func¶

Bindings for core::scoring::func namespace

class pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc¶

Bases: Func

function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) )

assign(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, : pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc) → pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc¶: C++: core::scoring::func::AmberPeriodicFunc::operator=(const class core::scoring::func::AmberPeriodicFunc &) –> class core::scoring::func::AmberPeriodicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::AmberPeriodicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, x: float) → float¶: C++: core::scoring::func::AmberPeriodicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.AmberPeriodicFunc, x: float) → float¶: C++: core::scoring::func::AmberPeriodicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::AmberPeriodicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::AmberPeriodicFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::AmberPeriodicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::AmberPeriodicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc¶

Bases: Func

function of type y = 0.5 * k * (1 - cos(n * (x - x0) ) )

assign(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, : pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc) → pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc¶: C++: core::scoring::func::CharmmPeriodicFunc::operator=(const class core::scoring::func::CharmmPeriodicFunc &) –> class core::scoring::func::CharmmPeriodicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CharmmPeriodicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, x: float) → float¶: C++: core::scoring::func::CharmmPeriodicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CharmmPeriodicFunc, x: float) → float¶: C++: core::scoring::func::CharmmPeriodicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::CharmmPeriodicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CharmmPeriodicFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::CharmmPeriodicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::CharmmPeriodicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func¶

Bases: Func

Function that allows return of arbitrary FArrays – this time circularized.

assign(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, : pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func) → pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func¶: C++: core::scoring::func::CircularGeneral1D_Func::operator=(const class core::scoring::func::CircularGeneral1D_Func &) –> class core::scoring::func::CircularGeneral1D_Func &

clone(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CircularGeneral1D_Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, x: float) → float¶: C++: core::scoring::func::CircularGeneral1D_Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CircularGeneral1D_Func, x: float) → float¶: C++: core::scoring::func::CircularGeneral1D_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(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CircularGeneral1D_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(std::ostream &) 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(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc¶

Bases: Func

Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints.

assign(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, : pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc¶: C++: core::scoring::func::CircularHarmonicFunc::operator=(const class core::scoring::func::CircularHarmonicFunc &) –> class core::scoring::func::CircularHarmonicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CircularHarmonicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, x: float) → float¶: C++: core::scoring::func::CircularHarmonicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CircularHarmonicFunc, x: float) → float¶: C++: core::scoring::func::CircularHarmonicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::CircularHarmonicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CircularHarmonicFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc) → float¶: C++: core::scoring::func::CircularHarmonicFunc::sd() const –> double

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::CircularHarmonicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

x0(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc) → float¶: C++: core::scoring::func::CircularHarmonicFunc::x0() const –> double

class pyrosetta.rosetta.core.scoring.func.CircularPowerFunc¶

Bases: Func

Generalization of CircularCircularPowerFunc – other exponents allowed.

Operates in radians, like DihedralConstraint.

assign(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.core.scoring.func.Func) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::Func::operator=(const class core::scoring::func::Func &) –> class core::scoring::func::Func &

clone(self: pyrosetta.rosetta.core.scoring.func.CircularPowerFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CircularPowerFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CircularPowerFunc, x: float) → float¶: C++: core::scoring::func::CircularPowerFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CircularPowerFunc, x: float) → float¶: C++: core::scoring::func::CircularPowerFunc::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(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CircularPowerFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CircularPowerFunc::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(std::ostream &) 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(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc¶

Bases: Func

Function that operates in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints.

assign(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, : pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc) → pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc¶: C++: core::scoring::func::CircularSigmoidalFunc::operator=(const class core::scoring::func::CircularSigmoidalFunc &) –> class core::scoring::func::CircularSigmoidalFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CircularSigmoidalFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, x: float) → float¶: C++: core::scoring::func::CircularSigmoidalFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CircularSigmoidalFunc, x: float) → float¶: C++: core::scoring::func::CircularSigmoidalFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::CircularSigmoidalFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CircularSigmoidalFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::CircularSigmoidalFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CircularSplineFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, : pyrosetta.rosetta.core.scoring.func.CircularSplineFunc) → pyrosetta.rosetta.core.scoring.func.CircularSplineFunc¶: C++: core::scoring::func::CircularSplineFunc::operator=(const class core::scoring::func::CircularSplineFunc &) –> class core::scoring::func::CircularSplineFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CircularSplineFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, x: float) → float¶: C++: core::scoring::func::CircularSplineFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CircularSplineFunc, x: float) → float¶: C++: core::scoring::func::CircularSplineFunc::func(const double) const –> double

get_weight(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc) → float¶: C++: core::scoring::func::CircularSplineFunc::get_weight() –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::CircularSplineFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CircularSplineFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::CircularSplineFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::CircularSplineFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

train(self: pyrosetta.rosetta.core.scoring.func.CircularSplineFunc, energies_in: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: core::scoring::func::CircularSplineFunc::train(class utility::vector1<double, class std::allocator<double> >) –> void

class pyrosetta.rosetta.core.scoring.func.ConformationXYZ¶

Bases: XYZ_Func

assign(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) → pyrosetta.rosetta.core.scoring.func.XYZ_Func¶: C++: core::scoring::func::XYZ_Func::operator=(const class core::scoring::func::XYZ_Func &) –> class core::scoring::func::XYZ_Func &

residue(self: pyrosetta.rosetta.core.scoring.func.ConformationXYZ, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::scoring::func::ConformationXYZ::residue(unsigned long) const –> const class core::conformation::Residue &

class pyrosetta.rosetta.core.scoring.func.ConstantFunc¶

Bases: Func

Derived class of class Func representing a Constant distribution with a user-specified mean and standard deviation.

assign(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, : pyrosetta.rosetta.core.scoring.func.ConstantFunc) → pyrosetta.rosetta.core.scoring.func.ConstantFunc¶: C++: core::scoring::func::ConstantFunc::operator=(const class core::scoring::func::ConstantFunc &) –> class core::scoring::func::ConstantFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this ConstantFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, : float) → float¶

Returns the value of the first derivative of this ConstantFunc at distance x.

