <HBEvalType.hbe_dAHXaCXL: 50>
hbe_dAHXaH2O = <HBEvalType.hbe_dAHXaH2O: 208>
hbe_dAHXaHXL = <HBEvalType.hbe_dAHXaHXL: 98>
hbe_dAHXaIMD = <HBEvalType.hbe_dAHXaIMD: 62>
hbe_dAHXaIME = <HBEvalType.hbe_dAHXaIME: 74>
hbe_dAHXaPBAsepPM1 = <HBEvalType.hbe_dAHXaPBAsepPM1: 17>
hbe_dAHXaPBAsepother = <HBEvalType.hbe_dAHXaPBAsepother: 26>
hbe_dAHXaPCA_DNA = <HBEvalType.hbe_dAHXaPCA_DNA: 110>
hbe_dAHXaPCA_RNAsepPM1 = <HBEvalType.hbe_dAHXaPCA_RNAsepPM1: 129>
hbe_dAHXaPCA_RNAsepother = <HBEvalType.hbe_dAHXaPCA_RNAsepother: 130>
hbe_dAHXaPES_DNA = <HBEvalType.hbe_dAHXaPES_DNA: 143>
hbe_dAHXaPES_RNAsepPM1 = <HBEvalType.hbe_dAHXaPES_RNAsepPM1: 162>
hbe_dAHXaPES_RNAsepother = <HBEvalType.hbe_dAHXaPES_RNAsepother: 163>
hbe_dAHXaRRI_DNA = <HBEvalType.hbe_dAHXaRRI_DNA: 176>
hbe_dAHXaRRI_RNAsepPM1 = <HBEvalType.hbe_dAHXaRRI_RNAsepPM1: 195>
hbe_dAHXaRRI_RNAsepother = <HBEvalType.hbe_dAHXaRRI_RNAsepother: 196>
hbe_dAMINOaAROMATIC_HYDROXYL = <HBEvalType.hbe_dAMOaAHX: 83>
hbe_dAMINOaCARBOXAMIDE = <HBEvalType.hbe_dAMOaCXA: 35>
hbe_dAMINOaCARBOXYL = <HBEvalType.hbe_dAMOaCXL: 47>
hbe_dAMINOaHYDROXYL = <HBEvalType.hbe_dAMOaHXL: 95>
hbe_dAMINOaIMIDAZOL_DELTA = <HBEvalType.hbe_dAMOaIMD: 59>
hbe_dAMINOaIMIDAZOL_EPSILON = <HBEvalType.hbe_dAMOaIME: 71>
hbe_dAMINOaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dAMOaPCA_DNA: 107>
hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dAMOaPCA_RNAsepPM1: 123>
hbe_dAMINOaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dAMOaPCA_RNAsepother: 124>
hbe_dAMINOaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dAMOaPES_DNA: 140>
hbe_dAMINOaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dAMOaPES_RNAsepPM1: 156>
hbe_dAMINOaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dAMOaPES_RNAsepother: 157>
hbe_dAMINOaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dAMOaPBAsepPM1: 14>
hbe_dAMINOaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dAMOaPBAsepother: 23>
hbe_dAMINOaRIBOSE_RING_DNA = <HBEvalType.hbe_dAMOaRRI_DNA: 173>
hbe_dAMINOaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dAMOaRRI_RNAsepPM1: 189>
hbe_dAMINOaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dAMOaRRI_RNAsepother: 190>
hbe_dAMINOaWATER = <HBEvalType.hbe_dAMOaH2O: 205>
hbe_dAMOaAHX = <HBEvalType.hbe_dAMOaAHX: 83>
hbe_dAMOaCXA = <HBEvalType.hbe_dAMOaCXA: 35>
hbe_dAMOaCXL = <HBEvalType.hbe_dAMOaCXL: 47>
hbe_dAMOaH2O = <HBEvalType.hbe_dAMOaH2O: 205>
hbe_dAMOaHXL = <HBEvalType.hbe_dAMOaHXL: 95>
hbe_dAMOaIMD = <HBEvalType.hbe_dAMOaIMD: 59>
hbe_dAMOaIME = <HBEvalType.hbe_dAMOaIME: 71>
hbe_dAMOaPBAsepPM1 = <HBEvalType.hbe_dAMOaPBAsepPM1: 14>
hbe_dAMOaPBAsepother = <HBEvalType.hbe_dAMOaPBAsepother: 23>
hbe_dAMOaPCA_DNA = <HBEvalType.hbe_dAMOaPCA_DNA: 107>
hbe_dAMOaPCA_RNAsepPM1 = <HBEvalType.hbe_dAMOaPCA_RNAsepPM1: 123>
hbe_dAMOaPCA_RNAsepother = <HBEvalType.hbe_dAMOaPCA_RNAsepother: 124>
hbe_dAMOaPES_DNA = <HBEvalType.hbe_dAMOaPES_DNA: 140>
hbe_dAMOaPES_RNAsepPM1 = <HBEvalType.hbe_dAMOaPES_RNAsepPM1: 156>
hbe_dAMOaPES_RNAsepother = <HBEvalType.hbe_dAMOaPES_RNAsepother: 157>
hbe_dAMOaRRI_DNA = <HBEvalType.hbe_dAMOaRRI_DNA: 173>
hbe_dAMOaRRI_RNAsepPM1 = <HBEvalType.hbe_dAMOaRRI_RNAsepPM1: 189>
hbe_dAMOaRRI_RNAsepother = <HBEvalType.hbe_dAMOaRRI_RNAsepother: 190>
hbe_dAROMATIC_HYDROXYLaAROMATIC_HYDROXYL = <HBEvalType.hbe_dAHXaAHX: 86>
hbe_dAROMATIC_HYDROXYLaCARBOXAMIDE = <HBEvalType.hbe_dAHXaCXA: 38>
hbe_dAROMATIC_HYDROXYLaCARBOXYL = <HBEvalType.hbe_dAHXaCXL: 50>
hbe_dAROMATIC_HYDROXYLaHYDROXYL = <HBEvalType.hbe_dAHXaHXL: 98>
hbe_dAROMATIC_HYDROXYLaIMIDAZOL_DELTA = <HBEvalType.hbe_dAHXaIMD: 62>
hbe_dAROMATIC_HYDROXYLaIMIDAZOL_EPSILON = <HBEvalType.hbe_dAHXaIME: 74>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dAHXaPCA_DNA: 110>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dAHXaPCA_RNAsepPM1: 129>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dAHXaPCA_RNAsepother: 130>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dAHXaPES_DNA: 143>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dAHXaPES_RNAsepPM1: 162>
hbe_dAROMATIC_HYDROXYLaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dAHXaPES_RNAsepother: 163>
hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dAHXaPBAsepPM1: 17>
hbe_dAROMATIC_HYDROXYLaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dAHXaPBAsepother: 26>
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_DNA = <HBEvalType.hbe_dAHXaRRI_DNA: 176>
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dAHXaRRI_RNAsepPM1: 195>
hbe_dAROMATIC_HYDROXYLaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dAHXaRRI_RNAsepother: 196>
hbe_dAROMATIC_HYDROXYLaWATER = <HBEvalType.hbe_dAHXaH2O: 208>
hbe_dCARBOXAMIDEaAROMATIC_HYDROXYL = <HBEvalType.hbe_dCXAaAHX: 79>
hbe_dCARBOXAMIDEaCARBOXAMIDE = <HBEvalType.hbe_dCXAaCXA: 31>
hbe_dCARBOXAMIDEaCARBOXYL = <HBEvalType.hbe_dCXAaCXL: 43>
hbe_dCARBOXAMIDEaHYDROXYL = <HBEvalType.hbe_dCXAaHXL: 91>
hbe_dCARBOXAMIDEaIMIDAZOL_DELTA = <HBEvalType.hbe_dCXAaIMD: 55>
hbe_dCARBOXAMIDEaIMIDAZOL_EPSILON = <HBEvalType.hbe_dCXAaIME: 67>
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dCXAaPCA_DNA: 103>
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dCXAaPCA_RNAsepPM1: 115>
hbe_dCARBOXAMIDEaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dCXAaPCA_RNAsepother: 116>
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dCXAaPES_DNA: 136>
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dCXAaPES_RNAsepPM1: 148>
hbe_dCARBOXAMIDEaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dCXAaPES_RNAsepother: 149>
hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dCXAaPBAsepPM1: 10>
hbe_dCARBOXAMIDEaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dCXAaPBAsepother: 19>
hbe_dCARBOXAMIDEaRIBOSE_RING_DNA = <HBEvalType.hbe_dCXAaRRI_DNA: 169>
hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dCXAaRRI_RNAsepPM1: 181>
hbe_dCARBOXAMIDEaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dCXAaRRI_RNAsepother: 182>
hbe_dCARBOXAMIDEaWATER = <HBEvalType.hbe_dCXAaH2O: 201>
hbe_dCXAaAHX = <HBEvalType.hbe_dCXAaAHX: 79>
hbe_dCXAaCXA = <HBEvalType.hbe_dCXAaCXA: 31>
hbe_dCXAaCXL = <HBEvalType.hbe_dCXAaCXL: 43>
hbe_dCXAaH2O = <HBEvalType.hbe_dCXAaH2O: 201>
hbe_dCXAaHXL = <HBEvalType.hbe_dCXAaHXL: 91>
hbe_dCXAaIMD = <HBEvalType.hbe_dCXAaIMD: 55>
hbe_dCXAaIME = <HBEvalType.hbe_dCXAaIME: 67>
hbe_dCXAaPBAsepPM1 = <HBEvalType.hbe_dCXAaPBAsepPM1: 10>
hbe_dCXAaPBAsepother = <HBEvalType.hbe_dCXAaPBAsepother: 19>
hbe_dCXAaPCA_DNA = <HBEvalType.hbe_dCXAaPCA_DNA: 103>
hbe_dCXAaPCA_RNAsepPM1 = <HBEvalType.hbe_dCXAaPCA_RNAsepPM1: 115>
hbe_dCXAaPCA_RNAsepother = <HBEvalType.hbe_dCXAaPCA_RNAsepother: 116>
hbe_dCXAaPES_DNA = <HBEvalType.hbe_dCXAaPES_DNA: 136>
hbe_dCXAaPES_RNAsepPM1 = <HBEvalType.hbe_dCXAaPES_RNAsepPM1: 148>
hbe_dCXAaPES_RNAsepother = <HBEvalType.hbe_dCXAaPES_RNAsepother: 149>
hbe_dCXAaRRI_DNA = <HBEvalType.hbe_dCXAaRRI_DNA: 169>
hbe_dCXAaRRI_RNAsepPM1 = <HBEvalType.hbe_dCXAaRRI_RNAsepPM1: 181>
hbe_dCXAaRRI_RNAsepother = <HBEvalType.hbe_dCXAaRRI_RNAsepother: 182>
hbe_dDIHYDRO_GUANIDINIUMaAROMATIC_HYDROXYL = <HBEvalType.hbe_dGDHaAHX: 85>
