disulfides

Bindings for core::scoring::disulfides namespace

class pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func

Bases: pyrosetta.rosetta.core.scoring.func.Func

Score based on the dihedral formed by N Ca Ca C

assign(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func, : pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func) → pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func

C++: core::scoring::disulfides::CaCbCbCa_Dihedral_Func::operator=(const class core::scoring::disulfides::CaCbCbCa_Dihedral_Func &) –> class core::scoring::disulfides::CaCbCbCa_Dihedral_Func &

clone(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::disulfides::CaCbCbCa_Dihedral_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func, : float) → float

C++: core::scoring::disulfides::CaCbCbCa_Dihedral_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func, : float) → float

C++: core::scoring::disulfides::CaCbCbCa_Dihedral_Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(class std::basic_istream<char> &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::disulfides::CaCbCbCa_Dihedral_Func::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

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

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func

Bases: pyrosetta.rosetta.core.scoring.func.Func

Score based on the angle Ca Cb Cb

assign(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func, : pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func) → pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func

C++: core::scoring::disulfides::CaCbCb_Angle_Func::operator=(const class core::scoring::disulfides::CaCbCb_Angle_Func &) –> class core::scoring::disulfides::CaCbCb_Angle_Func &

clone(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::disulfides::CaCbCb_Angle_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func, : float) → float

C++: core::scoring::disulfides::CaCbCb_Angle_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func, : float) → float

C++: core::scoring::disulfides::CaCbCb_Angle_Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(class std::basic_istream<char> &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::disulfides::CaCbCb_Angle_Func::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

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

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func

Bases: pyrosetta.rosetta.core.scoring.func.Func

Score based on the distance between Cb

Based on the rosetta++ scores by Bill Schief in 2002.

Uses a sum of three gaussians.

assign(self: pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func, : pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func) → pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func

C++: core::scoring::disulfides::Cb_Distance_Func::operator=(const class core::scoring::disulfides::Cb_Distance_Func &) –> class core::scoring::disulfides::Cb_Distance_Func &

clone(self: pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::disulfides::Cb_Distance_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func, : float) → float

C++: core::scoring::disulfides::Cb_Distance_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func, : float) → float

C++: core::scoring::disulfides::Cb_Distance_Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(class std::basic_istream<char> &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::disulfides::Cb_Distance_Func::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

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

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func

Bases: pyrosetta.rosetta.core.scoring.func.Func

Score based on the distance between the two residues’ centroids

assign(self: pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func, : pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func) → pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func

C++: core::scoring::disulfides::Cen_Distance_Func::operator=(const class core::scoring::disulfides::Cen_Distance_Func &) –> class core::scoring::disulfides::Cen_Distance_Func &

clone(self: pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::disulfides::Cen_Distance_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func, : float) → float

C++: core::scoring::disulfides::Cen_Distance_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func, : float) → float

C++: core::scoring::disulfides::Cen_Distance_Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(class std::basic_istream<char> &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::disulfides::Cen_Distance_Func::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

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

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents

Bases: pybind11_builtins.pybind11_object

Storage for Disulfide Energy Terms

Although the full atom and centroid terms will not be defined

at the same time for a particular disulfide bond, it is convienient to be able to store either in the same object.

dslfc_ang(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents) → float

C++: core::scoring::disulfides::CentroidDisulfideEnergyComponents::dslfc_ang() –> double &

dslfc_bb_dih(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents) → float

C++: core::scoring::disulfides::CentroidDisulfideEnergyComponents::dslfc_bb_dih() –> double &

dslfc_cb_dih(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents) → float

C++: core::scoring::disulfides::CentroidDisulfideEnergyComponents::dslfc_cb_dih() –> double &

dslfc_cb_dst(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents) → float

C++: core::scoring::disulfides::CentroidDisulfideEnergyComponents::dslfc_cb_dst() –> double &

dslfc_cen_dst(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyComponents) → float

C++: core::scoring::disulfides::CentroidDisulfideEnergyComponents::dslfc_cen_dst() –> double &

class pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator

Bases: pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

Just a const version of CentroidDisulfideNeighborIterator

accumulate_energy(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::accumulate_energy(class core::scoring::EMapVector &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator, : pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::operator=(const class core::scoring::ResidueNeighborConstIterator &) –> class core::scoring::ResidueNeighborConstIterator &

energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → bool

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::energy_computed() const –> bool

lower_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::lower_neighbor_id() const –> unsigned long

neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::neighbor_id() const –> unsigned long

plus_plus(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::operator++() –> const class core::scoring::ResidueNeighborConstIterator &

residue_iterated_on(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::residue_iterated_on() const –> unsigned long

retrieve_energy(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::retrieve_energy(class core::scoring::EMapVector &) const –> void

upper_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborConstIterator::upper_neighbor_id() const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator

Bases: pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

An iterator over the disulfide bonds a residue forms

When scoring a pose, a long range energy container must be able to iterate over all the residues which interact with a particular residue. For disulfide bonds, this is either zero or one items depending on whether the residue specified forms a disulfide bond or not.