C++: core::scoring::func::ConstantFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.ConstantFunc, : float) → float¶

Returns the value of this ConstantFunc evaluated at distance x.

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

read_data(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::ConstantFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::ConstantFunc::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(std::ostream &) const –> void

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

show the definition of this ConstantFunc to the specified output stream.

C++: core::scoring::func::ConstantFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.CountViolFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, : pyrosetta.rosetta.core.scoring.func.CountViolFunc) → pyrosetta.rosetta.core.scoring.func.CountViolFunc¶: C++: core::scoring::func::CountViolFunc::operator=(const class core::scoring::func::CountViolFunc &) –> class core::scoring::func::CountViolFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::CountViolFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, x: float) → float¶: C++: core::scoring::func::CountViolFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.CountViolFunc, x: float) → float¶: C++: core::scoring::func::CountViolFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::CountViolFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::CountViolFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, 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::CountViolFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc, 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::CountViolFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

viols(self: pyrosetta.rosetta.core.scoring.func.CountViolFunc) → int¶: C++: core::scoring::func::CountViolFunc::viols() const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.EtableFunc¶

Bases: Func

Class for representing arbitrarily defined functions.

assign(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, : pyrosetta.rosetta.core.scoring.func.EtableFunc) → pyrosetta.rosetta.core.scoring.func.EtableFunc¶: C++: core::scoring::func::EtableFunc::operator=(const class core::scoring::func::EtableFunc &) –> class core::scoring::func::EtableFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.EtableFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this EtableFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, x: float) → float¶

Returns the value of the first derivative of this EtableFunc at distance x.

C++: core::scoring::func::EtableFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.EtableFunc, x: float) → float¶

Returns the value of this EtableFunc evaluated at distance x.

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

read_data(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::EtableFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::EtableFunc::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(std::ostream &) const –> void

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

show the definitio of this EtableFunc to the specified output stream.

C++: core::scoring::func::EtableFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.FadeFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, : pyrosetta.rosetta.core.scoring.func.FadeFunc) → pyrosetta.rosetta.core.scoring.func.FadeFunc¶: C++: core::scoring::func::FadeFunc::operator=(const class core::scoring::func::FadeFunc &) –> class core::scoring::func::FadeFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.FadeFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::FadeFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

cutoff_lower(*args, **kwargs)¶

Overloaded function.

cutoff_lower(self: pyrosetta.rosetta.core.scoring.func.FadeFunc) -> float

C++: core::scoring::func::FadeFunc::cutoff_lower() const –> double

cutoff_lower(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, x: float) -> None

C++: core::scoring::func::FadeFunc::cutoff_lower(double) –> void

cutoff_upper(*args, **kwargs)¶

Overloaded function.

cutoff_upper(self: pyrosetta.rosetta.core.scoring.func.FadeFunc) -> float

C++: core::scoring::func::FadeFunc::cutoff_upper() const –> double

cutoff_upper(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, x: float) -> None

C++: core::scoring::func::FadeFunc::cutoff_upper(double) –> void

dfunc(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, x: float) → float¶: C++: core::scoring::func::FadeFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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

fade_zone(*args, **kwargs)¶

Overloaded function.

fade_zone(self: pyrosetta.rosetta.core.scoring.func.FadeFunc) -> float

C++: core::scoring::func::FadeFunc::fade_zone() const –> double

fade_zone(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, x: float) -> None

C++: core::scoring::func::FadeFunc::fade_zone(double) –> void

func(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, x: float) → float¶: C++: core::scoring::func::FadeFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::FadeFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::FadeFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::FadeFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.FadeFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::FadeFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, : pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc¶: C++: core::scoring::func::FlatHarmonicFunc::operator=(const class core::scoring::func::FlatHarmonicFunc &) –> class core::scoring::func::FlatHarmonicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::FlatHarmonicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, x: float) → float¶: C++: core::scoring::func::FlatHarmonicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.FlatHarmonicFunc, x: float) → float¶: C++: core::scoring::func::FlatHarmonicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::FlatHarmonicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::FlatHarmonicFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(*args, **kwargs)¶

Overloaded function.

sd(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc) -> float

C++: core::scoring::func::FlatHarmonicFunc::sd() const –> double

sd(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, sd: float) -> None

C++: core::scoring::func::FlatHarmonicFunc::sd(double) –> void

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::FlatHarmonicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::FlatHarmonicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

tol(*args, **kwargs)¶

Overloaded function.

tol(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc) -> float

C++: core::scoring::func::FlatHarmonicFunc::tol() const –> double

tol(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, tol: float) -> None

C++: core::scoring::func::FlatHarmonicFunc::tol(double) –> void

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc) -> float

C++: core::scoring::func::FlatHarmonicFunc::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc, x: float) -> None

C++: core::scoring::func::FlatHarmonicFunc::x0(double) –> void

class pyrosetta.rosetta.core.scoring.func.FourPointsFunc¶

Bases: XYZ_Func

A simple class that represents the coordinates of four points, pretending that they all belong to residue 1. The residue() method is not implemented and cause a utility_exit.

assign(self: pyrosetta.rosetta.core.scoring.func.FourPointsFunc, : pyrosetta.rosetta.core.scoring.func.FourPointsFunc) → pyrosetta.rosetta.core.scoring.func.FourPointsFunc¶: C++: core::scoring::func::FourPointsFunc::operator=(const class core::scoring::func::FourPointsFunc &) –> class core::scoring::func::FourPointsFunc &

residue(self: pyrosetta.rosetta.core.scoring.func.FourPointsFunc, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::scoring::func::FourPointsFunc::residue(unsigned long) const –> const class core::conformation::Residue &

xyz(self: pyrosetta.rosetta.core.scoring.func.FourPointsFunc, atomid: int, coord: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

set the coordinate for one of the four atoms

C++: core::scoring::func::FourPointsFunc::xyz(unsigned long, const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.core.scoring.func.Func¶

Bases: pybind11_object

Func is an abstract base class representing a function used to define constraints, in which func(r) gives the constraint score for the given value r.

assign(self: pyrosetta.rosetta.core.scoring.func.Func, : pyrosetta.rosetta.core.scoring.func.Func) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::Func::operator=(const class core::scoring::func::Func &) –> class core::scoring::func::Func &

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

This method must return a deep copy of this %Func, meaning if this %Func holds pointers: to other %Func objects, that it must clone those %Func objects as well.