hbe_dDIHYDRO_GUANIDINIUMaCARBOXAMIDE = <HBEvalType.hbe_dGDHaCXA: 37>
hbe_dDIHYDRO_GUANIDINIUMaCARBOXYL = <HBEvalType.hbe_dGDHaCXL: 49>
hbe_dDIHYDRO_GUANIDINIUMaHYDROXYL = <HBEvalType.hbe_dGDHaHXL: 97>
hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_DELTA = <HBEvalType.hbe_dGDHaIMD: 61>
hbe_dDIHYDRO_GUANIDINIUMaIMIDAZOL_EPSILON = <HBEvalType.hbe_dGDHaIME: 73>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_DNA = <HBEvalType.hbe_dGDHaPCA_DNA: 109>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepPM1 = <HBEvalType.hbe_dGDHaPCA_RNAsepPM1: 127>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_CARBONY_RNAsepother = <HBEvalType.hbe_dGDHaPCA_RNAsepother: 128>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dGDHaPES_DNA: 142>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dGDHaPES_RNAsepPM1: 160>
hbe_dDIHYDRO_GUANIDINIUMaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dGDHaPES_RNAsepother: 161>
hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dGDHaPBAsepPM1: 16>
hbe_dDIHYDRO_GUANIDINIUMaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dGDHaPBAsepother: 25>
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_DNA = <HBEvalType.hbe_dGDHaRRI_DNA: 175>
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dGDHaRRI_RNAsepPM1: 193>
hbe_dDIHYDRO_GUANIDINIUMaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dGDHaRRI_RNAsepother: 194>
hbe_dDIHYDRO_GUANIDINIUMaWATER = <HBEvalType.hbe_dGDHaH2O: 207>
hbe_dGDEaAHX = <HBEvalType.hbe_dGDEaAHX: 84>
hbe_dGDEaCXA = <HBEvalType.hbe_dGDEaCXA: 36>
hbe_dGDEaCXL = <HBEvalType.hbe_dGDEaCXL: 48>
hbe_dGDEaH2O = <HBEvalType.hbe_dGDEaH2O: 206>
hbe_dGDEaHXL = <HBEvalType.hbe_dGDEaHXL: 96>
hbe_dGDEaIMD = <HBEvalType.hbe_dGDEaIMD: 60>
hbe_dGDEaIME = <HBEvalType.hbe_dGDEaIME: 72>
hbe_dGDEaPBAsepPM1 = <HBEvalType.hbe_dGDEaPBAsepPM1: 15>
hbe_dGDEaPBAsepother = <HBEvalType.hbe_dGDEaPBAsepother: 24>
hbe_dGDEaPCA_DNA = <HBEvalType.hbe_dGDEaPCA_DNA: 108>
hbe_dGDEaPCA_RNAsepPM1 = <HBEvalType.hbe_dGDEaPCA_RNAsepPM1: 125>
hbe_dGDEaPCA_RNAsepother = <HBEvalType.hbe_dGDEaPCA_RNAsepother: 126>
hbe_dGDEaPES_DNA = <HBEvalType.hbe_dGDEaPES_DNA: 141>
hbe_dGDEaPES_RNAsepPM1 = <HBEvalType.hbe_dGDEaPES_RNAsepPM1: 158>
hbe_dGDEaPES_RNAsepother = <HBEvalType.hbe_dGDEaPES_RNAsepother: 159>
hbe_dGDEaRRI_DNA = <HBEvalType.hbe_dGDEaRRI_DNA: 174>
hbe_dGDEaRRI_RNAsepPM1 = <HBEvalType.hbe_dGDEaRRI_RNAsepPM1: 191>
hbe_dGDEaRRI_RNAsepother = <HBEvalType.hbe_dGDEaRRI_RNAsepother: 192>
hbe_dGDHaAHX = <HBEvalType.hbe_dGDHaAHX: 85>
hbe_dGDHaCXA = <HBEvalType.hbe_dGDHaCXA: 37>
hbe_dGDHaCXL = <HBEvalType.hbe_dGDHaCXL: 49>
hbe_dGDHaH2O = <HBEvalType.hbe_dGDHaH2O: 207>
hbe_dGDHaHXL = <HBEvalType.hbe_dGDHaHXL: 97>
hbe_dGDHaIMD = <HBEvalType.hbe_dGDHaIMD: 61>
hbe_dGDHaIME = <HBEvalType.hbe_dGDHaIME: 73>
hbe_dGDHaPBAsepPM1 = <HBEvalType.hbe_dGDHaPBAsepPM1: 16>
hbe_dGDHaPBAsepother = <HBEvalType.hbe_dGDHaPBAsepother: 25>
hbe_dGDHaPCA_DNA = <HBEvalType.hbe_dGDHaPCA_DNA: 109>
hbe_dGDHaPCA_RNAsepPM1 = <HBEvalType.hbe_dGDHaPCA_RNAsepPM1: 127>
hbe_dGDHaPCA_RNAsepother = <HBEvalType.hbe_dGDHaPCA_RNAsepother: 128>
hbe_dGDHaPES_DNA = <HBEvalType.hbe_dGDHaPES_DNA: 142>
hbe_dGDHaPES_RNAsepPM1 = <HBEvalType.hbe_dGDHaPES_RNAsepPM1: 160>
hbe_dGDHaPES_RNAsepother = <HBEvalType.hbe_dGDHaPES_RNAsepother: 161>
hbe_dGDHaRRI_DNA = <HBEvalType.hbe_dGDHaRRI_DNA: 175>
hbe_dGDHaRRI_RNAsepPM1 = <HBEvalType.hbe_dGDHaRRI_RNAsepPM1: 193>
hbe_dGDHaRRI_RNAsepother = <HBEvalType.hbe_dGDHaRRI_RNAsepother: 194>
hbe_dGUANIDINIUM_EPSILONaAROMATIC_HYDROXYL = <HBEvalType.hbe_dGDEaAHX: 84>
hbe_dGUANIDINIUM_EPSILONaCARBOXAMIDE = <HBEvalType.hbe_dGDEaCXA: 36>
hbe_dGUANIDINIUM_EPSILONaCARBOXYL = <HBEvalType.hbe_dGDEaCXL: 48>
hbe_dGUANIDINIUM_EPSILONaHYDROXYL = <HBEvalType.hbe_dGDEaHXL: 96>
hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_DELTA = <HBEvalType.hbe_dGDEaIMD: 60>
hbe_dGUANIDINIUM_EPSILONaIMIDAZOL_EPSILON = <HBEvalType.hbe_dGDEaIME: 72>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dGDEaPCA_DNA: 108>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dGDEaPCA_RNAsepPM1: 125>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dGDEaPCA_RNAsepother: 126>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dGDEaPES_DNA: 141>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dGDEaPES_RNAsepPM1: 158>
hbe_dGUANIDINIUM_EPSILONaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dGDEaPES_RNAsepother: 159>
hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dGDEaPBAsepPM1: 15>
hbe_dGUANIDINIUM_EPSILONaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dGDEaPBAsepother: 24>
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_DNA = <HBEvalType.hbe_dGDEaRRI_DNA: 174>
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dGDEaRRI_RNAsepPM1: 191>
hbe_dGUANIDINIUM_EPSILONaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dGDEaRRI_RNAsepother: 192>
hbe_dGUANIDINIUM_EPSILONaWATER = <HBEvalType.hbe_dGDEaH2O: 206>
hbe_dH2OaAHX = <HBEvalType.hbe_dH2OaAHX: 88>
hbe_dH2OaCXA = <HBEvalType.hbe_dH2OaCXA: 40>
hbe_dH2OaCXL = <HBEvalType.hbe_dH2OaCXL: 52>
hbe_dH2OaH2O = <HBEvalType.hbe_dH2OaH2O: 210>
hbe_dH2OaHXL = <HBEvalType.hbe_dH2OaHXL: 100>
hbe_dH2OaIMD = <HBEvalType.hbe_dH2OaIMD: 64>
hbe_dH2OaIME = <HBEvalType.hbe_dH2OaIME: 76>
hbe_dH2OaPBA = <HBEvalType.hbe_dH2OaPBA: 28>
hbe_dH2OaPCA_DNA = <HBEvalType.hbe_dH2OaPCA_DNA: 112>
hbe_dH2OaPCA_RNA = <HBEvalType.hbe_dH2OaPCA_RNA: 133>
hbe_dH2OaPES_DNA = <HBEvalType.hbe_dH2OaPES_DNA: 145>
hbe_dH2OaPES_RNA = <HBEvalType.hbe_dH2OaPES_RNA: 166>
hbe_dH2OaRRI_DNA = <HBEvalType.hbe_dH2OaRRI_DNA: 178>
hbe_dH2OaRRI_RNA = <HBEvalType.hbe_dH2OaRRI_RNA: 199>
hbe_dHXLaAHX = <HBEvalType.hbe_dHXLaAHX: 87>
hbe_dHXLaCXA = <HBEvalType.hbe_dHXLaCXA: 39>
hbe_dHXLaCXL = <HBEvalType.hbe_dHXLaCXL: 51>
hbe_dHXLaH2O = <HBEvalType.hbe_dHXLaH2O: 209>
hbe_dHXLaHXL = <HBEvalType.hbe_dHXLaHXL: 99>
hbe_dHXLaIMD = <HBEvalType.hbe_dHXLaIMD: 63>
hbe_dHXLaIME = <HBEvalType.hbe_dHXLaIME: 75>
hbe_dHXLaPBAsepPM1 = <HBEvalType.hbe_dHXLaPBAsepPM1: 18>
hbe_dHXLaPBAsepother = <HBEvalType.hbe_dHXLaPBAsepother: 27>
hbe_dHXLaPCA_DNA = <HBEvalType.hbe_dHXLaPCA_DNA: 111>
hbe_dHXLaPCA_RNAsepPM1 = <HBEvalType.hbe_dHXLaPCA_RNAsepPM1: 131>
hbe_dHXLaPCA_RNAsepother = <HBEvalType.hbe_dHXLaPCA_RNAsepother: 132>
hbe_dHXLaPES_DNA = <HBEvalType.hbe_dHXLaPES_DNA: 144>
hbe_dHXLaPES_RNAsepPM1 = <HBEvalType.hbe_dHXLaPES_RNAsepPM1: 164>
hbe_dHXLaPES_RNAsepother = <HBEvalType.hbe_dHXLaPES_RNAsepother: 165>
hbe_dHXLaRRI_DNA = <HBEvalType.hbe_dHXLaRRI_DNA: 177>
hbe_dHXLaRRI_RNAsepPM1 = <HBEvalType.hbe_dHXLaRRI_RNAsepPM1: 197>
hbe_dHXLaRRI_RNAsepother = <HBEvalType.hbe_dHXLaRRI_RNAsepother: 198>
hbe_dHYDROXYLaAROMATIC_HYDROXYL = <HBEvalType.hbe_dHXLaAHX: 87>
hbe_dHYDROXYLaCARBOXAMIDE = <HBEvalType.hbe_dHXLaCXA: 39>
hbe_dHYDROXYLaCARBOXYL = <HBEvalType.hbe_dHXLaCXL: 51>
hbe_dHYDROXYLaHYDROXYL = <HBEvalType.hbe_dHXLaHXL: 99>
hbe_dHYDROXYLaIMIDAZOL_DELTA = <HBEvalType.hbe_dHXLaIMD: 63>
hbe_dHYDROXYLaIMIDAZOL_EPSILON = <HBEvalType.hbe_dHXLaIME: 75>
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dHXLaPCA_DNA: 111>
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dHXLaPCA_RNAsepPM1: 131>
