lkball¶

lkbtrie

Bindings for core::scoring::lkball namespace

class pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

__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).

__getitem__(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo, index: int) → pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo¶: C++: core::scoring::lkball::LKB_ResiduesInfo::operator[](const unsigned long) –> class core::scoring::lkball::LKB_ResidueInfo &

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) -> None
__init__(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo, arg0: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) -> 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).

append(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo, rsd_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) → None¶: C++: core::scoring::lkball::LKB_ResiduesInfo::append(class std::shared_ptr<class core::scoring::lkball::LKB_ResidueInfo>) –> void

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

clone(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::scoring::lkball::LKB_ResiduesInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

size(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) → int¶: C++: core::scoring::lkball::LKB_ResiduesInfo::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase¶

Bases: pyrosetta.rosetta.utility.SingletonBase_core_scoring_lkball_LKBallDatabase_t

A singleton class which stores data for LKBall terms. This is a separate singleton class, rather than static data on the LKB_ResidueInfo class so that the ResidueType destruction observer has a stable object to call back to.

__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__¶: Initialize self. See help(type(self)) for accurate signature.

__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).

get_atom_weights(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t¶

Get the atom_weights for the ResidueType

IMPORTANT LIFETIME NOTE: The return value is only valid so long as the passed residue type is

C++: core::scoring::lkball::LKBallDatabase::get_atom_weights(const class core::chemical::ResidueType &) const –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

get_instance() → core::scoring::lkball::LKBallDatabase¶: C++: utility::SingletonBase<core::scoring::lkball::LKBallDatabase>::get_instance() –> class core::scoring::lkball::LKBallDatabase *

has(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Returns true if the passed rsd_type is in the database

C++: core::scoring::lkball::LKBallDatabase::has(const class core::chemical::ResidueType &) const –> bool

initialize_residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::scoring::lkball::LKBallDatabase::initialize_residue_type(const class core::chemical::ResidueType &) –> void

reset_arrays_danger_expert_only(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase) → None¶

danger

C++: core::scoring::lkball::LKBallDatabase::reset_arrays_danger_expert_only() –> void

class pyrosetta.rosetta.core.scoring.lkball.WaterBuilder¶

Bases: pybind11_builtins.pybind11_object

Stores the internal coordinates of an ideal water position

__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.lkball.WaterBuilder, water: pyrosetta.rosetta.numeric.xyzVector_double_t, rsd: pyrosetta.rosetta.core.conformation.Residue, atom1: int, atom2: int, atom3: int) → 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).

atom1(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) → int¶: C++: core::scoring::lkball::WaterBuilder::atom1() const –> unsigned long

atom2(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) → int¶: C++: core::scoring::lkball::WaterBuilder::atom2() const –> unsigned long

atom3(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) → int¶: C++: core::scoring::lkball::WaterBuilder::atom3() const –> unsigned long

build(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder, rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::scoring::lkball::WaterBuilder::build(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

derivatives(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder, rsd: pyrosetta.rosetta.core.conformation.Residue, dw_da1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, dw_da2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, dw_da3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) → None¶: C++: core::scoring::lkball::WaterBuilder::derivatives(const class core::conformation::Residue &, class numeric::xyzMatrix<double> &, class numeric::xyzMatrix<double> &, class numeric::xyzMatrix<double> &) const –> void