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.Func, : float) → float¶

Returns a value representing the derivative of this function: evaluated at a given point.

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

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.Func, : float) → float¶

Returns a value representing this function evaluated at a given: point.

C++: core::scoring::func::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(std::istream &) –> void

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

Does the input Func, “other”, have the same type as me? Necessary for the: equality operator to function correctly. All derived Func classes must implement this function.

C++: core::scoring::func::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(std::ostream &) 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(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.FuncFactory¶

Bases: pybind11_object

add_type(self: pyrosetta.rosetta.core.scoring.func.FuncFactory, type_name: str, new_func: pyrosetta.rosetta.core.scoring.func.Func) → None¶: C++: core::scoring::func::FuncFactory::add_type(std::string, class std::shared_ptr<class core::scoring::func::Func>) –> void

assign(self: pyrosetta.rosetta.core.scoring.func.FuncFactory, : pyrosetta.rosetta.core.scoring.func.FuncFactory) → pyrosetta.rosetta.core.scoring.func.FuncFactory¶: C++: core::scoring::func::FuncFactory::operator=(const class core::scoring::func::FuncFactory &) –> class core::scoring::func::FuncFactory &

new_func(self: pyrosetta.rosetta.core.scoring.func.FuncFactory, type: str) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::FuncFactory::new_func(const std::string &) const –> class std::shared_ptr<class core::scoring::func::Func>

class pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc¶: C++: core::scoring::func::GaussianChainDoubleFunc::operator=(const class core::scoring::func::GaussianChainDoubleFunc &) –> class core::scoring::func::GaussianChainDoubleFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainDoubleFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainDoubleFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.GaussianChainDoubleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainDoubleFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainDoubleFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainDoubleFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainDoubleFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianChainFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainFunc¶: C++: core::scoring::func::GaussianChainFunc::operator=(const class core::scoring::func::GaussianChainFunc &) –> class core::scoring::func::GaussianChainFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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

force_combined_gaussian_approximation(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc) → bool¶: C++: core::scoring::func::GaussianChainFunc::force_combined_gaussian_approximation() const –> bool

func(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

set_force_combined_gaussian_approximation(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, setting: bool) → None¶: C++: core::scoring::func::GaussianChainFunc::set_force_combined_gaussian_approximation(const bool &) –> void

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc¶: C++: core::scoring::func::GaussianChainGeneralFunc::operator=(const class core::scoring::func::GaussianChainGeneralFunc &) –> class core::scoring::func::GaussianChainGeneralFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainGeneralFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainGeneralFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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(*args, **kwargs)¶

Overloaded function.

func(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, z: float, calc_deriv: bool, deriv: float) -> float

C++: core::scoring::func::GaussianChainGeneralFunc::func(const double, const bool, double &) const –> double

func(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, x: float) -> float

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

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainGeneralFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainGeneralFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainGeneralFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::operator=(const class core::scoring::func::GaussianChainQuadrupleFunc &) –> class core::scoring::func::GaussianChainQuadrupleFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.GaussianChainQuadrupleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainQuadrupleFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc¶: C++: core::scoring::func::GaussianChainSingleFunc::operator=(const class core::scoring::func::GaussianChainSingleFunc &) –> class core::scoring::func::GaussianChainSingleFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainSingleFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainSingleFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.GaussianChainSingleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainSingleFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainSingleFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainSingleFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainSingleFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc, : pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc) → pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc¶: C++: core::scoring::func::GaussianChainTripleFunc::operator=(const class core::scoring::func::GaussianChainTripleFunc &) –> class core::scoring::func::GaussianChainTripleFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::GaussianChainTripleFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainTripleFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.GaussianChainTripleFunc, x: float) → float¶: C++: core::scoring::func::GaussianChainTripleFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::GaussianChainTripleFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianChainTripleFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::GaussianChainTripleFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.GaussianFunc¶

Bases: Func

Derived class of class Func representing a Gaussian distribution with a user-specified mean and standard deviation.

assign(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, : pyrosetta.rosetta.core.scoring.func.GaussianFunc) → pyrosetta.rosetta.core.scoring.func.GaussianFunc¶: C++: core::scoring::func::GaussianFunc::operator=(const class core::scoring::func::GaussianFunc &) –> class core::scoring::func::GaussianFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this GaussianFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, x: float) → float¶

Returns the value of the first derivative of this GaussianFunc at distance x.

C++: core::scoring::func::GaussianFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.GaussianFunc, x: float) → float¶

Returns the value of this GaussianFunc evaluated at distance x.

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

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

The parameters are:

Initializes this GaussianFunc from the given istream. An example of the type of string from which the istream should be constructed is: “GAUSSIANFUNC 19.396 7.643”. The interpretation is to create initialize this GaussianFunc object with the following parameters: - mean 19.396 - sd 7.643

C++: core::scoring::func::GaussianFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::GaussianFunc::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(std::ostream &) const –> void

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

show the definitio of this GaussianFunc to the specified output stream.