hbe_dHYDROXYLaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dHXLaPCA_RNAsepother: 132>
hbe_dHYDROXYLaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dHXLaPES_DNA: 144>
hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dHXLaPES_RNAsepPM1: 164>
hbe_dHYDROXYLaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dHXLaPES_RNAsepother: 165>
hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dHXLaPBAsepPM1: 18>
hbe_dHYDROXYLaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dHXLaPBAsepother: 27>
hbe_dHYDROXYLaRIBOSE_RING_DNA = <HBEvalType.hbe_dHXLaRRI_DNA: 177>
hbe_dHYDROXYLaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dHXLaRRI_RNAsepPM1: 197>
hbe_dHYDROXYLaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dHXLaRRI_RNAsepother: 198>
hbe_dHYDROXYLaWATER = <HBEvalType.hbe_dHXLaH2O: 209>
hbe_dIMDaAHX = <HBEvalType.hbe_dIMDaAHX: 80>
hbe_dIMDaCXA = <HBEvalType.hbe_dIMDaCXA: 32>
hbe_dIMDaCXL = <HBEvalType.hbe_dIMDaCXL: 44>
hbe_dIMDaH2O = <HBEvalType.hbe_dIMDaH2O: 202>
hbe_dIMDaHXL = <HBEvalType.hbe_dIMDaHXL: 92>
hbe_dIMDaIMD = <HBEvalType.hbe_dIMDaIMD: 56>
hbe_dIMDaIME = <HBEvalType.hbe_dIMDaIME: 68>
hbe_dIMDaPBAsepPM1 = <HBEvalType.hbe_dIMDaPBAsepPM1: 11>
hbe_dIMDaPBAsepother = <HBEvalType.hbe_dIMDaPBAsepother: 20>
hbe_dIMDaPCA_DNA = <HBEvalType.hbe_dIMDaPCA_DNA: 104>
hbe_dIMDaPCA_RNAsepPM1 = <HBEvalType.hbe_dIMDaPCA_RNAsepPM1: 117>
hbe_dIMDaPCA_RNAsepother = <HBEvalType.hbe_dIMDaPCA_RNAsepother: 118>
hbe_dIMDaPES_DNA = <HBEvalType.hbe_dIMDaPES_DNA: 137>
hbe_dIMDaPES_RNAsepPM1 = <HBEvalType.hbe_dIMDaPES_RNAsepPM1: 150>
hbe_dIMDaPES_RNAsepother = <HBEvalType.hbe_dIMDaPES_RNAsepother: 151>
hbe_dIMDaRRI_DNA = <HBEvalType.hbe_dIMDaRRI_DNA: 170>
hbe_dIMDaRRI_RNAsepPM1 = <HBEvalType.hbe_dIMDaRRI_RNAsepPM1: 183>
hbe_dIMDaRRI_RNAsepother = <HBEvalType.hbe_dIMDaRRI_RNAsepother: 184>
hbe_dIMEaAHX = <HBEvalType.hbe_dIMEaAHX: 81>
hbe_dIMEaCXA = <HBEvalType.hbe_dIMEaCXA: 33>
hbe_dIMEaCXL = <HBEvalType.hbe_dIMEaCXL: 45>
hbe_dIMEaH2O = <HBEvalType.hbe_dIMEaH2O: 203>
hbe_dIMEaHXL = <HBEvalType.hbe_dIMEaHXL: 93>
hbe_dIMEaIMD = <HBEvalType.hbe_dIMEaIMD: 57>
hbe_dIMEaIME = <HBEvalType.hbe_dIMEaIME: 69>
hbe_dIMEaPBAsepPM1 = <HBEvalType.hbe_dIMEaPBAsepPM1: 12>
hbe_dIMEaPBAsepother = <HBEvalType.hbe_dIMEaPBAsepother: 21>
hbe_dIMEaPCA_DNA = <HBEvalType.hbe_dIMEaPCA_DNA: 105>
hbe_dIMEaPCA_RNAsepPM1 = <HBEvalType.hbe_dIMEaPCA_RNAsepPM1: 119>
hbe_dIMEaPCA_RNAsepother = <HBEvalType.hbe_dIMEaPCA_RNAsepother: 120>
hbe_dIMEaPES_DNA = <HBEvalType.hbe_dIMEaPES_DNA: 138>
hbe_dIMEaPES_RNAsepPM1 = <HBEvalType.hbe_dIMEaPES_RNAsepPM1: 152>
hbe_dIMEaPES_RNAsepother = <HBEvalType.hbe_dIMEaPES_RNAsepother: 153>
hbe_dIMEaRRI_DNA = <HBEvalType.hbe_dIMEaRRI_DNA: 171>
hbe_dIMEaRRI_RNAsepPM1 = <HBEvalType.hbe_dIMEaRRI_RNAsepPM1: 185>
hbe_dIMEaRRI_RNAsepother = <HBEvalType.hbe_dIMEaRRI_RNAsepother: 186>
hbe_dIMIDAZOL_DELTAaAROMATIC_HYDROXYL = <HBEvalType.hbe_dIMDaAHX: 80>
hbe_dIMIDAZOL_DELTAaCARBOXAMIDE = <HBEvalType.hbe_dIMDaCXA: 32>
hbe_dIMIDAZOL_DELTAaCARBOXYL = <HBEvalType.hbe_dIMDaCXL: 44>
hbe_dIMIDAZOL_DELTAaHYDROXYL = <HBEvalType.hbe_dIMDaHXL: 92>
hbe_dIMIDAZOL_DELTAaIMIDAZOL_DELTA = <HBEvalType.hbe_dIMDaIMD: 56>
hbe_dIMIDAZOL_DELTAaIMIDAZOL_EPSILON = <HBEvalType.hbe_dIMDaIME: 68>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dIMDaPCA_DNA: 104>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dIMDaPCA_RNAsepPM1: 117>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dIMDaPCA_RNAsepother: 118>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dIMDaPES_DNA: 137>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dIMDaPES_RNAsepPM1: 150>
hbe_dIMIDAZOL_DELTAaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dIMDaPES_RNAsepother: 151>
hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dIMDaPBAsepPM1: 11>
hbe_dIMIDAZOL_DELTAaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dIMDaPBAsepother: 20>
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_DNA = <HBEvalType.hbe_dIMDaRRI_DNA: 170>
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dIMDaRRI_RNAsepPM1: 183>
hbe_dIMIDAZOL_DELTAaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dIMDaRRI_RNAsepother: 184>
hbe_dIMIDAZOL_DELTAaWATER = <HBEvalType.hbe_dIMDaH2O: 202>
hbe_dIMIDAZOL_EPSILONaAROMATIC_HYDROXYL = <HBEvalType.hbe_dIMEaAHX: 81>
hbe_dIMIDAZOL_EPSILONaCARBOXAMIDE = <HBEvalType.hbe_dIMEaCXA: 33>
hbe_dIMIDAZOL_EPSILONaCARBOXYL = <HBEvalType.hbe_dIMEaCXL: 45>
hbe_dIMIDAZOL_EPSILONaHYDXROXYL = <HBEvalType.hbe_dIMEaHXL: 93>
hbe_dIMIDAZOL_EPSILONaIMIDAZOL_DELTA = <HBEvalType.hbe_dIMEaIMD: 57>
hbe_dIMIDAZOL_EPSILONaIMIDAZOL_EPSILON = <HBEvalType.hbe_dIMEaIME: 69>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dIMEaPCA_DNA: 105>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dIMEaPCA_RNAsepPM1: 119>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dIMEaPCA_RNAsepother: 120>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dIMEaPES_DNA: 138>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dIMEaPES_RNAsepPM1: 152>
hbe_dIMIDAZOL_EPSILONaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dIMEaPES_RNAsepother: 153>
hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dIMEaPBAsepPM1: 12>
hbe_dIMIDAZOL_EPSILONaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dIMEaPBAsepother: 21>
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_DNA = <HBEvalType.hbe_dIMEaRRI_DNA: 171>
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dIMEaRRI_RNAsepPM1: 185>
hbe_dIMIDAZOL_EPSILONaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dIMEaRRI_RNAsepother: 186>
hbe_dIMIDAZOL_EPSILONaWATER = <HBEvalType.hbe_dIMEaH2O: 203>
hbe_dINDOLaAROMATIC_HYDROXYL = <HBEvalType.hbe_dINDaAHX: 82>
hbe_dINDOLaCARBOXAMIDE = <HBEvalType.hbe_dINDaCXA: 34>
hbe_dINDOLaCARBOXYL = <HBEvalType.hbe_dINDaCXL: 46>
hbe_dINDOLaHYDROXYL = <HBEvalType.hbe_dINDaHXL: 94>
hbe_dINDOLaIMIDAZOL_DELTA = <HBEvalType.hbe_dINDaIMD: 58>
hbe_dINDOLaIMIDAZOL_EPSILON = <HBEvalType.hbe_dINDaIME: 70>
hbe_dINDOLaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dINDaPCA_DNA: 106>
hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dINDaPCA_RNAsepPM1: 121>
hbe_dINDOLaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dINDaPCA_RNAsepother: 122>
hbe_dINDOLaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dINDaPES_DNA: 139>
hbe_dINDOLaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dINDaPES_RNAsepPM1: 154>
hbe_dINDOLaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dINDaPES_RNAsepother: 155>
hbe_dINDOLaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dINDaPBAsepPM1: 13>
hbe_dINDOLaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dINDaPBAsepother: 22>
hbe_dINDOLaRIBOSE_RING_DNA = <HBEvalType.hbe_dINDaRRI_DNA: 172>
hbe_dINDOLaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dINDaRRI_RNAsepPM1: 187>
hbe_dINDOLaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dINDaRRI_RNAsepother: 188>
hbe_dINDOLaWATER = <HBEvalType.hbe_dINDaH2O: 204>
hbe_dINDaAHX = <HBEvalType.hbe_dINDaAHX: 82>
hbe_dINDaCXA = <HBEvalType.hbe_dINDaCXA: 34>
