electron_density

Bindings for core::scoring::electron_density namespace

class pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator

creator for the ElectronDensityLoader class

__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.electron_density.ElectronDensityLoaderCreator) → 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.electron_density.ElectronDensityLoaderCreator, : pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator) → pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator

C++: core::scoring::electron_density::ElectronDensityLoaderCreator::operator=(const class core::scoring::electron_density::ElectronDensityLoaderCreator &) –> class core::scoring::electron_density::ElectronDensityLoaderCreator &

create_resource_loader(self: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator) → pyrosetta.rosetta.basic.resource_manager.ResourceLoader

C++: core::scoring::electron_density::ElectronDensityLoaderCreator::create_resource_loader() const –> class std::shared_ptr<class basic::resource_manager::ResourceLoader>

loader_type(self: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityLoaderCreator) → str

C++: core::scoring::electron_density::ElectronDensityLoaderCreator::loader_type() const –> std::string

class pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator

Bases: pyrosetta.rosetta.basic.resource_manager.ResourceOptionsCreator

creator for the ElectronDensityOptions class

__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.electron_density.ElectronDensityOptionsCreator) → 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.electron_density.ElectronDensityOptionsCreator, : pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator) → pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator

C++: core::scoring::electron_density::ElectronDensityOptionsCreator::operator=(const class core::scoring::electron_density::ElectronDensityOptionsCreator &) –> class core::scoring::electron_density::ElectronDensityOptionsCreator &

create_options(self: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator) → pyrosetta.rosetta.basic.resource_manager.ResourceOptions

C++: core::scoring::electron_density::ElectronDensityOptionsCreator::create_options() const –> class std::shared_ptr<class basic::resource_manager::ResourceOptions>

options_type(self: pyrosetta.rosetta.core.scoring.electron_density.ElectronDensityOptionsCreator) → str

C++: core::scoring::electron_density::ElectronDensityOptionsCreator::options_type() const –> std::string

class pyrosetta.rosetta.core.scoring.electron_density.KromerMann

Bases: pybind11_builtins.pybind11_object

__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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.electron_density.KromerMann) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.electron_density.KromerMann, c: float, a1: float, a2: float, a3: float, a4: float, b1: float, b2: float, b3: float, b4: 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__

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).

f0(self: pyrosetta.rosetta.core.scoring.electron_density.KromerMann, S2: float) → float

C++: core::scoring::electron_density::KromerMann::f0(double) –> double

class pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering

Bases: pybind11_builtins.pybind11_object

B(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, k: float) → float

C++: core::scoring::electron_density::OneGaussianScattering::B(double) const –> double

C(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, k: float) → float

C++: core::scoring::electron_density::OneGaussianScattering::C(double) const –> 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__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering) -> None
2. __init__(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, w: float, s: 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__

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).

a(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering) → int

C++: core::scoring::electron_density::OneGaussianScattering::a() const –> int

dk(*args, **kwargs)

Overloaded function.

1. dk(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, B: float) -> float
2. dk(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, B: float, lim: float) -> float

C++: core::scoring::electron_density::OneGaussianScattering::dk(double, double) const –> double

k(*args, **kwargs)

Overloaded function.

1. k(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, B: float) -> float
2. k(self: pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering, B: float, lim: float) -> float

C++: core::scoring::electron_density::OneGaussianScattering::k(double, double) const –> double

pyrosetta.rosetta.core.scoring.electron_density.add_dens_scores_from_cmdline_to_scorefxn(scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

update scorefxn with density scores from commandline

C++: core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.scoring.electron_density.conj_map_times(map_product: ObjexxFCL::FArray3D<std::complex<double> >, mapA: ObjexxFCL::FArray3D<std::complex<double> >, mapB: ObjexxFCL::FArray3D<std::complex<double> >) → None

C++: core::scoring::electron_density::conj_map_times(class ObjexxFCL::FArray3D<struct std::complex<double> > &, const class ObjexxFCL::FArray3D<struct std::complex<double> > &, const class ObjexxFCL::FArray3D<struct std::complex<double> > &) –> void

pyrosetta.rosetta.core.scoring.electron_density.convolute_maps(mapA: ObjexxFCL::FArray3D<double>, mapB: ObjexxFCL::FArray3D<double>) → ObjexxFCL::FArray3D<double>

C++: core::scoring::electron_density::convolute_maps(const class ObjexxFCL::FArray3D<double> &, const class ObjexxFCL::FArray3D<double> &) –> class ObjexxFCL::FArray3D<double>

pyrosetta.rosetta.core.scoring.electron_density.factorsLTE19(X: int) → bool

C++: core::scoring::electron_density::factorsLTE19(int) –> bool

pyrosetta.rosetta.core.scoring.electron_density.factorsLTE5(X: int) → bool

C++: core::scoring::electron_density::factorsLTE5(int) –> bool

pyrosetta.rosetta.core.scoring.electron_density.findSampling(MINSMP: float, NMUL: int) → int

C++: core::scoring::electron_density::findSampling(double, int) –> int

pyrosetta.rosetta.core.scoring.electron_density.findSampling5(MINSMP: float, NMUL: int) → int

C++: core::scoring::electron_density::findSampling5(double, int) –> int

pyrosetta.rosetta.core.scoring.electron_density.getDensityMap(*args, **kwargs)

Overloaded function.