C++: core::scoring::func::GaussianFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.HarmonicFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, : pyrosetta.rosetta.core.scoring.func.HarmonicFunc) → pyrosetta.rosetta.core.scoring.func.HarmonicFunc¶: C++: core::scoring::func::HarmonicFunc::operator=(const class core::scoring::func::HarmonicFunc &) –> class core::scoring::func::HarmonicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::HarmonicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, x: float) → float¶: C++: core::scoring::func::HarmonicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.HarmonicFunc, x: float) → float¶: C++: core::scoring::func::HarmonicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::HarmonicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::HarmonicFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(*args, **kwargs)¶

Overloaded function.

sd(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc) -> float

C++: core::scoring::func::HarmonicFunc::sd() const –> double

sd(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, sd: float) -> None

C++: core::scoring::func::HarmonicFunc::sd(double) –> void

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::HarmonicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::HarmonicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc) -> float

C++: core::scoring::func::HarmonicFunc::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.HarmonicFunc, x: float) -> None

C++: core::scoring::func::HarmonicFunc::x0(double) –> void

class pyrosetta.rosetta.core.scoring.func.IdentityFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, : pyrosetta.rosetta.core.scoring.func.IdentityFunc) → pyrosetta.rosetta.core.scoring.func.IdentityFunc¶: C++: core::scoring::func::IdentityFunc::operator=(const class core::scoring::func::IdentityFunc &) –> class core::scoring::func::IdentityFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::IdentityFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, x: float) → float¶: C++: core::scoring::func::IdentityFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.IdentityFunc, x: float) → float¶: C++: core::scoring::func::IdentityFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::IdentityFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::IdentityFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::IdentityFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.IdentityFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::IdentityFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.KarplusFunc¶

Bases: Func

Function that evaluates a J-coupling from dihedral angles in radians, for applications like DihedralConstraint. Prevents discontinuities at 0/360 or -180/180 degrees for dihedral constraints.

assign(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, : pyrosetta.rosetta.core.scoring.func.KarplusFunc) → pyrosetta.rosetta.core.scoring.func.KarplusFunc¶: C++: core::scoring::func::KarplusFunc::operator=(const class core::scoring::func::KarplusFunc &) –> class core::scoring::func::KarplusFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::KarplusFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, x: float) → float¶: C++: core::scoring::func::KarplusFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.KarplusFunc, x: float) → float¶: C++: core::scoring::func::KarplusFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::KarplusFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::KarplusFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::KarplusFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, : pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction¶: C++: core::scoring::func::LinearPenaltyFunction::operator=(const class core::scoring::func::LinearPenaltyFunction &) –> class core::scoring::func::LinearPenaltyFunction &

clone(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::LinearPenaltyFunction::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, x: float) → float¶: C++: core::scoring::func::LinearPenaltyFunction::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.LinearPenaltyFunction, x: float) → float¶: C++: core::scoring::func::LinearPenaltyFunction::func(const double) const –> double

get_half_width(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → float¶: C++: core::scoring::func::LinearPenaltyFunction::get_half_width() const –> double

get_slope(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → float¶: C++: core::scoring::func::LinearPenaltyFunction::get_slope() const –> double

get_well_depth(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → float¶: C++: core::scoring::func::LinearPenaltyFunction::get_well_depth() const –> double

get_x_middle(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction) → float¶: C++: core::scoring::func::LinearPenaltyFunction::get_x_middle() const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::LinearPenaltyFunction::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::LinearPenaltyFunction::same_type_as_me(const class core::scoring::func::Func &) const –> bool

set_half_width(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, half_width: float) → None¶: C++: core::scoring::func::LinearPenaltyFunction::set_half_width(double) –> void

set_slope(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, slope: float) → None¶: C++: core::scoring::func::LinearPenaltyFunction::set_slope(double) –> void

set_well_depth(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, well_depth: float) → None¶: C++: core::scoring::func::LinearPenaltyFunction::set_well_depth(double) –> void

set_x_middle(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, x: float) → None¶: C++: core::scoring::func::LinearPenaltyFunction::set_x_middle(double) –> void

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::LinearPenaltyFunction::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::LinearPenaltyFunction::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, : pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc¶: C++: core::scoring::func::MinMultiHarmonicFunc::operator=(const class core::scoring::func::MinMultiHarmonicFunc &) –> class core::scoring::func::MinMultiHarmonicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::MinMultiHarmonicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, x: float) → float¶: C++: core::scoring::func::MinMultiHarmonicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.MinMultiHarmonicFunc, x: float) → float¶: C++: core::scoring::func::MinMultiHarmonicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::MinMultiHarmonicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::MinMultiHarmonicFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

sd(*args, **kwargs)¶

Overloaded function.

sd(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, n: int) -> float

C++: core::scoring::func::MinMultiHarmonicFunc::sd(int) const –> double

sd(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, n: int, sd: float) -> None

C++: core::scoring::func::MinMultiHarmonicFunc::sd(int, double) –> void

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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::MinMultiHarmonicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::MinMultiHarmonicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, n: int) -> float

C++: core::scoring::func::MinMultiHarmonicFunc::x0(int) const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc, n: int, x: float) -> None

C++: core::scoring::func::MinMultiHarmonicFunc::x0(int, double) –> void

class pyrosetta.rosetta.core.scoring.func.MixtureFunc¶

Bases: Func

Derived class of class Func representing a Mixture of several distinct functions. The function is of the form ln( g(r) / h(r) ), where g(r) is a mixture of a Gaussian and Exponential distributions, and h(r) is a Gaussian distribution. See methods and implementation for more information.

assign(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, : pyrosetta.rosetta.core.scoring.func.MixtureFunc) → pyrosetta.rosetta.core.scoring.func.MixtureFunc¶: C++: core::scoring::func::MixtureFunc::operator=(const class core::scoring::func::MixtureFunc &) –> class core::scoring::func::MixtureFunc &

calc_kl_divergence(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc) → float¶

Calculates the K-L divergence between the inferred and background distributions.

C++: core::scoring::func::MixtureFunc::calc_kl_divergence() const –> double

clone(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this MixtureFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, x: float) → float¶

Returns the value of the first derivative of this MixtureFunc at distance x.

C++: core::scoring::func::MixtureFunc::dfunc(const double) const –> double

dfunc_component(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, x: float, g: float, h: float, g_prime: float, h_prime: float) → float¶

Function that’s used for debugging. Given x, this calculates: g(x), h(x), g’(x) and h’(x).

C++: core::scoring::func::MixtureFunc::dfunc_component(const double, double &, double &, double &, double &) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.MixtureFunc, x: float) → float¶

Returns the value of this MixtureFunc evaluated at distance x.