Given the proper options, include all residues in the vicinity which could form a bond, not just the best one. Maybe even include non-cysteines!

accumulate_energy(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::accumulate_energy(class core::scoring::EMapVector &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator, : pyrosetta.rosetta.core.scoring.ResidueNeighborIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator=(const class core::scoring::ResidueNeighborIterator &) –> class core::scoring::ResidueNeighborIterator &

energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → bool

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::energy_computed() const –> bool

lower_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::lower_neighbor_id() const –> unsigned long

mark_energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::mark_energy_computed() –> void

mark_energy_uncomputed(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::mark_energy_uncomputed() –> void

neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::neighbor_id() const –> unsigned long

plus_plus(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator++() –> const class core::scoring::ResidueNeighborIterator &

residue_iterated_on(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::residue_iterated_on() const –> unsigned long

retrieve_energy(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::retrieve_energy(class core::scoring::EMapVector &) const –> void

save_energy(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::save_energy(const class core::scoring::EMapVector &) –> void

upper_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator) → int

C++: core::scoring::disulfides::CentroidDisulfideNeighborIterator::upper_neighbor_id() const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential

Bases: pybind11_builtins.pybind11_object

This class scores centroid disulfide bonds It is intended to be a singleton with a single instance held by ScoringManager.

The energy functions are derived from those present in Rosetta++

assign(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential, : pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential) → pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential

C++: core::scoring::disulfides::CentroidDisulfidePotential::operator=(const class core::scoring::disulfides::CentroidDisulfidePotential &) –> class core::scoring::disulfides::CentroidDisulfidePotential &

is_disulfide(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) → bool

Decide whether there is a disulfide bond between two residues.

Does not require that the residues be cysteines, so if this is important you should check for CYS first. (The relaxed requirements are useful for design.)

C++: core::scoring::disulfides::CentroidDisulfidePotential::is_disulfide(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

score_disulfide(*args, **kwargs)

Overloaded function.

1. score_disulfide(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, cbcb_distance_score: float, centroid_distance_score: float, cacbcb_angle_1_score: float, cacbcb_angle_2_score: float, cacbcbca_dihedral_score: float, backbone_dihedral_score: float) -> None

Calculates scoring terms for the disulfide bond specified

C++: core::scoring::disulfides::CentroidDisulfidePotential::score_disulfide(const class core::conformation::Residue &, const class core::conformation::Residue &, double &, double &, double &, double &, double &, double &) const –> void

2. score_disulfide(self: pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, cbcb_distance_sq: float, centroid_distance_sq: float, cacbcb_angle_1: float, cacbcb_angle_2: float, cacbcbca_dihedral: float, backbone_dihedral: float, cbcb_distance_score: float, centroid_distance_score: float, cacbcb_angle_1_score: float, cacbcb_angle_2_score: float, cacbcbca_dihedral_score: float, backbone_dihedral_score: float, cb_score_factor: float) -> None

Calculates scoring terms and geometry

C++: core::scoring::disulfides::CentroidDisulfidePotential::score_disulfide(const class core::conformation::Residue &, const class core::conformation::Residue &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &) const –> void

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices

Bases: pybind11_builtins.pybind11_object

This class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that’s known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow.

atom_gets_derivatives(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices, atom_index: int) → bool

C++: core::scoring::disulfides::DisulfideAtomIndices::atom_gets_derivatives(unsigned long) const –> bool

c_alpha_index(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices) → int

C++: core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index() const –> unsigned long

c_beta_index(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices) → int

C++: core::scoring::disulfides::DisulfideAtomIndices::c_beta_index() const –> unsigned long

derivative_atom(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices, atom_index: int) → pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom

C++: core::scoring::disulfides::DisulfideAtomIndices::derivative_atom(unsigned long) const –> enum core::scoring::disulfides::DisulfideDerivativeAtom

disulf_atom_index(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideAtomIndices) → int

The atom which participates in the disulfide bond

SG for fullatom or CEN for centroid

C++: core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index() const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideDerivativeAtom

Bases: pybind11_builtins.pybind11_object

Members:

NO_DERIVATIVES_FOR_ATOM

CYS_C_ALPHA

CYS_C_BETA

CYS_S_GAMMA

CYS_CEN

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents

Bases: pybind11_builtins.pybind11_object

Storage for Disulfide Energy Terms

dslfc_RT(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents) → float

C++: core::scoring::disulfides::DisulfideMatchingEnergyComponents::dslfc_RT() –> double &

dslfc_rot(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents) → float

C++: core::scoring::disulfides::DisulfideMatchingEnergyComponents::dslfc_rot() –> double &

dslfc_trans(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyComponents) → float

C++: core::scoring::disulfides::DisulfideMatchingEnergyComponents::dslfc_trans() –> double &