1. getDensityMap() -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity
2. getDensityMap(filename: str) -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity
3. getDensityMap(filename: str, force_reload: bool) -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity

The EDM instance

C++: core::scoring::electron_density::getDensityMap(class std::basic_string<char>, bool) –> class core::scoring::electron_density::ElectronDensity &

pyrosetta.rosetta.core.scoring.electron_density.getDensityMap_legacy(*args, **kwargs)

Overloaded function.

1. getDensityMap_legacy() -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity
2. getDensityMap_legacy(filename: str) -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity
3. getDensityMap_legacy(filename: str, force_reload: bool) -> pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity

The EDM instance

C++: core::scoring::electron_density::getDensityMap_legacy(class std::basic_string<char>, bool) –> class core::scoring::electron_density::ElectronDensity &

pyrosetta.rosetta.core.scoring.electron_density.get_A(elt: str) → pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering

C++: core::scoring::electron_density::get_A(class std::basic_string<char>) –> class core::scoring::electron_density::OneGaussianScattering

pyrosetta.rosetta.core.scoring.electron_density.get_km(elt: str) → pyrosetta.rosetta.core.scoring.electron_density.KromerMann

C++: core::scoring::electron_density::get_km(class std::basic_string<char>) –> class core::scoring::electron_density::KromerMann

pyrosetta.rosetta.core.scoring.electron_density.interp_dspline(*args, **kwargs)

Overloaded function.

1. interp_dspline(coeffs: ObjexxFCL::FArray3D<double>, idxX: pyrosetta.rosetta.numeric.xyzVector_double_t) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::electron_density::interp_dspline(class ObjexxFCL::FArray3D<double> &, const class numeric::xyzVector<double> &) –> class numeric::xyzVector<double>

2. interp_dspline(coeffs: ObjexxFCL::FArray4D<double>, idxX: pyrosetta.rosetta.numeric.xyzVector_double_t, slab: float, gradX: pyrosetta.rosetta.numeric.xyzVector_double_t, gradSlab: float) -> None

C++: core::scoring::electron_density::interp_dspline(class ObjexxFCL::FArray4D<double> &, const class numeric::xyzVector<double> &, double, class numeric::xyzVector<double> &, double &) –> void

pyrosetta.rosetta.core.scoring.electron_density.interp_spline(*args, **kwargs)

Overloaded function.

1. interp_spline(coeffs: ObjexxFCL::FArray3D<double>, idxX: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

spline interpolation with periodic boundaries

C++: core::scoring::electron_density::interp_spline(class ObjexxFCL::FArray3D<double> &, const class numeric::xyzVector<double> &) –> double

2. interp_spline(coeffs: ObjexxFCL::FArray4D<double>, slab: float, idxX: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

4d interpolants

C++: core::scoring::electron_density::interp_spline(class ObjexxFCL::FArray4D<double> &, double, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.core.scoring.electron_density.pos_mod(*args, **kwargs)

Overloaded function.

1. pos_mod(x: float, y: float) -> float

C++: core::scoring::electron_density::pos_mod(float, float) –> float

2. pos_mod(x: int, y: int) -> int

C++: core::scoring::electron_density::pos_mod(int, int) –> int

3. pos_mod(x: float, y: float) -> float

C++: core::scoring::electron_density::pos_mod(double, double) –> double

pyrosetta.rosetta.core.scoring.electron_density.pose_has_nonzero_Bs(pose: pyrosetta.rosetta.core.pose.Pose) → bool

helper function quickly guesses if a pose has non-zero B factors

C++: core::scoring::electron_density::pose_has_nonzero_Bs(const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.scoring.electron_density.spline_coeffs(*args, **kwargs)

Overloaded function.

1. spline_coeffs(data: ObjexxFCL::FArray3D<double>, coeffs: ObjexxFCL::FArray3D<double>) -> None

precompute spline coefficients (float array => double coeffs)

C++: core::scoring::electron_density::spline_coeffs(const class ObjexxFCL::FArray3D<double> &, class ObjexxFCL::FArray3D<double> &) –> void

2. spline_coeffs(data: ObjexxFCL::FArray3D<float>, coeffs: ObjexxFCL::FArray3D<double>) -> None

precompute spline coefficients (double array => double coeffs)

C++: core::scoring::electron_density::spline_coeffs(const class ObjexxFCL::FArray3D<float> &, class ObjexxFCL::FArray3D<double> &) –> void

3. spline_coeffs(data: ObjexxFCL::FArray4D<double>, coeffs: ObjexxFCL::FArray4D<double>) -> None

C++: core::scoring::electron_density::spline_coeffs(const class ObjexxFCL::FArray4D<double> &, class ObjexxFCL::FArray4D<double> &) –> void