packing

Bindings for core::scoring::packing namespace

class pyrosetta.rosetta.core.scoring.packing.HolesResult

Bases: pybind11_builtins.pybind11_object

the result class holding the three scores and the per-atom scores

__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.packing.HolesResult) → 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.packing.HolesResult, : pyrosetta.rosetta.core.scoring.packing.HolesResult) → pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::HolesResult::operator=(const class core::scoring::packing::HolesResult &) –> class core::scoring::packing::HolesResult &

pyrosetta.rosetta.core.scoring.packing.compute_dec15_score(pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::packing::compute_dec15_score(const class core::pose::Pose &) –> double

pyrosetta.rosetta.core.scoring.packing.compute_holes_deriv(*args, **kwargs)

Overloaded function.

1. compute_holes_deriv(pose: pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.core.scoring.packing.HolesParams, deriv: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

computes the cartesian space derivative WRT the given params

C++: core::scoring::packing::compute_holes_deriv(const class core::pose::Pose &, const class core::scoring::packing::HolesParams &, class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> class core::scoring::packing::HolesResult

2. compute_holes_deriv(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParams, deriv: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

///

C++: core::scoring::packing::compute_holes_deriv(const class core::pose::Pose &, class core::scoring::packing::PoseBalls &, const class core::scoring::packing::HolesParams &, class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> class core::scoring::packing::HolesResult

pyrosetta.rosetta.core.scoring.packing.compute_holes_deriv_res(*args, **kwargs)

Overloaded function.

1. compute_holes_deriv_res(pose: pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.core.scoring.packing.HolesParamsRes, derivs: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> float

C++: core::scoring::packing::compute_holes_deriv_res(const class core::pose::Pose &, const class core::scoring::packing::HolesParamsRes &, class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> double

2. compute_holes_deriv_res(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParamsRes, derivs: pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t) -> float

C++: core::scoring::packing::compute_holes_deriv_res(const class core::pose::Pose &, const class core::scoring::packing::PoseBalls &, const class core::scoring::packing::HolesParamsRes &, class core::id::AtomID_Map<class numeric::xyzVector<double> > &) –> double

pyrosetta.rosetta.core.scoring.packing.compute_holes_score(*args, **kwargs)

Overloaded function.

1. compute_holes_score(pose: pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.core.scoring.packing.HolesParams) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

if you have custom parameters, or want per-atom scores for a specific score

result goes into the “score” field

C++: core::scoring::packing::compute_holes_score(const class core::pose::Pose &, const class core::scoring::packing::HolesParams &) –> class core::scoring::packing::HolesResult

2. compute_holes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParams) -> pyrosetta.rosetta.core.scoring.packing.HolesResult
3. compute_holes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParams, use_cached_surfs: bool) -> pyrosetta.rosetta.core.scoring.packing.HolesResult
4. compute_holes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParams, use_cached_surfs: bool, cmd: str) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::compute_holes_score(const class core::pose::Pose &, class core::scoring::packing::PoseBalls &, const class core::scoring::packing::HolesParams &, bool, class std::basic_string<char>) –> class core::scoring::packing::HolesResult

5. compute_holes_score(pose: pyrosetta.rosetta.core.pose.Pose, cmd: str) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::compute_holes_score(const class core::pose::Pose &, const class std::basic_string<char> &) –> class core::scoring::packing::HolesResult

pyrosetta.rosetta.core.scoring.packing.compute_holes_score_res(*args, **kwargs)

Overloaded function.

1. compute_holes_score_res(pose: pyrosetta.rosetta.core.pose.Pose, params: pyrosetta.rosetta.core.scoring.packing.HolesParamsRes) -> float

C++: core::scoring::packing::compute_holes_score_res(const class core::pose::Pose &, const class core::scoring::packing::HolesParamsRes &) –> double

2. compute_holes_score_res(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, params: pyrosetta.rosetta.core.scoring.packing.HolesParamsRes) -> float

C++: core::scoring::packing::compute_holes_score_res(const class core::pose::Pose &, const class core::scoring::packing::PoseBalls &, const class core::scoring::packing::HolesParamsRes &) –> double

pyrosetta.rosetta.core.scoring.packing.compute_rosettaholes_score(*args, **kwargs)

Overloaded function.

1. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

for the standard scores

C++: core::scoring::packing::compute_rosettaholes_score(const class core::pose::Pose &) –> class core::scoring::packing::HolesResult

2. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, resl_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec15_params: pyrosetta.rosetta.core.scoring.packing.HolesParams) -> pyrosetta.rosetta.core.scoring.packing.HolesResult
3. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, resl_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec15_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, use_cached_surfs: bool) -> pyrosetta.rosetta.core.scoring.packing.HolesResult
4. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls, resl_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec15_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, use_cached_surfs: bool, cmd: str) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::compute_rosettaholes_score(const class core::pose::Pose &, class core::scoring::packing::PoseBalls &, const class core::scoring::packing::HolesParams &, const class core::scoring::packing::HolesParams &, const class core::scoring::packing::HolesParams &, bool, class std::basic_string<char>) –> class core::scoring::packing::HolesResult

5. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose, pb: pyrosetta.rosetta.core.scoring.packing.PoseBalls) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::compute_rosettaholes_score(const class core::pose::Pose &, class core::scoring::packing::PoseBalls &) –> class core::scoring::packing::HolesResult

6. compute_rosettaholes_score(pose: pyrosetta.rosetta.core.pose.Pose, resl_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec_params: pyrosetta.rosetta.core.scoring.packing.HolesParams, dec15_params: pyrosetta.rosetta.core.scoring.packing.HolesParams) -> pyrosetta.rosetta.core.scoring.packing.HolesResult

C++: core::scoring::packing::compute_rosettaholes_score(const class core::pose::Pose &, const class core::scoring::packing::HolesParams &, const class core::scoring::packing::HolesParams &, const class core::scoring::packing::HolesParams &) –> class core::scoring::packing::HolesResult

pyrosetta.rosetta.core.scoring.packing.get_surf_tot(pose: pyrosetta.rosetta.core.pose.Pose, probe_radius: float) → float

C++: core::scoring::packing::get_surf_tot(const class core::pose::Pose &, const double) –> double

pyrosetta.rosetta.core.scoring.packing.get_surf_vol(*args, **kwargs)

Overloaded function.

1. get_surf_vol(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.packing.SurfVol
2. get_surf_vol(pose: pyrosetta.rosetta.core.pose.Pose, probe_radius: float) -> pyrosetta.rosetta.core.scoring.packing.SurfVol

C++: core::scoring::packing::get_surf_vol(const class core::pose::Pose &, const double) –> struct core::scoring::packing::SurfVol

3. get_surf_vol(pose: pyrosetta.rosetta.core.pose.Pose, whichatoms: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> pyrosetta.rosetta.core.scoring.packing.SurfVol
4. get_surf_vol(pose: pyrosetta.rosetta.core.pose.Pose, whichatoms: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, probe_radius: float) -> pyrosetta.rosetta.core.scoring.packing.SurfVol

C++: core::scoring::packing::get_surf_vol(const class core::pose::Pose &, const class core::id::AtomID_Map<bool> &, const double) –> struct core::scoring::packing::SurfVol

pyrosetta.rosetta.core.scoring.packing.get_surf_vol_deriv(*args, **kwargs)

Overloaded function.

1. get_surf_vol_deriv(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv
2. get_surf_vol_deriv(pose: pyrosetta.rosetta.core.pose.Pose, probe_radius: float) -> pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv

C++: core::scoring::packing::get_surf_vol_deriv(const class core::pose::Pose &, const double) –> struct core::scoring::packing::SurfVolDeriv

3. get_surf_vol_deriv(pose: pyrosetta.rosetta.core.pose.Pose, whichatoms: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv
4. get_surf_vol_deriv(pose: pyrosetta.rosetta.core.pose.Pose, whichatoms: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, probe_radius: float) -> pyrosetta.rosetta.core.scoring.packing.SurfVolDeriv

C++: core::scoring::packing::get_surf_vol_deriv(const class core::pose::Pose &, const class core::id::AtomID_Map<bool> &, const double) –> struct core::scoring::packing::SurfVolDeriv