hbe_dINDaCXL = <HBEvalType.hbe_dINDaCXL: 46>
hbe_dINDaH2O = <HBEvalType.hbe_dINDaH2O: 204>
hbe_dINDaHXL = <HBEvalType.hbe_dINDaHXL: 94>
hbe_dINDaIMD = <HBEvalType.hbe_dINDaIMD: 58>
hbe_dINDaIME = <HBEvalType.hbe_dINDaIME: 70>
hbe_dINDaPBAsepPM1 = <HBEvalType.hbe_dINDaPBAsepPM1: 13>
hbe_dINDaPBAsepother = <HBEvalType.hbe_dINDaPBAsepother: 22>
hbe_dINDaPCA_DNA = <HBEvalType.hbe_dINDaPCA_DNA: 106>
hbe_dINDaPCA_RNAsepPM1 = <HBEvalType.hbe_dINDaPCA_RNAsepPM1: 121>
hbe_dINDaPCA_RNAsepother = <HBEvalType.hbe_dINDaPCA_RNAsepother: 122>
hbe_dINDaPES_DNA = <HBEvalType.hbe_dINDaPES_DNA: 139>
hbe_dINDaPES_RNAsepPM1 = <HBEvalType.hbe_dINDaPES_RNAsepPM1: 154>
hbe_dINDaPES_RNAsepother = <HBEvalType.hbe_dINDaPES_RNAsepother: 155>
hbe_dINDaRRI_DNA = <HBEvalType.hbe_dINDaRRI_DNA: 172>
hbe_dINDaRRI_RNAsepPM1 = <HBEvalType.hbe_dINDaRRI_RNAsepPM1: 187>
hbe_dINDaRRI_RNAsepother = <HBEvalType.hbe_dINDaRRI_RNAsepother: 188>
hbe_dPBAaAHXsepPM1 = <HBEvalType.hbe_dPBAaAHXsepPM1: 77>
hbe_dPBAaAHXsepother = <HBEvalType.hbe_dPBAaAHXsepother: 78>
hbe_dPBAaCXAsepPM1 = <HBEvalType.hbe_dPBAaCXAsepPM1: 29>
hbe_dPBAaCXAsepother = <HBEvalType.hbe_dPBAaCXAsepother: 30>
hbe_dPBAaCXLsepPM1 = <HBEvalType.hbe_dPBAaCXLsepPM1: 41>
hbe_dPBAaCXLsepother = <HBEvalType.hbe_dPBAaCXLsepother: 42>
hbe_dPBAaH2O = <HBEvalType.hbe_dPBAaH2O: 200>
hbe_dPBAaHXLsepPM1 = <HBEvalType.hbe_dPBAaHXLsepPM1: 89>
hbe_dPBAaHXLsepother = <HBEvalType.hbe_dPBAaHXLsepother: 90>
hbe_dPBAaIMDsepPM1 = <HBEvalType.hbe_dPBAaIMDsepPM1: 53>
hbe_dPBAaIMDsepother = <HBEvalType.hbe_dPBAaIMDsepother: 54>
hbe_dPBAaIMEsepPM1 = <HBEvalType.hbe_dPBAaIMEsepPM1: 65>
hbe_dPBAaIMEsepother = <HBEvalType.hbe_dPBAaIMEsepother: 66>
hbe_dPBAaPBAsepM2turn = <HBEvalType.hbe_dPBAaPBAsepM2turn: 4>
hbe_dPBAaPBAsepM3turn = <HBEvalType.hbe_dPBAaPBAsepM3turn: 3>
hbe_dPBAaPBAsepM4helix = <HBEvalType.hbe_dPBAaPBAsepM4helix: 2>
hbe_dPBAaPBAsepP2turn = <HBEvalType.hbe_dPBAaPBAsepP2turn: 6>
hbe_dPBAaPBAsepP3turn = <HBEvalType.hbe_dPBAaPBAsepP3turn: 7>
hbe_dPBAaPBAsepP4helix = <HBEvalType.hbe_dPBAaPBAsepP4helix: 8>
hbe_dPBAaPBAsepPM1 = <HBEvalType.hbe_dPBAaPBAsepPM1: 5>
hbe_dPBAaPBAsepother = <HBEvalType.hbe_dPBAaPBAsepother: 9>
hbe_dPBAaPCA_DNAsepPM1 = <HBEvalType.hbe_dPBAaPCA_DNAsepPM1: 101>
hbe_dPBAaPCA_DNAsepother = <HBEvalType.hbe_dPBAaPCA_DNAsepother: 102>
hbe_dPBAaPCA_RNAsepPM1 = <HBEvalType.hbe_dPBAaPCA_RNAsepPM1: 113>
hbe_dPBAaPCA_RNAsepother = <HBEvalType.hbe_dPBAaPCA_RNAsepother: 114>
hbe_dPBAaPES_DNAsepPM1 = <HBEvalType.hbe_dPBAaPES_DNAsepPM1: 134>
hbe_dPBAaPES_DNAsepother = <HBEvalType.hbe_dPBAaPES_DNAsepother: 135>
hbe_dPBAaPES_RNAsepPM1 = <HBEvalType.hbe_dPBAaPES_RNAsepPM1: 146>
hbe_dPBAaPES_RNAsepother = <HBEvalType.hbe_dPBAaPES_RNAsepother: 147>
hbe_dPBAaRRI_DNAsepPM1 = <HBEvalType.hbe_dPBAaRRI_DNAsepPM1: 167>
hbe_dPBAaRRI_DNAsepother = <HBEvalType.hbe_dPBAaRRI_DNAsepother: 168>
hbe_dPBAaRRI_RNAsepPM1 = <HBEvalType.hbe_dPBAaRRI_RNAsepPM1: 179>
hbe_dPBAaRRI_RNAsepother = <HBEvalType.hbe_dPBAaRRI_RNAsepother: 180>
hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepPM1 = <HBEvalType.hbe_dPBAaHXLsepPM1: 89>
hbe_dPROTEINS_BB_AMIDEaHYDROXYLsepother = <HBEvalType.hbe_dPBAaHXLsepother: 90>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepPM1 = <HBEvalType.hbe_dPBAaPCA_DNAsepPM1: 101>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_DNAsepother = <HBEvalType.hbe_dPBAaPCA_DNAsepother: 102>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepPM1 = <HBEvalType.hbe_dPBAaPCA_RNAsepPM1: 113>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_CARBONYL_RNAsepother = <HBEvalType.hbe_dPBAaPCA_RNAsepother: 114>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepPM1 = <HBEvalType.hbe_dPBAaPES_DNAsepPM1: 134>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_DNAsepother = <HBEvalType.hbe_dPBAaPES_DNAsepother: 135>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepPM1 = <HBEvalType.hbe_dPBAaPES_RNAsepPM1: 146>
hbe_dPROTEINS_BB_AMIDEaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dPBAaPES_RNAsepother: 147>
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepPM1 = <HBEvalType.hbe_dPBAaRRI_DNAsepPM1: 167>
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_DNAsepother = <HBEvalType.hbe_dPBAaRRI_DNAsepother: 168>
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepPM1 = <HBEvalType.hbe_dPBAaRRI_RNAsepPM1: 179>
hbe_dPROTEINS_BB_AMIDEaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dPBAaRRI_RNAsepother: 180>
hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepPM1 = <HBEvalType.hbe_dPBAaAHXsepPM1: 77>
hbe_dPROTEIN_BB_AMIDEaAROMATIC_HYDROXYLsepother = <HBEvalType.hbe_dPBAaAHXsepother: 78>
hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepPM1 = <HBEvalType.hbe_dPBAaCXAsepPM1: 29>
hbe_dPROTEIN_BB_AMIDEaCARBOXAMIDEsepother = <HBEvalType.hbe_dPBAaCXAsepother: 30>
hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepPM1 = <HBEvalType.hbe_dPBAaCXLsepPM1: 41>
hbe_dPROTEIN_BB_AMIDEaCARBOXYLsepother = <HBEvalType.hbe_dPBAaCXLsepother: 42>
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepPM1 = <HBEvalType.hbe_dPBAaIMDsepPM1: 53>
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_DELTAsepother = <HBEvalType.hbe_dPBAaIMDsepother: 54>
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepPM1 = <HBEvalType.hbe_dPBAaIMEsepPM1: 65>
hbe_dPROTEIN_BB_AMIDEaIMIDAZOL_EPSILONsepother = <HBEvalType.hbe_dPBAaIMEsepother: 66>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM2turn = <HBEvalType.hbe_dPBAaPBAsepM2turn: 4>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM3turn = <HBEvalType.hbe_dPBAaPBAsepM3turn: 3>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepM4helix = <HBEvalType.hbe_dPBAaPBAsepM4helix: 2>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP2turn = <HBEvalType.hbe_dPBAaPBAsepP2turn: 6>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP3turn = <HBEvalType.hbe_dPBAaPBAsepP3turn: 7>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepP4helix = <HBEvalType.hbe_dPBAaPBAsepP4helix: 8>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepPM1 = <HBEvalType.hbe_dPBAaPBAsepPM1: 5>
hbe_dPROTEIN_BB_AMIDEaPROTEIN_BB_AMIDEsepother = <HBEvalType.hbe_dPBAaPBAsepother: 9>
hbe_dPROTEIN_BB_AMIDEaWATER = <HBEvalType.hbe_dPBAaH2O: 200>
hbe_dWATERaAROMATIC_HYDROXYL = <HBEvalType.hbe_dH2OaAHX: 88>
hbe_dWATERaCARBOXAMIDE = <HBEvalType.hbe_dH2OaCXA: 40>
hbe_dWATERaCARBOXYL = <HBEvalType.hbe_dH2OaCXL: 52>
hbe_dWATERaHYDROXYL = <HBEvalType.hbe_dH2OaHXL: 100>
hbe_dWATERaIMIDAZOL_DELTA = <HBEvalType.hbe_dH2OaIMD: 64>
hbe_dWATERaIMIDAZOL_EPSILON = <HBEvalType.hbe_dH2OaIME: 76>
hbe_dWATERaPHOSPHATE_CARBONYL_DNA = <HBEvalType.hbe_dH2OaPCA_DNA: 112>
hbe_dWATERaPHOSPHATE_CARBONYL_RNA = <HBEvalType.hbe_dH2OaPCA_RNA: 133>
hbe_dWATERaPHOSPHATE_ESTER_DNA = <HBEvalType.hbe_dH2OaPES_DNA: 145>
hbe_dWATERaPHOSPHATE_ESTER_RNAsepother = <HBEvalType.hbe_dH2OaPES_RNA: 166>
hbe_dWATERaRIBOSE_RING_DNA = <HBEvalType.hbe_dH2OaRRI_DNA: 178>
hbe_dWATERaRIBOSE_RING_RNAsepother = <HBEvalType.hbe_dH2OaRRI_RNA: 199>
hbe_dWATERaWATER = <HBEvalType.hbe_dH2OaH2O: 210>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType