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

func_(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, x: float) → float¶

Returns the value of this MixtureFunc evaluated at distance x.

C++: core::scoring::func::MixtureFunc::func_(double) const –> double

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

The parameters are:

Initializes this MixtureFunc from the given istream. An example of the type of string from which the istream should be constructed is: “MIXTUREFUNC 6.9734 3.598 0.222 0.872 19.396 7.643”. The interpretation is to create initialize this MixtureFunc object with the following parameters: - anchor 6.9734 - gaussian_param 3.598 - exp_param 0.222 - mixture_param 0.872 - bg_mean 19.396 - bg_sd 7.643

C++: core::scoring::func::MixtureFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::MixtureFunc::same_type_as_me(const class core::scoring::func::Func &) const –> bool

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

Prints this MixtureFunc to the given ostream.

C++: core::scoring::func::MixtureFunc::show(std::ostream &) const –> void

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

show the definitio of this MixtureFunc to the specified output stream.

C++: core::scoring::func::MixtureFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.PeriodicFunc¶

Bases: Func

function of type y = ( k * cos(n * (x - x0) ) ) + C

assign(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, : pyrosetta.rosetta.core.scoring.func.PeriodicFunc) → pyrosetta.rosetta.core.scoring.func.PeriodicFunc¶: C++: core::scoring::func::PeriodicFunc::operator=(const class core::scoring::func::PeriodicFunc &) –> class core::scoring::func::PeriodicFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::PeriodicFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, x: float) → float¶: C++: core::scoring::func::PeriodicFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.PeriodicFunc, x: float) → float¶: C++: core::scoring::func::PeriodicFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::PeriodicFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::PeriodicFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::PeriodicFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::PeriodicFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.ResiduePairXYZ¶

Bases: XYZ_Func

assign(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) → pyrosetta.rosetta.core.scoring.func.XYZ_Func¶: C++: core::scoring::func::XYZ_Func::operator=(const class core::scoring::func::XYZ_Func &) –> class core::scoring::func::XYZ_Func &

residue(self: pyrosetta.rosetta.core.scoring.func.ResiduePairXYZ, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::scoring::func::ResiduePairXYZ::residue(unsigned long) const –> const class core::conformation::Residue &

class pyrosetta.rosetta.core.scoring.func.ResidueXYZ¶

Bases: XYZ_Func

assign(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) → pyrosetta.rosetta.core.scoring.func.XYZ_Func¶: C++: core::scoring::func::XYZ_Func::operator=(const class core::scoring::func::XYZ_Func &) –> class core::scoring::func::XYZ_Func &

residue(self: pyrosetta.rosetta.core.scoring.func.ResidueXYZ, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::scoring::func::ResidueXYZ::residue(unsigned long) const –> const class core::conformation::Residue &

class pyrosetta.rosetta.core.scoring.func.SOGFunc¶

Bases: Func

Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation.

assign(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, : pyrosetta.rosetta.core.scoring.func.SOGFunc) → pyrosetta.rosetta.core.scoring.func.SOGFunc¶: C++: core::scoring::func::SOGFunc::operator=(const class core::scoring::func::SOGFunc &) –> class core::scoring::func::SOGFunc &

check_bounds(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, x: float, val: float) → None¶: C++: core::scoring::func::SOGFunc::check_bounds(const double, const double) const –> void

clone(self: pyrosetta.rosetta.core.scoring.func.SOGFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this SOGFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, x: float) → float¶

Returns the value of the first derivative of this SOGFunc at distance x.

C++: core::scoring::func::SOGFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SOGFunc, x: float) → float¶

Returns the value of this SOGFunc evaluated at distance x.

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

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

Initializes this SOGFunc from the given istream.

The parameters are:

Initializes this SOGFunc from the given istream. An example of the type of string from which the istream should be constructed is: “SOGFUNC 2 19.396 7.643 0.4 17.312 2.4 0.6”. The interpretation is to create initialize this SOGFunc object with the following parameters: - one Gaussian function with mean 19.396 and sd 7.643, weighted with a weight of 0.4 - another Gaussian function with mean of 17.312 and sd 2.4, with a weight of 0.6. Weights need not add up to 1, but many times they will.

C++: core::scoring::func::SOGFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SOGFunc::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(std::ostream &) const –> void

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

show the definition of this SOGFunc to the specified output stream.

C++: core::scoring::func::SOGFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl¶

Bases: pybind11_object

Derived class of class Func representing a SOG distribution with a user-specified mean and standard deviation.

assign(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, : pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl¶: C++: core::scoring::func::SOGFunc_Impl::operator=(const class core::scoring::func::SOGFunc_Impl &) –> class core::scoring::func::SOGFunc_Impl &

check_bounds(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, x: float, val: float) → None¶: C++: core::scoring::func::SOGFunc_Impl::check_bounds(const double, const double) const –> void

clear_(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → None¶: C++: core::scoring::func::SOGFunc_Impl::clear_() –> void

dfunc(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, x: float) → float¶

Returns the value of the first derivative of this SOGFunc_Impl at distance x.

C++: core::scoring::func::SOGFunc_Impl::dfunc(const double) const –> double

func(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, x: float) → float¶

Returns the value of this SOGFunc_Impl evaluated at distance x.

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

get_alt_score_(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, x: float) → float¶: C++: core::scoring::func::SOGFunc_Impl::get_alt_score_(const double) const –> double

prob_sum_of_gaussians(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, x: float) → float¶: C++: core::scoring::func::SOGFunc_Impl::prob_sum_of_gaussians(const double) const –> double

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

Initializes this SOGFunc_Impl from the given istream.

The parameters are:

Initializes this SOGFunc_Impl from the given istream. An example of the type of string from which the istream should be constructed is: “SOGFUNC 2 19.396 7.643 0.4 17.312 2.4 0.6”. The interpretation is to create initialize this SOGFunc_Impl object with the following parameters: - one Gaussian function with mean 19.396 and sd 7.643, weighted with a weight of 0.4 - another Gaussian function with mean of 17.312 and sd 2.4, with a weight of 0.6. Weights need not add up to 1, but many times they will.

