func

Bindings for core::scoring::func namespace

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::AmberPeriodicFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, x0_in: float, k_in: float, n_periodic_in: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, arg0: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
2. 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(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::CharmmPeriodicFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, x0_in: float, k_in: float, n_periodic_in: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, arg0: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
2. 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(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::CircularGeneral1D_Func::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, data: ObjexxFCL::FArray1D<double>, xmin: float, xbin: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, filename: str) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func, arg0: pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

function and the parameters passed in to the constructor.

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::CircularHarmonicFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, x0_radians: float, sd_radians: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, x0_radians: float, sd_radians: float, offset: float) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc, arg0: pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

Generalization of CircularCircularPowerFunc – other exponents allowed.

Operates in radians, like DihedralConstraint.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.CircularPowerFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::CircularPowerFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.func.CircularPowerFunc, x0_radians: float, sd_radians: float, power: int, weight: float) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

function and the parameters passed in to the constructor.

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::CircularSigmoidalFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, center_radians: float, width_radians: float, slope_radians: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, center_radians: float, width_radians: float, slope_radians: float, offset: float) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc, arg0: pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::ConstantFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, return_val: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc, arg0: pyrosetta.rosetta.core.scoring.func.ConstantFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.ConstantFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

Class for representing arbitrarily defined functions.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::EtableFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, min_: float, max_: float, stepsize_: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.EtableFunc, arg0: pyrosetta.rosetta.core.scoring.func.EtableFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.EtableFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

__call__(self: pyrosetta.rosetta.core.scoring.func.FourPointsFunc, id: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::func::FourPointsFunc::operator()(const class core::id::AtomID &) const –> const class numeric::xyzVector<double> &

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.func.FourPointsFunc) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_builtins.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

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

Equality operator. Looks for strict equality. Floating-point comparison is the

rule rather than the exception.

C++: core::scoring::func::Func::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.Func, arg0: pyrosetta.rosetta.core.scoring.func.Func) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.Func) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

function and the parameters passed in to the constructor.

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::GaussianFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, mean: float, sd: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc, arg0: pyrosetta.rosetta.core.scoring.func.GaussianFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.GaussianFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::KarplusFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float, arg5: float) -> None

doc

2. __init__(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, A_Hertz: float, B_Hertz: float, C_Hertz: float, Dphi_radians: float, x0_Hertz: float, sd_Hertz: float, offset: float) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.KarplusFunc, arg0: pyrosetta.rosetta.core.scoring.func.KarplusFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::MixtureFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, anchor: float, gaussian_param: float, exp_param: float, mixture_param: float, bg_mean: float, bg_sd: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc, arg0: pyrosetta.rosetta.core.scoring.func.MixtureFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.MixtureFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::PeriodicFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, x0_in: float, k_in: float, n_periodic_in: float, C_in: float) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, arg0: pyrosetta.rosetta.core.scoring.func.PeriodicFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

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

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

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.func.PeriodicFunc, out: pyrosetta.rosetta.std.ostream, x: float, verbose_level: int) -> int
2. 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(class std::basic_ostream<char> &, double, unsigned long, double) const –> unsigned long

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

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::SOGFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, means: pyrosetta.rosetta.utility.vector1_double, sdevs: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, mean: float, sdev: float) -> None
4. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc, arg0: pyrosetta.rosetta.core.scoring.func.SOGFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

Bases: pybind11_builtins.pybind11_object

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, other: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) → bool

C++: core::scoring::func::SOGFunc_Impl::operator==(const class core::scoring::func::SOGFunc_Impl &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, means: pyrosetta.rosetta.utility.vector1_double, sdevs: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) -> None
3. __init__(self: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl, arg0: pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) const –> void

smooth_to_zero(*args, **kwargs)

Overloaded function.

1. 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

2. 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.

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

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

2. 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.

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

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

2. 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.SoedingFunc

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

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

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::SoedingFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc, arg0: pyrosetta.rosetta.core.scoring.func.SoedingFunc) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.SoedingFunc) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

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

Unnormalized, unbounded sum of Gaussians constraint

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, other: pyrosetta.rosetta.core.scoring.func.Func) → bool

C++: core::scoring::func::USOGFunc::operator==(const class core::scoring::func::Func &) const –> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.func.USOGFunc) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, arg0: float, arg1: float) -> None

doc

3. __init__(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, mean: float, std_dev: float, weight: float) -> None
4. __init__(self: pyrosetta.rosetta.core.scoring.func.USOGFunc, means: pyrosetta.rosetta.utility.vector1_double, std_devs: pyrosetta.rosetta.utility.vector1_double, weights: pyrosetta.rosetta.utility.vector1_double) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

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

inequality operator – simply the negation of the (virtual) equality operator

C++: core::scoring::func::Func::operator!=(const class core::scoring::func::Func &) const –> bool

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.core.scoring.func.Func) → str

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.

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

Estimates the derivative of this function at a given radius by

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

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

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

Estimates the derivative of this function at a given radius by

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

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

func(self: pyrosetta.rosetta.core.scoring.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(class std::basic_istream<char> &) –> 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(class std::basic_ostream<char> &) 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(class std::basic_ostream<char> &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

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

show some sort of stringified representation of the violations for

this constraint.

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

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

Bases: pybind11_builtins.pybind11_object

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

__call__(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func, id: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::func::XYZ_Func::operator()(const class core::id::AtomID &) const –> const class numeric::xyzVector<double> &

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.core.scoring.func.XYZ_Func) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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(class std::basic_istream<char> &) –> double