Bases: pybind11_object

Members:

hbgd_NONE

hbgd_AHdist

hbgd_cosBAH

hbgd_cosAHD

hbgd_AHD

hbgd_chi

hbgd_MAX

hbgd_AHD = <HBGeoDimType.hbgd_AHD: 5>
hbgd_AHdist = <HBGeoDimType.hbgd_AHdist: 2>
hbgd_MAX = <HBGeoDimType.hbgd_chi: 6>
hbgd_NONE = <HBGeoDimType.hbgd_NONE: 1>
hbgd_chi = <HBGeoDimType.hbgd_chi: 6>
hbgd_cosAHD = <HBGeoDimType.hbgd_cosAHD: 4>
hbgd_cosBAH = <HBGeoDimType.hbgd_cosBAH: 3>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep

Bases: 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

property name
seq_sep_M2 = <HBSeqSep.seq_sep_M2: 4>
seq_sep_M3 = <HBSeqSep.seq_sep_M3: 3>
seq_sep_M4 = <HBSeqSep.seq_sep_M4: 2>
seq_sep_MAX = <HBSeqSep.seq_sep_P4: 8>
seq_sep_P2 = <HBSeqSep.seq_sep_P2: 6>
seq_sep_P3 = <HBSeqSep.seq_sep_P3: 7>
seq_sep_P4 = <HBSeqSep.seq_sep_P4: 8>
seq_sep_PM1 = <HBSeqSep.seq_sep_PM1: 5>
seq_sep_other = <HBSeqSep.seq_sep_other: 1>
property value
class pyrosetta.rosetta.core.scoring.hbonds.HBond

Bases: pybind11_object

acc_atm(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → int

C++: core::scoring::hbonds::HBond::acc_atm() const –> unsigned long

acc_atm_is_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

needed for silly allow logic

C++: core::scoring::hbonds::HBond::acc_atm_is_backbone() const –> bool

acc_atm_is_protein_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

needed for silly allow logic

C++: core::scoring::hbonds::HBond::acc_atm_is_protein_backbone() const –> bool

acc_index(*args, **kwargs)

Overloaded function.

  1. acc_index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> int

C++: core::scoring::hbonds::HBond::acc_index() const –> unsigned long

  1. acc_index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, setting: int) -> None

C++: core::scoring::hbonds::HBond::acc_index(unsigned long) –> void

acc_npd_weight(*args, **kwargs)

Overloaded function.

  1. acc_npd_weight(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> float

C++: core::scoring::hbonds::HBond::acc_npd_weight() const –> double

  1. acc_npd_weight(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, setting: float) -> None

C++: core::scoring::hbonds::HBond::acc_npd_weight(double) –> void

acc_res(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → int

C++: core::scoring::hbonds::HBond::acc_res() const –> unsigned long

acc_res_is_dna(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: core::scoring::hbonds::HBond::acc_res_is_dna() const –> bool

acc_res_is_protein(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: core::scoring::hbonds::HBond::acc_res_is_protein() const –> bool

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

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

atom_is_acceptor(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, atom: pyrosetta.rosetta.core.id.AtomID) → bool

C++: core::scoring::hbonds::HBond::atom_is_acceptor(const class core::id::AtomID &) const –> bool

atom_is_donorH(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, atom: pyrosetta.rosetta.core.id.AtomID) → bool

C++: core::scoring::hbonds::HBond::atom_is_donorH(const class core::id::AtomID &) const –> bool

derivs(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs

C++: core::scoring::hbonds::HBond::derivs() const –> const struct core::scoring::hbonds::HBondDerivs &

don_hatm(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → int

C++: core::scoring::hbonds::HBond::don_hatm() const –> unsigned long

don_hatm_is_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

needed for silly allow logic

C++: core::scoring::hbonds::HBond::don_hatm_is_backbone() const –> bool

don_hatm_is_protein_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

needed for silly allow logic

C++: core::scoring::hbonds::HBond::don_hatm_is_protein_backbone() const –> bool

don_index(*args, **kwargs)

Overloaded function.

  1. don_index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> int

C++: core::scoring::hbonds::HBond::don_index() const –> unsigned long

  1. don_index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, setting: int) -> None

C++: core::scoring::hbonds::HBond::don_index(unsigned long) –> void

don_npd_weight(*args, **kwargs)

Overloaded function.

  1. don_npd_weight(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> float

C++: core::scoring::hbonds::HBond::don_npd_weight() const –> double

  1. don_npd_weight(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, setting: float) -> None

C++: core::scoring::hbonds::HBond::don_npd_weight(double) –> void

don_res(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → int

C++: core::scoring::hbonds::HBond::don_res() const –> unsigned long

don_res_is_dna(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: core::scoring::hbonds::HBond::don_res_is_dna() const –> bool

don_res_is_protein(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: core::scoring::hbonds::HBond::don_res_is_protein() const –> bool

energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → float
NOTE: this is unweighted energy, see weight() for the weight

(weight ==> environmental weight; hbonds closer to the surface are weaker)

C++: core::scoring::hbonds::HBond::energy() const –> double

eval_tuple(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple

The HBEvalTuple is a tuple of enums for each dimension of the evaluation type

C++: core::scoring::hbonds::HBond::eval_tuple() const –> const class core::scoring::hbonds::HBEvalTuple &

eval_type(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → pyrosetta.rosetta.core.scoring.hbonds.HBEvalType

The HBEval type encodes the evaluation type as a single enum value

C++: core::scoring::hbonds::HBond::eval_type() const –> enum core::scoring::hbonds::HBEvalType

get_AHDangle(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::hbonds::HBond::get_AHDangle(const class core::pose::Pose &) const –> double

get_BAHangle(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::hbonds::HBond::get_BAHangle(const class core::pose::Pose &) const –> double

get_BAtorsion(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::hbonds::HBond::get_BAtorsion(const class core::pose::Pose &) const –> double

get_HAdist(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::hbonds::HBond::get_HAdist(const class core::pose::Pose &) const –> double

get_self_ptr(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → pyrosetta.rosetta.core.scoring.hbonds.HBond

C++: core::scoring::hbonds::HBond::get_self_ptr() –> class std::shared_ptr<class core::scoring::hbonds::HBond>

static hbond_energy_comparer(a: pyrosetta.rosetta.core.scoring.hbonds.HBond, b: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool

C++: core::scoring::hbonds::HBond::hbond_energy_comparer(class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::shared_ptr<const class core::scoring::hbonds::HBond>) –> bool

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> int

C++: core::scoring::hbonds::HBond::index() const –> unsigned long

  1. index(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, setting: int) -> None

C++: core::scoring::hbonds::HBond::index(unsigned long) –> void

show(*args, **kwargs)

Overloaded function.

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

a bare bones description of the data contained in the hbond object

C++: core::scoring::hbonds::HBond::show(std::ostream &) const –> void

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

a prettier, more interpretable description of an hbond, including pdb identified residues and the geometric dimensions of the hydrogen bond.