C++: core::scoring::func::SOGFunc_Impl::read_data(std::istream &) –> void

renormalize_weights(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → None¶: C++: core::scoring::func::SOGFunc_Impl::renormalize_weights() –> void

set_defaults(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → None¶: C++: core::scoring::func::SOGFunc_Impl::set_defaults() –> void

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

show the definitio of this SOGFunc_Impl to the specified output stream.

C++: core::scoring::func::SOGFunc_Impl::show_definition(std::ostream &) const –> void

smooth_to_zero(*args, **kwargs)¶

Overloaded function.

smooth_to_zero(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, setting: bool) -> None

C++: core::scoring::func::SOGFunc_Impl::smooth_to_zero(const bool) –> void

smooth_to_zero(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) -> bool

C++: core::scoring::func::SOGFunc_Impl::smooth_to_zero() const –> bool

sog_cst_param(*args, **kwargs)¶

Overloaded function.

sog_cst_param(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) -> float

C++: core::scoring::func::SOGFunc_Impl::sog_cst_param() const –> double

sog_cst_param(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, param: float) -> None

C++: core::scoring::func::SOGFunc_Impl::sog_cst_param(const double) –> void

upper_bound(*args, **kwargs)¶

Overloaded function.

upper_bound(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, r: float) -> None

C++: core::scoring::func::SOGFunc_Impl::upper_bound(const double) –> void

upper_bound(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) -> float

C++: core::scoring::func::SOGFunc_Impl::upper_bound() const –> double

upper_bound_score(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → float¶: C++: core::scoring::func::SOGFunc_Impl::upper_bound_score() const –> double

class pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, : pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc) → pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc¶: C++: core::scoring::func::ScalarWeightedFunc::operator=(const class core::scoring::func::ScalarWeightedFunc &) –> class core::scoring::func::ScalarWeightedFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::ScalarWeightedFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, x: float) → float¶: C++: core::scoring::func::ScalarWeightedFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.ScalarWeightedFunc, x: float) → float¶: C++: core::scoring::func::ScalarWeightedFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::ScalarWeightedFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::ScalarWeightedFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::ScalarWeightedFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::ScalarWeightedFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SigmoidFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, : pyrosetta.rosetta.core.scoring.func.SigmoidFunc) → pyrosetta.rosetta.core.scoring.func.SigmoidFunc¶: C++: core::scoring::func::SigmoidFunc::operator=(const class core::scoring::func::SigmoidFunc &) –> class core::scoring::func::SigmoidFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::SigmoidFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, x: float) → float¶: C++: core::scoring::func::SigmoidFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SigmoidFunc, x: float) → float¶: C++: core::scoring::func::SigmoidFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SigmoidFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SigmoidFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::SigmoidFunc::show_definition(std::ostream &) const –> void

show_violations(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) → int¶: C++: core::scoring::func::SigmoidFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

slope(*args, **kwargs)¶

Overloaded function.

slope(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc) -> float

C++: core::scoring::func::SigmoidFunc::slope() const –> double

slope(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, slope: float) -> None

C++: core::scoring::func::SigmoidFunc::slope(double) –> void

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc) -> float

C++: core::scoring::func::SigmoidFunc::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.SigmoidFunc, x: float) -> None

C++: core::scoring::func::SigmoidFunc::x0(double) –> void

class pyrosetta.rosetta.core.scoring.func.SkipViolFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, : pyrosetta.rosetta.core.scoring.func.SkipViolFunc) → pyrosetta.rosetta.core.scoring.func.SkipViolFunc¶: C++: core::scoring::func::SkipViolFunc::operator=(const class core::scoring::func::SkipViolFunc &) –> class core::scoring::func::SkipViolFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::SkipViolFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, x: float) → float¶: C++: core::scoring::func::SkipViolFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SkipViolFunc, x: float) → float¶: C++: core::scoring::func::SkipViolFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SkipViolFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SkipViolFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, 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::SkipViolFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc, 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::SkipViolFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

viols(self: pyrosetta.rosetta.core.scoring.func.SkipViolFunc) → int¶: C++: core::scoring::func::SkipViolFunc::viols() const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SmoothStepFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc, : pyrosetta.rosetta.core.scoring.func.SmoothStepFunc) → pyrosetta.rosetta.core.scoring.func.SmoothStepFunc¶: C++: core::scoring::func::SmoothStepFunc::operator=(const class core::scoring::func::SmoothStepFunc &) –> class core::scoring::func::SmoothStepFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this SmoothStepFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc, x: float) → float¶: C++: core::scoring::func::SmoothStepFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SmoothStepFunc, x: float) → float¶: C++: core::scoring::func::SmoothStepFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SmoothStepFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SmoothStepFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.SmoothStepFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::SmoothStepFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SoedingFunc¶

Bases: Func

Derived class of class Func representing a Soeding distribution with a user-specified mean and standard deviation.

assign(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, : pyrosetta.rosetta.core.scoring.func.SoedingFunc) → pyrosetta.rosetta.core.scoring.func.SoedingFunc¶: C++: core::scoring::func::SoedingFunc::operator=(const class core::scoring::func::SoedingFunc &) –> class core::scoring::func::SoedingFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this SoedingFunc

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

compute_func(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, x: float) → float¶: C++: core::scoring::func::SoedingFunc::compute_func(const double) const –> double

dfunc(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, x: float) → float¶

Returns the value of the first derivative of this SoedingFunc at distance x.

C++: core::scoring::func::SoedingFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SoedingFunc, x: float) → float¶

Returns the value of this SoedingFunc evaluated at distance x.

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

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

Initializes this SoedingFunc from the given istream.

C++: core::scoring::func::SoedingFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SoedingFunc::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(std::ostream &) const –> void

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

show the definition of this SoedingFunc to the specified output stream.