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator

Bases: pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

Just a const version of DisulfideMatchingNeighborIterator

accumulate_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::accumulate_energy(class core::scoring::EMapVector &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator, : pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::operator=(const class core::scoring::ResidueNeighborConstIterator &) –> class core::scoring::ResidueNeighborConstIterator &

energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → bool

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::energy_computed() const –> bool

lower_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::lower_neighbor_id() const –> unsigned long

neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::neighbor_id() const –> unsigned long

plus_plus(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::operator++() –> const class core::scoring::ResidueNeighborConstIterator &

residue_iterated_on(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::residue_iterated_on() const –> unsigned long

retrieve_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::retrieve_energy(class core::scoring::EMapVector &) const –> void

upper_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::upper_neighbor_id() const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator

Bases: pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

An iterator over the disulfide bonds a residue forms

When scoring a pose, a long range energy container must be able to iterate over all the residues which interact with a particular residue. For disulfide bonds, this is either zero or one items depending on whether the residue specified forms a disulfide bond or not.

Given the proper options, include all residues in the vicinity which could form a bond, not just the best one. Maybe even include non-cysteines!

accumulate_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::accumulate_energy(class core::scoring::EMapVector &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator, : pyrosetta.rosetta.core.scoring.ResidueNeighborIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator=(const class core::scoring::ResidueNeighborIterator &) –> class core::scoring::ResidueNeighborIterator &

energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → bool

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::energy_computed() const –> bool

lower_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::lower_neighbor_id() const –> unsigned long

mark_energy_computed(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_computed() –> void

mark_energy_uncomputed(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_uncomputed() –> void

neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::neighbor_id() const –> unsigned long

plus_plus(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → pyrosetta.rosetta.core.scoring.ResidueNeighborIterator

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator++() –> const class core::scoring::ResidueNeighborIterator &

residue_iterated_on(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::residue_iterated_on() const –> unsigned long

retrieve_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::retrieve_energy(class core::scoring::EMapVector &) const –> void

save_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::save_energy(const class core::scoring::EMapVector &) –> void

upper_neighbor_id(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator) → int

C++: core::scoring::disulfides::DisulfideMatchingNeighborIterator::upper_neighbor_id() const –> unsigned long

class pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential

Bases: pybind11_builtins.pybind11_object

This class scores centroid disulfide bonds It is intended to be a singleton with a single instance held by ScoringManager.

The energy functions are derived from those present in Rosetta++

assign(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential, : pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential) → pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential

C++: core::scoring::disulfides::DisulfideMatchingPotential::operator=(const class core::scoring::disulfides::DisulfideMatchingPotential &) –> class core::scoring::disulfides::DisulfideMatchingPotential &

compute_matching_energy(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(const class core::pose::Pose &) const –> double

score_disulfide(*args, **kwargs)

Overloaded function.

1. score_disulfide(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, match_t: float, match_r: float, match_rt: float) -> None
2. score_disulfide(self: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, match_t: float, match_r: float, match_rt: float, mirror: bool) -> None

Calculates scoring terms for the disulfide bond specified

C++: core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(const class core::conformation::Residue &, const class core::conformation::Residue &, double &, double &, double &, const bool) const –> void

class pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func

Bases: pyrosetta.rosetta.core.scoring.func.Func

Score based on the dihedral formed by the two Ca and Cb

assign(self: pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func, : pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func) → pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func

C++: core::scoring::disulfides::NCaCaC_Dihedral_Func::operator=(const class core::scoring::disulfides::NCaCaC_Dihedral_Func &) –> class core::scoring::disulfides::NCaCaC_Dihedral_Func &

clone(self: pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func) → pyrosetta.rosetta.core.scoring.func.Func

C++: core::scoring::disulfides::NCaCaC_Dihedral_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func, : float) → float

C++: core::scoring::disulfides::NCaCaC_Dihedral_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)

Overloaded function.

1. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+1e-05).

C++: core::scoring::func::Func::estimate_dfunc(const double) const –> double

2. estimate_dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, r: float, h: float) -> float

Estimates the derivative of this function at a given radius by

calculating the slope of the secant line from func(r) and func(r+h).

C++: core::scoring::func::Func::estimate_dfunc(const double, const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func, : float) → float

C++: core::scoring::disulfides::NCaCaC_Dihedral_Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.std.istream) → None

initialize this Func from the given std::istream.

C++: core::scoring::func::Func::read_data(class std::basic_istream<char> &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::disulfides::NCaCaC_Dihedral_Func::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints out space-delimited columns for r, func, dfunc and

dfunc_est. The values for func, dfunc and dfunc_est are plotted as a function of r, which is varied from 2-20 in steps of 0.5. The value for dfunc_est is the estimated by the method estimate_dfunc( r ).

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

show_definition(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream) → None

shows the definition of this function, usually the string type of

function and the parameters passed in to the constructor.

C++: core::scoring::func::Func::show_definition(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
2. show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for

this constraint.

C++: core::scoring::func::Func::show_violations(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long