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

  1. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBond, pose: pyrosetta.rosetta.core.pose.Pose, print_header: bool) -> None

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

weight(self: pyrosetta.rosetta.core.scoring.hbonds.HBond) → float
The environmental weight for a hydrogen bond – always 1 if environmental

dependence is not enabled

C++: core::scoring::hbonds::HBond::weight() const –> double

class pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase

Bases: pybind11_object

AHdist_long_fade_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::FadeInterval

find fading function for hbgd_AHdist long

C++: core::scoring::hbonds::HBondDatabase::AHdist_long_fade_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

AHdist_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_AHdist dimension

C++: core::scoring::hbonds::HBondDatabase::AHdist_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

AHdist_short_fade_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::FadeInterval

find fading function for hbgd_AHdist sort

C++: core::scoring::hbonds::HBondDatabase::AHdist_short_fade_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

HBFadeInterval_from_name(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, name: str) → core::scoring::hbonds::FadeInterval

find polynomial function given name

C++: core::scoring::hbonds::HBondDatabase::HBFadeInterval_from_name(const std::string &) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

HBPoly1D_from_name(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, name: str) → core::scoring::hbonds::Polynomial_1d

find polynomial function given name

C++: core::scoring::hbonds::HBondDatabase::HBPoly1D_from_name(const std::string &) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

acc_strength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, ac_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType) → float

get the bonding strength of an acceptor group

C++: core::scoring::hbonds::HBondDatabase::acc_strength(const enum core::scoring::hbonds::HBAccChemType) const –> double

chi_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_chi dimension

C++: core::scoring::hbonds::HBondDatabase::chi_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

cosAHD_fade_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::FadeInterval

find fading function for hbgd_cosAHD

C++: core::scoring::hbonds::HBondDatabase::cosAHD_fade_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

cosAHD_long_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is long

C++: core::scoring::hbonds::HBondDatabase::cosAHD_long_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

cosAHD_short_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_cosAHD dimension when hbgd_AHdist is short

C++: core::scoring::hbonds::HBondDatabase::cosAHD_short_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

cosBAH2_fade_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::FadeInterval

find fading function for hbgd_cosBAH2

C++: core::scoring::hbonds::HBondDatabase::cosBAH2_fade_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

cosBAH2_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_cosBAH2 dimension

C++: core::scoring::hbonds::HBondDatabase::cosBAH2_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

cosBAH_fade_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::FadeInterval

find fading function for hbgd_cosBAH

C++: core::scoring::hbonds::HBondDatabase::cosBAH_fade_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::FadeInterval>

cosBAH_long_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is long

C++: core::scoring::hbonds::HBondDatabase::cosBAH_long_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

cosBAH_short_poly_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → core::scoring::hbonds::Polynomial_1d

find polynomial to hbgd_cosBAH dimension when hbgd_AHdist is short

C++: core::scoring::hbonds::HBondDatabase::cosBAH_short_poly_lookup(const unsigned long) const –> class std::shared_ptr<const class core::scoring::hbonds::Polynomial_1d>

don_strength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, don_chem_type: pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType) → float

get the bonding strength of a donor group

C++: core::scoring::hbonds::HBondDatabase::don_strength(const enum core::scoring::hbonds::HBDonChemType) const –> double

static get_database(*args, **kwargs)

Overloaded function.

  1. get_database() -> pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase

only public way to create an HBondDatabase

C++: core::scoring::hbonds::HBondDatabase::get_database() –> class std::shared_ptr<const class core::scoring::hbonds::HBondDatabase>

  1. get_database(: str) -> pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase

only public way to create an HBondDatabase

C++: core::scoring::hbonds::HBondDatabase::get_database(const std::string &) –> class std::shared_ptr<const class core::scoring::hbonds::HBondDatabase>

initialize(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

C++: core::scoring::hbonds::HBondDatabase::initialize() –> void

initialize_HBEval(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

read table of evaluation types

C++: core::scoring::hbonds::HBondDatabase::initialize_HBEval() –> void

initialize_HBFadeInterval(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

read table of fade intervals

C++: core::scoring::hbonds::HBondDatabase::initialize_HBFadeInterval() –> void

initialize_HBPoly1D(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

read one dimensional polynomial definitions file

C++: core::scoring::hbonds::HBondDatabase::initialize_HBPoly1D() –> void

initialize_acc_strength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

read table of acceptor bonding strengths

C++: core::scoring::hbonds::HBondDatabase::initialize_acc_strength() –> void

initialize_don_strength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → None

read table of donor bonding strengths

C++: core::scoring::hbonds::HBondDatabase::initialize_don_strength() –> void

initialized(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → bool

C++: core::scoring::hbonds::HBondDatabase::initialized() const –> bool

report_parameter_features(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, db_session: pyrosetta.rosetta.utility.sql_database.session) → int

C++: core::scoring::hbonds::HBondDatabase::report_parameter_features(class std::shared_ptr<class utility::sql_database::session>) const –> unsigned long

report_parameter_features_schema_to_db(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, db_session: pyrosetta.rosetta.utility.sql_database.session) → None

C++: core::scoring::hbonds::HBondDatabase::report_parameter_features_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

use_incorrect_deriv(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase) → bool

Signal to use deprecated derivitive calculation in core::scoring::hbonds::hb_energy_deriv_u2(). Once old code has been modified to support the new behavior, remove this option. Since the options are not passe directly to to hb_energy_deriv_u2, access it through the HBondDatabase, rather then messing with the interfaces for the hb_energy_deriv functions.

C++: core::scoring::hbonds::HBondDatabase::use_incorrect_deriv() const –> bool

weight_type_lookup(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hb_eval_type: int) → pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType

find weight type for evaluation type

C++: core::scoring::hbonds::HBondDatabase::weight_type_lookup(const unsigned long) const –> enum core::scoring::hbonds::HBondWeightType

class pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs

Bases: pybind11_object

property abase2_deriv
property abase_deriv
property acc_deriv
assign(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs, : pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) → pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs

C++: core::scoring::hbonds::HBondDerivs::operator=(const struct core::scoring::hbonds::HBondDerivs &) –> struct core::scoring::hbonds::HBondDerivs &

deriv(self: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs, which: pyrosetta.rosetta.core.scoring.hbonds.which_atom_in_hbond) → pyrosetta.rosetta.core.scoring.DerivVectorPair

C++: core::scoring::hbonds::HBondDerivs::deriv(enum core::scoring::hbonds::which_atom_in_hbond) –> class core::scoring::DerivVectorPair &

property don_deriv
property h_deriv
class pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy

Bases: ContextDependentTwoBodyEnergy

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

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

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

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

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None
Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

backbone_backbone_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, 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
Evaluates the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulates the unweighted energy.

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, 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
Evaluates the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulates the unweighted energy.

C++: core::scoring::hbonds::HBondEnergy::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, : core::pose::Pose, : core::scoring::ScoreFunction, : 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, : core::pose::Pose, : core::scoring::ScoreFunction, : 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.HBondEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

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

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : 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: 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.HBondEnergy, weights: pyrosetta.rosetta.core.scoring.EMapVector) → bool

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) → bool
Returns false if two residues are not moving wrt each other; the two parts

of the HBondEnergy function which are non-pairwise-decomposable are held fixed during minimization – the neighbor counts, and the bb/bb hbond availability status. This means that the hbond-energy function can be efficiently evaluated during minimization.

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy) → bool

C++: core::scoring::hbonds::HBondEnergy::divides_backbone_and_sidechain_energetics() const –> bool

drawn_out_heavyatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, at1: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, at2: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, flipped: bool, cached_data: core::scoring::trie::TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::hbonds::HBondEnergy::drawn_out_heavyatom_hydrogenatom_energy(const class core::scoring::hbonds::hbtrie::HBAtom &, const class core::scoring::hbonds::hbtrie::HBAtom &, bool, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None
Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::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.hbonds.HBondEnergy, 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

C++: core::scoring::hbonds::HBondEnergy::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.HBondEnergy, 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::HBondEnergy::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: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: 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: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: 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.hbonds.HBondEnergy, 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

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, 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

C++: core::scoring::hbonds::HBondEnergy::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: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: 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: core::pose::Pose, sfxn: 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: core::pose::Pose, sfxn: 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.hbonds.HBondEnergy, 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: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) → None

C++: core::scoring::hbonds::HBondEnergy::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, : core::pose::Pose, : 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: 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.HBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

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

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool
Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?

Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy) → bool

Has pairwise energies, but no single-atom ones.

C++: core::scoring::hbonds::HBondEnergy::has_atomistic_pairwise_energies() const –> bool

hbond_derivs_1way(*args, **kwargs)

Overloaded function.

  1. hbond_derivs_1way(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, weights: pyrosetta.rosetta.core.scoring.EMapVector, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, pose: pyrosetta.rosetta.core.pose.Pose, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, exclude_bsc: bool, exclude_scb: bool, ssdep_weight_factor: float, don_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, acc_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) -> None

  2. hbond_derivs_1way(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, weights: pyrosetta.rosetta.core.scoring.EMapVector, hbond_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, pose: pyrosetta.rosetta.core.pose.Pose, don_rsd: pyrosetta.rosetta.core.conformation.Residue, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, don_nb: int, acc_nb: int, exclude_bsc: bool, exclude_scb: bool, ssdep_weight_factor: float, don_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, acc_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, bond_near_wat: bool) -> None

C++: core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(const class core::scoring::EMapVector &, const class core::scoring::hbonds::HBondSet &, class std::shared_ptr<const class core::scoring::hbonds::HBondDatabase>, const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long, const bool, const bool, const double, 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> > &, bool) const –> void

heavyatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, at1: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, at2: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, d2: float, : int) → float

C++: core::scoring::hbonds::HBondEnergy::heavyatom_heavyatom_energy(const class core::scoring::hbonds::hbtrie::HBAtom &, const class core::scoring::hbonds::hbtrie::HBAtom &, double &, unsigned long &) const –> double

heavyatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, at1: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, at2: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, flipped: bool, cached_data: core::scoring::trie::TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::hbonds::HBondEnergy::heavyatom_hydrogenatom_energy(const class core::scoring::hbonds::hbtrie::HBAtom &, const class core::scoring::hbonds::hbtrie::HBAtom &, const bool, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

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

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

hydrogenatom_heavyatom_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, at1: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, at2: pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, : int, cached_data: core::scoring::trie::TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::hbonds::HBondEnergy::hydrogenatom_heavyatom_energy(const class core::scoring::hbonds::hbtrie::HBAtom &, const class core::scoring::hbonds::hbtrie::HBAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

hydrogenatom_hydrogenatom_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, : pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, : pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom, : int, : core::scoring::trie::TrieVsTrieCachedDataContainerBase) → float

C++: core::scoring::hbonds::HBondEnergy::hydrogenatom_hydrogenatom_energy(const class core::scoring::hbonds::hbtrie::HBAtom &, const class core::scoring::hbonds::hbtrie::HBAtom &, unsigned long &, const class core::scoring::trie::TrieVsTrieCachedDataContainerBase *const) const –> double

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

HBondEnergy is context sensitive

C++: core::scoring::hbonds::HBondEnergy::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.HBondEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) → None

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

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Construct the set of all hydrogen bonds between two residues before

C++: core::scoring::hbonds::HBondEnergy::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: 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: 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: 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.HBondEnergy, 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

note that this only evaluates sc-sc and sc-bb energies

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, 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 energy between a pair of residues during minimization;

during minimization, the bb/bb hbond status is held fixed, so it is possible to evaluate the bb/bb, bb/sc and sc/sc hydrogen bonds in this function call.