C++: core::scoring::func::SoedingFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SplineFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, : pyrosetta.rosetta.core.scoring.func.SplineFunc) → pyrosetta.rosetta.core.scoring.func.SplineFunc¶: C++: core::scoring::func::SplineFunc::operator=(const class core::scoring::func::SplineFunc &) –> class core::scoring::func::SplineFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → pyrosetta.rosetta.core.scoring.func.Func¶

returns a clone of this SplineFunc

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

dfunc(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, x: float) → float¶

Returns the value of the first derivative of this SplineFunc at distance x.

C++: core::scoring::func::SplineFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SplineFunc, x: float) → float¶

Returns the value of this SplineFunc evaluated at distance x.

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

get_KB_description(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → str¶: C++: core::scoring::func::SplineFunc::get_KB_description() const –> const std::string &

get_bin_size(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_bin_size() const –> double

get_bins_vect(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → pyrosetta.rosetta.utility.vector1_double¶: C++: core::scoring::func::SplineFunc::get_bins_vect() const –> const class utility::vector1<double, class std::allocator<double> > &

get_bins_vect_size(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → int¶: C++: core::scoring::func::SplineFunc::get_bins_vect_size() const –> unsigned long

get_exp_val(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶

return SplineFunc member variables

C++: core::scoring::func::SplineFunc::get_exp_val() const –> double

get_filename(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → str¶: C++: core::scoring::func::SplineFunc::get_filename() const –> const std::string &

get_lower_bound_dy(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_lower_bound_dy() const –> double

get_lower_bound_x(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_lower_bound_x() const –> double

get_lower_bound_y(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_lower_bound_y() const –> double

get_potential_vect(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → pyrosetta.rosetta.utility.vector1_double¶: C++: core::scoring::func::SplineFunc::get_potential_vect() const –> const class utility::vector1<double, class std::allocator<double> > &

get_potential_vect_size(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → int¶: C++: core::scoring::func::SplineFunc::get_potential_vect_size() const –> unsigned long

get_upper_bound_dy(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_upper_bound_dy() const –> double

get_upper_bound_x(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_upper_bound_x() const –> double

get_upper_bound_y(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_upper_bound_y() const –> double

get_weight(self: pyrosetta.rosetta.core.scoring.func.SplineFunc) → float¶: C++: core::scoring::func::SplineFunc::get_weight() const –> double

is_approximately_equal(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, other: pyrosetta.rosetta.core.scoring.func.SplineFunc, float_threshold: float) → bool¶

Compare this SplineFunc to another one, and determine whether

the two are equal within some threshold.

The float threshold is used for comparing floating-point values.

C++: core::scoring::func::SplineFunc::is_approximately_equal(const class core::scoring::func::SplineFunc &, const double) const –> bool

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

Initialize this SplineFunc from the given izstream.

Triggers read from disk UNLESS the first entry (filename) is “NONE” (upper or lower case or any mixture). In that case, the spline is read from the rest of the line.

C++: core::scoring::func::SplineFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SplineFunc::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(std::ostream &) const –> void

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

show the definition of this SplineFunc to the specified output stream.

C++: core::scoring::func::SplineFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.SplineFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

show some sort of stringified representation of the violations for this constraint.

C++: core::scoring::func::SplineFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.SquareWell2Func¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, : pyrosetta.rosetta.core.scoring.func.SquareWell2Func) → pyrosetta.rosetta.core.scoring.func.SquareWell2Func¶: C++: core::scoring::func::SquareWell2Func::operator=(const class core::scoring::func::SquareWell2Func &) –> class core::scoring::func::SquareWell2Func &

clone(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::SquareWell2Func::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, x: float) → float¶: C++: core::scoring::func::SquareWell2Func::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SquareWell2Func, x: float) → float¶: C++: core::scoring::func::SquareWell2Func::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SquareWell2Func::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SquareWell2Func::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::SquareWell2Func::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::SquareWell2Func::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

well_depth(*args, **kwargs)¶

Overloaded function.

well_depth(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func) -> float

C++: core::scoring::func::SquareWell2Func::well_depth() const –> double

well_depth(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, well_depth: float) -> None

C++: core::scoring::func::SquareWell2Func::well_depth(double) –> void

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func) -> float

C++: core::scoring::func::SquareWell2Func::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, x: float) -> None

C++: core::scoring::func::SquareWell2Func::x0(double) –> void

x_range(*args, **kwargs)¶

Overloaded function.

x_range(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func) -> float

C++: core::scoring::func::SquareWell2Func::x_range() const –> double

x_range(self: pyrosetta.rosetta.core.scoring.func.SquareWell2Func, x_range: float) -> None

C++: core::scoring::func::SquareWell2Func::x_range(double) –> void

class pyrosetta.rosetta.core.scoring.func.SquareWellFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, : pyrosetta.rosetta.core.scoring.func.SquareWellFunc) → pyrosetta.rosetta.core.scoring.func.SquareWellFunc¶: C++: core::scoring::func::SquareWellFunc::operator=(const class core::scoring::func::SquareWellFunc &) –> class core::scoring::func::SquareWellFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::SquareWellFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, x: float) → float¶: C++: core::scoring::func::SquareWellFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SquareWellFunc, x: float) → float¶: C++: core::scoring::func::SquareWellFunc::func(const double) const –> double

read_data(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SquareWellFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SquareWellFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::SquareWellFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::SquareWellFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

well_depth(*args, **kwargs)¶

Overloaded function.

well_depth(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc) -> float

C++: core::scoring::func::SquareWellFunc::well_depth() const –> double

well_depth(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, well_depth: float) -> None

C++: core::scoring::func::SquareWellFunc::well_depth(double) –> void

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc) -> float

C++: core::scoring::func::SquareWellFunc::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.SquareWellFunc, x: float) -> None

