rings

Bindings for core::chemical::rings namespace

class pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Bases: pybind11_builtins.pybind11_object

: The axial/equatorial designation for bonds/substituents on ring systems.

Axial: “…[B]onds to ring atoms (and molecular entities attached to such bonds) are… axial… [if] the bonds make a relatively large… angle… with the plane containing or passing closest to a majority of the ring atoms. …[A]xial bonds are approximately parallel to the C3 axis…. Equatorial: “…[B]onds to ring atoms (and molecular entities attached to such bonds) are… equatorial… [if] the bonds make a relatively small… angle… with the plane containing or passing closest to a majority of the ring atoms. …[E]quatorial bonds [are] approximately parallel to two of the ring bonds.

NEITHER has the value of 0 and so can be used in conditionals as false.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) -> bool
2. __eq__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) → int

__init__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: 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.

__int__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) -> bool
2. __ne__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.chemical.rings.AxEqDesignation, arg0: tuple) → None

__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).

class pyrosetta.rosetta.core.chemical.rings.CPParameter

Bases: pybind11_builtins.pybind11_object

Enumerators for the three Cremer-Pople “ring-puckering” parameters used to describe 4-, 5-, and 6-membered ring conformers

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: pyrosetta.rosetta.core.chemical.rings.CPParameter) -> bool
2. __eq__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter) → int

__init__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: 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.

__int__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: pyrosetta.rosetta.core.chemical.rings.CPParameter) -> bool
2. __ne__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.chemical.rings.CPParameter, arg0: tuple) → None

__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).

class pyrosetta.rosetta.core.chemical.rings.RingConformer

Bases: pybind11_builtins.pybind11_object

A structure for storing information for specific, idealized ring conformers.

__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.chemical.rings.RingConformer, arg0: pyrosetta.rosetta.core.chemical.rings.RingConformer) -> None
2. __init__(self: pyrosetta.rosetta.core.chemical.rings.RingConformer) -> 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__(self: pyrosetta.rosetta.core.chemical.rings.RingConformer) → 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.chemical.rings.RingConformer, : pyrosetta.rosetta.core.chemical.rings.RingConformer) → pyrosetta.rosetta.core.chemical.rings.RingConformer

C++: core::chemical::rings::RingConformer::operator=(const struct core::chemical::rings::RingConformer &) –> struct core::chemical::rings::RingConformer &

class pyrosetta.rosetta.core.chemical.rings.RingConformerManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_chemical_rings_RingConformerManager_t

This class is a singleton and manages RingConformer data that should only be read from the database one time and shared among all RingConformerSets.

__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).

conformers_for_ring_size(ring_size: int) → pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

Return a set of ring conformers for the requested ring size.

C++: core::chemical::rings::RingConformerManager::conformers_for_ring_size(unsigned long) –> const class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> > &

get_instance() → core::chemical::rings::RingConformerManager

C++: utility::SingletonBase<core::chemical::rings::RingConformerManager>::get_instance() –> class core::chemical::rings::RingConformerManager *

pyrosetta.rosetta.core.chemical.rings.is_atom_axial_or_equatorial_to_ring(query_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, attachment_atom: pyrosetta.rosetta.numeric.xyzVector_double_t, ring_atoms: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → pyrosetta.rosetta.core.chemical.rings.AxEqDesignation

Are the query atom coordinates axial or equatorial to the given ring or neither?

C++: core::chemical::rings::is_atom_axial_or_equatorial_to_ring(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> enum core::chemical::rings::AxEqDesignation

pyrosetta.rosetta.core.chemical.rings.read_conformers_from_database_file_for_ring_size(filename: str, ring_size: int) → pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer

Return a list of ring conformers, read from a database file.

C++: core::chemical::rings::read_conformers_from_database_file_for_ring_size(const class std::basic_string<char> &, unsigned long) –> class utility::vector1<struct core::chemical::rings::RingConformer, class std::allocator<struct core::chemical::rings::RingConformer> >