C++: core::scoring::hbonds::HBondEnergy::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.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None
Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::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: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: 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: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: 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, : core::pose::Pose, : core::scoring::ScoreFunction, : 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.hbonds.HBondEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) → None
Setup the bb/bb hbond presence data for a particular residue – this data

is taken out of the HbondSet in the Pose.

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, 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
Link the bb/bb hbond information in the ResidueSingleMinimizationData

to the ResiduePairMinimizationData.

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::scoring::hbonds::HBondEnergy::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_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None
if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

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

C++: core::scoring::hbonds::HBondEnergy::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: core::pose::Pose, sfxn: 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: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: 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: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: 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, : core::pose::Pose, : bool) → None

show additional information of the energy method

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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy, 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
Evaluates the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulates the unweighted energy.

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) → None

C++: core::scoring::hbonds::HBondEnergy::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.hbonds.HBondEnergy) → bool
Use the extended residue pair energy interface to distinguish between

score function evaluation during minimization from score function evaluation during regular scoring.

C++: core::scoring::hbonds::HBondEnergy::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.HBondEnergyCreator

Bases: EnergyMethodCreator

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

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

create_energy_method(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new HBondEnergy

C++: core::scoring::hbonds::HBondEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.scoring.hbonds.HBondEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType
Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: core::scoring::hbonds::HBondEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.scoring.hbonds.HBondOptions

Bases: pybind11_object

Mbhbond(*args, **kwargs)

Overloaded function.

  1. Mbhbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

pba

C++: core::scoring::hbonds::HBondOptions::Mbhbond() const –> bool

  1. Mbhbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

pba

C++: core::scoring::hbonds::HBondOptions::Mbhbond(const bool) –> void

static append_schema_attributes(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: core::scoring::hbonds::HBondOptions::append_schema_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

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

copy operator

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

bb_donor_acceptor_check(*args, **kwargs)

Overloaded function.

  1. bb_donor_acceptor_check(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check() const –> bool

  1. bb_donor_acceptor_check(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check(const bool) –> void

decompose_bb_hb_into_pair_energies(*args, **kwargs)

Overloaded function.

  1. decompose_bb_hb_into_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies() const –> bool

  1. decompose_bb_hb_into_pair_energies(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(const bool) –> void

exclude_DNA_DNA(*args, **kwargs)

Overloaded function.

  1. exclude_DNA_DNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::exclude_DNA_DNA() const –> bool

  1. exclude_DNA_DNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(const bool) –> void

exclude_ether_oxygens(*args, **kwargs)

Overloaded function.

  1. exclude_ether_oxygens(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

No H-bonds to ether oxygens, like O4’ in DNA or DNA. Replaces -chemical::no_hbond_to_ether_oxygens.

C++: core::scoring::hbonds::HBondOptions::exclude_ether_oxygens() const –> bool

  1. exclude_ether_oxygens(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::exclude_ether_oxygens(bool) –> void

exclude_intra_res_RNA(*args, **kwargs)

Overloaded function.

  1. exclude_intra_res_RNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA() const –> bool

  1. exclude_intra_res_RNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA(const bool) –> void

exclude_intra_res_protein(*args, **kwargs)

Overloaded function.

  1. exclude_intra_res_protein(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::exclude_intra_res_protein() const –> bool

  1. exclude_intra_res_protein(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(const bool) –> void

exclude_self_hbonds(*args, **kwargs)

Overloaded function.

  1. exclude_self_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

Double counted hbonds include:

  • Hydrogen bonds to self

  • Backbone - sidechain hydrogen bonds where the backbone partner is forming a backbone - backbone hydrogen bond.

Turning off this exclusion rule is useful for collecting statistics on hydrogen bond site satisfaction

C++: core::scoring::hbonds::HBondOptions::exclude_self_hbonds() const –> bool

  1. exclude_self_hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::exclude_self_hbonds(const bool) –> void

fade_energy(*args, **kwargs)

Overloaded function.

  1. fade_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

Rather than having a strict cutoff of hbond definition at

0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function. -corrections:score:hb_fade_energy Default: false

C++: core::scoring::hbonds::HBondOptions::fade_energy() const –> bool

  1. fade_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::fade_energy(bool) –> void

hbond_energy_shift(*args, **kwargs)

Overloaded function.

  1. hbond_energy_shift(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

C++: core::scoring::hbonds::HBondOptions::hbond_energy_shift() const –> double

  1. hbond_energy_shift(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, : float) -> None

C++: core::scoring::hbonds::HBondOptions::hbond_energy_shift(double) –> void

initialize_from_options(*args, **kwargs)

Overloaded function.

  1. initialize_from_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> None

Initialize this object from the global option collection

C++: core::scoring::hbonds::HBondOptions::initialize_from_options() –> void

  1. initialize_from_options(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, option_list: pyrosetta.rosetta.utility.options.OptionCollection) -> None

Initialize this object from a (possibly local) option collection

C++: core::scoring::hbonds::HBondOptions::initialize_from_options(const class utility::options::OptionCollection &) –> void

length_dependent_srbb(*args, **kwargs)

Overloaded function.

  1. length_dependent_srbb(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

Enable helix-length-dependent sr bb hbonds

Default: false

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb() const –> bool

  1. length_dependent_srbb(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb(bool) –> void

length_dependent_srbb_highscale(*args, **kwargs)

Overloaded function.

  1. length_dependent_srbb_highscale(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_highscale() const –> double

  1. length_dependent_srbb_highscale(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: float) -> None

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_highscale(double) –> void

length_dependent_srbb_lowscale(*args, **kwargs)

Overloaded function.

  1. length_dependent_srbb_lowscale(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_lowscale() const –> double

  1. length_dependent_srbb_lowscale(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: float) -> None

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_lowscale(double) –> void

length_dependent_srbb_maxlength(*args, **kwargs)

Overloaded function.

  1. length_dependent_srbb_maxlength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> int

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength() const –> unsigned long

  1. length_dependent_srbb_maxlength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: int) -> None

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength(unsigned long) –> void

length_dependent_srbb_minlength(*args, **kwargs)

Overloaded function.

  1. length_dependent_srbb_minlength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> int

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength() const –> unsigned long

  1. length_dependent_srbb_minlength(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: int) -> None

C++: core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength(unsigned long) –> void

static list_options_read(option_list: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None

Documentation functon that lists the options that are read in the initialize_from_options function

C++: core::scoring::hbonds::HBondOptions::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

max_hb_energy(*args, **kwargs)

Overloaded function.

  1. max_hb_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

Max possible hbond energy

Under nearly all circumstances this should be set to 0.0

Originally made an option to allow BuriedUnsatFilter to allow really bad hbonds

C++: core::scoring::hbonds::HBondOptions::max_hb_energy() const –> double

  1. max_hb_energy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: float) -> None

C++: core::scoring::hbonds::HBondOptions::max_hb_energy(const double) –> void

measure_sp3acc_BAH_from_hvy(*args, **kwargs)

Overloaded function.

  1. measure_sp3acc_BAH_from_hvy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

When calculating the BAH angle for sp3 hybridized acceptors: true: the angle should be measured

from the heavy-atom base (CB for S/T); false: from the base-2 atom (HG for S/T).

C++: core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy() const –> bool

  1. measure_sp3acc_BAH_from_hvy(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(bool) –> void

mphbond(*args, **kwargs)

Overloaded function.

  1. mphbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

Membrane framework hbonding correction

C++: core::scoring::hbonds::HBondOptions::mphbond() const –> bool

  1. mphbond(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::mphbond(const bool) –> void

params_database_tag(*args, **kwargs)

Overloaded function.

  1. params_database_tag(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: str) -> None

C++: core::scoring::hbonds::HBondOptions::params_database_tag(const std::string &) –> void

  1. params_database_tag(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> str

C++: core::scoring::hbonds::HBondOptions::params_database_tag() const –> const std::string &

parse_my_tag(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, tag: utility::tag::Tag) → None

set hbond options from key value options in a Tag structure, e.g. from a block in the SCOREFXNS section of a RosettaScripts file.

C++: core::scoring::hbonds::HBondOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

put_intra_into_total(*args, **kwargs)

Overloaded function.

  1. put_intra_into_total(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::put_intra_into_total() const –> bool

  1. put_intra_into_total(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::put_intra_into_total(const bool) –> void

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

C++: core::scoring::hbonds::HBondOptions::show(std::ostream &) const –> void

smooth_hb_env_dep(*args, **kwargs)

Overloaded function.

  1. smooth_hb_env_dep(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::smooth_hb_env_dep() const –> bool

  1. smooth_hb_env_dep(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::smooth_hb_env_dep(const bool) –> void

sp2_BAH180_rise(*args, **kwargs)

Overloaded function.

  1. sp2_BAH180_rise(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

Parameter for the sp2 potential that dictates how much worse a head-on hydrogen bond is

relative to one at a BAH angle of 120 degrees. Controlled by the command-line flag -corrections:score:hb_sp2_BAH180_rise. Default of 0.75.

C++: core::scoring::hbonds::HBondOptions::sp2_BAH180_rise() const –> double

  1. sp2_BAH180_rise(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: float) -> None

C++: core::scoring::hbonds::HBondOptions::sp2_BAH180_rise(double) –> void

sp2_outer_width(*args, **kwargs)

Overloaded function.

  1. sp2_outer_width(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> float

Parameter for the sp2 potential that dictates the width

between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). -corrections:score:hb_sp2_outer_width Default: 0.357

C++: core::scoring::hbonds::HBondOptions::sp2_outer_width() const –> double

  1. sp2_outer_width(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: float) -> None

C++: core::scoring::hbonds::HBondOptions::sp2_outer_width(double) –> void

use_hb_env_dep(*args, **kwargs)

Overloaded function.

  1. use_hb_env_dep(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::use_hb_env_dep() const –> bool

  1. use_hb_env_dep(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::use_hb_env_dep(const bool) –> void

use_hb_env_dep_DNA(*args, **kwargs)

Overloaded function.

  1. use_hb_env_dep_DNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA() const –> bool

  1. use_hb_env_dep_DNA(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA(const bool) –> void

use_sp2_chi_penalty(*args, **kwargs)

Overloaded function.