C++: core::scoring::func::SquareWellFunc::x0(double) –> void

class pyrosetta.rosetta.core.scoring.func.SumFunc¶

Bases: Func

add_func(self: pyrosetta.rosetta.core.scoring.func.SumFunc, f: pyrosetta.rosetta.core.scoring.func.Func) → None¶: C++: core::scoring::func::SumFunc::add_func(class std::shared_ptr<class core::scoring::func::Func>) –> void

assign(self: pyrosetta.rosetta.core.scoring.func.SumFunc, : pyrosetta.rosetta.core.scoring.func.SumFunc) → pyrosetta.rosetta.core.scoring.func.SumFunc¶: C++: core::scoring::func::SumFunc::operator=(const class core::scoring::func::SumFunc &) –> class core::scoring::func::SumFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.SumFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::SumFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.SumFunc, x: float) → float¶: C++: core::scoring::func::SumFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.SumFunc, x: float) → float¶: C++: core::scoring::func::SumFunc::func(const double) const –> double

funcs(*args, **kwargs)¶

Overloaded function.

funcs(self: pyrosetta.rosetta.core.scoring.func.SumFunc) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_Func_t

C++: core::scoring::func::SumFunc::funcs() const –> class utility::vector1<class std::shared_ptr<class core::scoring::func::Func>, class std::allocator<class std::shared_ptr<class core::scoring::func::Func> > >

funcs(self: pyrosetta.rosetta.core.scoring.func.SumFunc, funcs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_Func_t) -> None

C++: core::scoring::func::SumFunc::funcs(class utility::vector1<class std::shared_ptr<class core::scoring::func::Func>, class std::allocator<class std::shared_ptr<class core::scoring::func::Func> > >) –> void

read_data(self: pyrosetta.rosetta.core.scoring.func.SumFunc, : pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::SumFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.SumFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::SumFunc::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(std::ostream &) 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(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.TopOutFunc¶

Bases: Func

assign(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, : pyrosetta.rosetta.core.scoring.func.TopOutFunc) → pyrosetta.rosetta.core.scoring.func.TopOutFunc¶: C++: core::scoring::func::TopOutFunc::operator=(const class core::scoring::func::TopOutFunc &) –> class core::scoring::func::TopOutFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::TopOutFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, x: float) → float¶: C++: core::scoring::func::TopOutFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.TopOutFunc, x: float) → float¶: C++: core::scoring::func::TopOutFunc::func(const double) const –> double

limit(*args, **kwargs)¶

Overloaded function.

limit(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc) -> float

C++: core::scoring::func::TopOutFunc::limit() const –> double

limit(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, limit: float) -> None

C++: core::scoring::func::TopOutFunc::limit(double) –> void

read_data(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::func::TopOutFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::TopOutFunc::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(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::func::TopOutFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
show_violations(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int, threshold: float) -> int

C++: core::scoring::func::TopOutFunc::show_violations(std::ostream &, double, unsigned long, double) const –> unsigned long

weight(*args, **kwargs)¶

Overloaded function.

weight(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc) -> float

C++: core::scoring::func::TopOutFunc::weight() const –> double

weight(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, weight: float) -> None

C++: core::scoring::func::TopOutFunc::weight(double) –> void

x0(*args, **kwargs)¶

Overloaded function.

x0(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc) -> float

C++: core::scoring::func::TopOutFunc::x0() const –> double

x0(self: pyrosetta.rosetta.core.scoring.func.TopOutFunc, x: float) -> None

C++: core::scoring::func::TopOutFunc::x0(double) –> void

class pyrosetta.rosetta.core.scoring.func.USOGFunc¶

Bases: Func

Unnormalized, unbounded sum of Gaussians constraint

assign(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, : pyrosetta.rosetta.core.scoring.func.USOGFunc) → pyrosetta.rosetta.core.scoring.func.USOGFunc¶: C++: core::scoring::func::USOGFunc::operator=(const class core::scoring::func::USOGFunc &) –> class core::scoring::func::USOGFunc &

clone(self: pyrosetta.rosetta.core.scoring.func.USOGFunc) → pyrosetta.rosetta.core.scoring.func.Func¶: C++: core::scoring::func::USOGFunc::clone() const –> class std::shared_ptr<class core::scoring::func::Func>

dfunc(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, x: float) → float¶

Returns a value representing the derivative of this function evaluated at a given point

C++: core::scoring::func::USOGFunc::dfunc(const double) const –> double

estimate_dfunc(*args, **kwargs)¶

Overloaded function.

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

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.func.USOGFunc, x: float) → float¶

Returns a value representing this function evaluated at a given point

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

numGaussians(self: pyrosetta.rosetta.core.scoring.func.USOGFunc) → int¶

Returns the number of Gaussian components

C++: core::scoring::func::USOGFunc::numGaussians() const –> unsigned long

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

Initializes this function from the given input stream

C++: core::scoring::func::USOGFunc::read_data(std::istream &) –> void

same_type_as_me(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool¶: C++: core::scoring::func::USOGFunc::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(std::ostream &) const –> void

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

Writes the definition of this function to the specific output stream

C++: core::scoring::func::USOGFunc::show_definition(std::ostream &) const –> void

show_violations(*args, **kwargs)¶

Overloaded function.

show_violations(self: pyrosetta.rosetta.core.scoring.func.Func, out: pyrosetta.rosetta.std.ostream, r: float, verbose_level: int) -> int
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(std::ostream &, double, unsigned long, double) const –> unsigned long

class pyrosetta.rosetta.core.scoring.func.XYZ_Func¶

Bases: pybind11_object

just a simple class that takes an AtomID and returns a Vector (position)

assign(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, : pyrosetta.rosetta.core.scoring.func.XYZ_Func) → pyrosetta.rosetta.core.scoring.func.XYZ_Func¶: C++: core::scoring::func::XYZ_Func::operator=(const class core::scoring::func::XYZ_Func &) –> class core::scoring::func::XYZ_Func &

residue(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue¶: C++: core::scoring::func::XYZ_Func::residue(unsigned long) const –> const class core::conformation::Residue &

pyrosetta.rosetta.core.scoring.func.readValueOrDie(in: pyrosetta.rosetta.std.istream) → float¶

Reads and returns a single floating point value from the specified: input stream, aborting if either the failbit or badbit is flipped.

C++: core::scoring::func::readValueOrDie(std::istream &) –> double