  1. use_sp2_chi_penalty(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty() const –> bool

  1. use_sp2_chi_penalty(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty(bool) –> void

water_hybrid_sf(*args, **kwargs)

Overloaded function.

  1. water_hybrid_sf(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) -> bool

C++: core::scoring::hbonds::HBondOptions::water_hybrid_sf() const –> bool

  1. water_hybrid_sf(self: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, setting: bool) -> None

C++: core::scoring::hbonds::HBondOptions::water_hybrid_sf(const bool) –> void

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

Bases: 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

  1. 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) → pyrosetta.rosetta.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

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

  2. 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

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

  2. 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: pyrosetta.rosetta.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(std::ostream &) const –> void

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

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

  1. 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, std::ostream &) const –> void

  1. show(self: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. 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

  1. 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, std::ostream &) const –> void

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

  2. 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.HBondTypeManager

Bases: pybind11_object

static acc_chem_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType

Acceptor Chemical Type

C++: core::scoring::hbonds::HBondTypeManager::acc_chem_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBAccChemType

static deriv_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBDerivType

Derivative Type

C++: core::scoring::hbonds::HBondTypeManager::deriv_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBDerivType

static don_chem_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType

Donor Chemical Type

C++: core::scoring::hbonds::HBondTypeManager::don_chem_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBDonChemType

static geo_dim_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType

C++: core::scoring::hbonds::HBondTypeManager::geo_dim_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBGeoDimType

static hybridization_type_from_name(name: str) → pyrosetta.rosetta.core.chemical.Hybridization

C++: core::scoring::hbonds::HBondTypeManager::hybridization_type_from_name(const std::string &) –> enum core::chemical::Hybridization

static is_acc_chem_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_acc_chem_type(const std::string &) –> bool

static is_deriv_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_deriv_type(const std::string &) –> bool

static is_don_chem_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_don_chem_type(const std::string &) –> bool

static is_geo_dim_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_geo_dim_type(const std::string &) –> bool

static is_hybridization_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_hybridization_type(const std::string &) –> bool

static is_seq_sep_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_seq_sep_type(const std::string &) –> bool

static is_weight_type(name: str) → bool

C++: core::scoring::hbonds::HBondTypeManager::is_weight_type(const std::string &) –> bool

static name_from_acc_chem_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBAccChemType) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_acc_chem_type(enum core::scoring::hbonds::HBAccChemType) –> std::string

static name_from_deriv_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_deriv_type(enum core::scoring::hbonds::HBDerivType) –> std::string

static name_from_don_chem_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBDonChemType) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_don_chem_type(enum core::scoring::hbonds::HBDonChemType) –> std::string

static name_from_geo_dim_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_geo_dim_type(enum core::scoring::hbonds::HBGeoDimType) –> std::string

static name_from_hybridization_type(: pyrosetta.rosetta.core.chemical.Hybridization) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_hybridization_type(enum core::chemical::Hybridization) –> std::string

static name_from_seq_sep_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_seq_sep_type(enum core::scoring::hbonds::HBSeqSep) –> std::string

static name_from_weight_type(score_type: pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType) → str

C++: core::scoring::hbonds::HBondTypeManager::name_from_weight_type(enum core::scoring::hbonds::HBondWeightType) –> std::string

static seq_sep_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBSeqSep

Sequence Separation Type

C++: core::scoring::hbonds::HBondTypeManager::seq_sep_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBSeqSep

static weight_type_from_name(name: str) → pyrosetta.rosetta.core.scoring.hbonds.HBondWeightType

Bond Weight Type

C++: core::scoring::hbonds::HBondTypeManager::weight_type_from_name(const std::string &) –> enum core::scoring::hbonds::HBondWeightType

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

Bases: 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

hbw_LR_BB = <HBondWeightType.hbw_LR_BB: 3>
hbw_LR_BB_SC = <HBondWeightType.hbw_LR_BB_SC: 5>
hbw_MAX = <HBondWeightType.hbw_SC: 6>
hbw_NONE = <HBondWeightType.hbw_NONE: 1>
hbw_SC = <HBondWeightType.hbw_SC: 6>
hbw_SR_BB = <HBondWeightType.hbw_SR_BB: 2>
hbw_SR_BB_SC = <HBondWeightType.hbw_SR_BB_SC: 4>
property name
property value
class pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet

Bases: 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

  1. 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) → pyrosetta.rosetta.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

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

  2. 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

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

  2. 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: pyrosetta.rosetta.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(std::ostream &) const –> void

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

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

  1. 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, std::ostream &) const –> void

  1. show(self: pyrosetta.rosetta.core.scoring.hbonds.NPDHBondSet, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. 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

  1. 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, std::ostream &) const –> void

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

  2. 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

class pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d

Bases: Polynomial_1d

assign(self: pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d, : pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d) → pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d

C++: core::scoring::hbonds::Polynomial_1d::operator=(const class core::scoring::hbonds::Polynomial_1d &) –> class core::scoring::hbonds::Polynomial_1d &

check_invariants(self: pyrosetta.rosetta.numeric.Polynomial_1d) → None

C++: numeric::Polynomial_1d::check_invariants() const –> void

coefficients(self: pyrosetta.rosetta.numeric.Polynomial_1d) → pyrosetta.rosetta.utility.vector1_double

C++: numeric::Polynomial_1d::coefficients() const –> const class utility::vector1<double, class std::allocator<double> > &

degree(self: pyrosetta.rosetta.numeric.Polynomial_1d) → int

C++: numeric::Polynomial_1d::degree() const –> unsigned long

eval(self: pyrosetta.rosetta.numeric.Polynomial_1d, variable: float) → float

just evaluate the polynomial, w/o derivatives

C++: numeric::Polynomial_1d::eval(const double) –> double

geometric_dimension(self: pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d) → pyrosetta.rosetta.core.scoring.hbonds.HBGeoDimType

C++: core::scoring::hbonds::Polynomial_1d::geometric_dimension() const –> enum core::scoring::hbonds::HBGeoDimType

max_val(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::max_val() const –> double

min_val(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::min_val() const –> double

name(self: pyrosetta.rosetta.numeric.Polynomial_1d) → str

C++: numeric::Polynomial_1d::name() const –> const std::string &

root1(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::root1() const –> double

root2(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::root2() const –> double

show(self: pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::hbonds::Polynomial_1d::show(std::ostream &) const –> void

show_values(self: pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d) → str

C++: core::scoring::hbonds::Polynomial_1d::show_values() const –> std::string

xmax(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::xmax() const –> double

xmin(self: pyrosetta.rosetta.numeric.Polynomial_1d) → float

C++: numeric::Polynomial_1d::xmin() const –> double

class pyrosetta.rosetta.core.scoring.hbonds.SSWeightParameters

Bases: pybind11_object

Weights and Options ///

property h_
property l_
property len_h_
property len_l_
property ssdep_
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

  1. 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

General Utilities ///

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.deep_copy(source: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions) → pyrosetta.rosetta.core.scoring.hbonds.HBondOptions

Needed to allow this to be used with DeepCopyOPs.

Vikram K. Mulligan (vmulligan.org).

C++: core::scoring::hbonds::deep_copy(const class core::scoring::hbonds::HBondOptions &) –> class std::shared_ptr<class core::scoring::hbonds::HBondOptions>

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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

HBondSet Filling (Deprecated in favor of direct hbset functions)///

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.find_hb_paths(*args, **kwargs)

Overloaded function.

  1. find_hb_paths(local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bridge_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int) -> None

  2. find_hb_paths(local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bridge_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int) -> None

  3. find_hb_paths(local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bridge_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str) -> None

  4. find_hb_paths(local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bridge_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str, current_depth: int) -> None

  5. find_hb_paths(local_hb_set: pyrosetta.rosetta.core.scoring.hbonds.HBondSet, bridge_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, paths: pyrosetta.rosetta.std.map_std_string_unsigned_long, current_res: int, max_depth: int, current_path: str, current_depth: int, prev_hb: pyrosetta.rosetta.core.scoring.hbonds.HBond) -> None

Recursive function to find all unique HBond paths involving bridge_residue and ending

with a residue that is not in our bridged list.

Used in WaterMediatedHbondMetric where bridge_residues are waters

Populates paths as the non-const reference through recursion. Path is a splittable string of the connections.

ex: 191-221-333 where residue 221 is a bridge_residue in our list.

Jared Adolf-Bryfogle (jadolfbr.com)

C++: core::scoring::hbonds::find_hb_paths(const class core::scoring::hbonds::HBondSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > > &, const unsigned long, const unsigned long, const std::string &, const unsigned long, class std::shared_ptr<const class core::scoring::hbonds::HBond>) –> 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, Hrsd: int, Arsd: int, Hatm: int, Aatm: 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 int, const int, const int, const int, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

  1. 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

  1. 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

  1. 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

  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, deriv_type: pyrosetta.rosetta.core.scoring.hbonds.HBDerivType) -> 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, 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

  1. 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

HBond Database ///

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

  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, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> 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, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, 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, 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

  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, options: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, emap: pyrosetta.rosetta.core.scoring.EMapVector, 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, 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

  1. 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.next_hb_res(c_hb: pyrosetta.rosetta.core.scoring.hbonds.HBond, res: int) → int
Get the residue that this residue connects to through this particular hbond

We treat hbonds as directed connections (we ignore donor/acceptor).

Jared Adolf-Bryfogle (jadolfbr.com)

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

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

Waters ///

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 std::string &) –> 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_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

n_hb_atoms = <which_atom_in_hbond.which_hb_abase2: 6>
property name
property value
which_hb_aatm = <which_atom_in_hbond.which_hb_aatm: 3>
which_hb_abase = <which_atom_in_hbond.which_hb_abase: 4>
which_hb_abase2 = <which_atom_in_hbond.which_hb_abase2: 6>
which_hb_abase_prime = <which_atom_in_hbond.which_hb_abase_prime: 5>
which_hb_datm = <which_atom_in_hbond.which_hb_datm: 2>
which_hb_hatm = <which_atom_in_hbond.which_hb_hatm: 1>
which_hb_unassigned = <which_atom_in_hbond.which_hb_unassigned: 0>
which_last_donor_atm = <which_atom_in_hbond.which_hb_datm: 2>