reference_pose

Bindings for core::pose::reference_pose namespace

class pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

Bases: pybind11_builtins.pybind11_object

ReferencePose class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol.

__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.pose.reference_pose.ReferencePose) -> None
2. __init__(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, arg0: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) -> 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.pose.reference_pose.ReferencePose, : pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

C++: core::pose::reference_pose::ReferencePose::operator=(const class core::pose::reference_pose::ReferencePose &) –> class core::pose::reference_pose::ReferencePose &

clone(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

Make a copy of this ReferencePose object (allocate actual memory for it)

and return an owning pointer to the copy.

C++: core::pose::reference_pose::ReferencePose::clone() const –> class std::shared_ptr<class core::pose::reference_pose::ReferencePose>

corresponding_residue_in_current(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, res_in_ref: int) → int

Get the residue in the current pose corresponding to a particular residue in the

reference pose.

Should return 0 if there is no corresponding residue in the current pose (e.g. if the residue was deleted.) Throws an error if there was no residue with the given index in the reference pose.

C++: core::pose::reference_pose::ReferencePose::corresponding_residue_in_current(const unsigned long) const –> unsigned long

decrement_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, seqpos: int) → None

Find all mappings to indices in the new pose after seqpos, and decrement them by 1.

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePose::decrement_reference_pose_mapping_after_seqpos(const unsigned long) –> void

get_self_ptr(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

Get owning pointer (e.g. from a reference).

C++: core::pose::reference_pose::ReferencePose::get_self_ptr() –> class std::shared_ptr<class core::pose::reference_pose::ReferencePose>

get_self_weak_ptr(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) → pyrosetta.rosetta.std.weak_ptr_core_pose_reference_pose_ReferencePose_t

Get access (weak) pointer (e.g. from a reference).

C++: core::pose::reference_pose::ReferencePose::get_self_weak_ptr() –> class std::weak_ptr<class core::pose::reference_pose::ReferencePose>

increment_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, seqpos: int) → None

Find all mappings to indices in the new pose after seqpos, and increment them by 1.

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePose::increment_reference_pose_mapping_after_seqpos(const unsigned long) –> void

initialize_residue_map_from_pose(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, pose: pyrosetta.rosetta.core.pose.Pose) → None

Initializes the residue_map_ based on an input reference pose.

After this operation, the residue_map_ is a very uninteresting map that maps every residue index in the pose onto itself. This also sets the stores_residue_map_ bit to true.

C++: core::pose::reference_pose::ReferencePose::initialize_residue_map_from_pose(const class core::pose::Pose &) –> void

stores_residue_map(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose) → bool

Returns true if this ReferencePose object stores a map of

(old residue indices->new residue indices), false otherwise.

C++: core::pose::reference_pose::ReferencePose::stores_residue_map() const –> bool

zero_reference_pose_mapping_at_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePose, seqpos: int) → None

Find all mappings to indices in the new pose to seqpos, and set them to point to residue 0 (deletion signal).

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePose::zero_reference_pose_mapping_at_seqpos(const unsigned long) –> void

class pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet

Bases: pybind11_builtins.pybind11_object

ReferencePoseSet class, used to store sets of ReferencePose data for tracking how a pose changes over the course of a protocol.

__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.pose.reference_pose.ReferencePoseSet) -> None
2. __init__(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, arg0: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) -> 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).

add_and_initialize_reference_pose(*args, **kwargs)

Overloaded function.

1. add_and_initialize_reference_pose(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, key_string: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. add_and_initialize_reference_pose(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, key_string: str, pose: pyrosetta.rosetta.core.pose.Pose, override_current: bool) -> None

Given a reference pose, create a new ReferencePose object and initialize it

based on the reference pose, then add it to the current map.

After this operation, the map holds a new ReferencePoseOP pointing to a very uninteresting ReferencePose object that maps a list of residues onto themselves, accessible by the key string. If override_current is set to true, will overrwrite any reference pose with the key_string.

C++: core::pose::reference_pose::ReferencePoseSet::add_and_initialize_reference_pose(const class std::basic_string<char> &, const class core::pose::Pose &, bool) –> void

assign(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, : pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet

C++: core::pose::reference_pose::ReferencePoseSet::operator=(const class core::pose::reference_pose::ReferencePoseSet &) –> class core::pose::reference_pose::ReferencePoseSet &

clone(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet

Make a copy of this ReferencePoseSet object (allocate actual memory for it)

and return an owning pointer to the copy.

C++: core::pose::reference_pose::ReferencePoseSet::clone() const –> class std::shared_ptr<class core::pose::reference_pose::ReferencePoseSet>

corresponding_residue_in_current(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, res_index_in_ref: int, ref_pose_key_string: str) → int

Get the corresponding residue in the current pose to a residue in a reference pose.

Should return 0 if no corresponding residue exists in the current pose, and throw an error if the residue index provided as a key did not exist in the reference pose.

C++: core::pose::reference_pose::ReferencePoseSet::corresponding_residue_in_current(const unsigned long, const class std::basic_string<char> &) const –> unsigned long

decrement_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, seqpos: int) → None

Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and decrement them by 1.

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePoseSet::decrement_reference_pose_mapping_after_seqpos(const unsigned long) –> void

empty(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → bool

Returns true if and only if there are no ReferencePose objects in this ReferencePoseSet.

C++: core::pose::reference_pose::ReferencePoseSet::empty() const –> bool

get_self_ptr(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet

Get owning pointer (e.g. from a reference).

C++: core::pose::reference_pose::ReferencePoseSet::get_self_ptr() –> class std::shared_ptr<class core::pose::reference_pose::ReferencePoseSet>

get_self_weak_ptr(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → pyrosetta.rosetta.std.weak_ptr_core_pose_reference_pose_ReferencePoseSet_t

Get access (weak) pointer (e.g. from a reference).

C++: core::pose::reference_pose::ReferencePoseSet::get_self_weak_ptr() –> class std::weak_ptr<class core::pose::reference_pose::ReferencePoseSet>

increment_reference_pose_mapping_after_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, seqpos: int) → None

Find all mappings to indices in the new pose after seqpos in all ReferencePose objects, and increment them by 1.

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePoseSet::increment_reference_pose_mapping_after_seqpos(const unsigned long) –> void

n_reference_pose(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet) → int

Get the number of ReferencePose objects in this ReferencePoseSet.

C++: core::pose::reference_pose::ReferencePoseSet::n_reference_pose() const –> unsigned long

reference_pose(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, key_string: str) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

Get an owning pointer to a reference pose stored in the reference pose map, given a key string.

An error is thrown if the key string doesn’t associate with anything (i.e. if the reference pose doesn’t exist).

C++: core::pose::reference_pose::ReferencePoseSet::reference_pose(const class std::basic_string<char> &) –> class std::shared_ptr<class core::pose::reference_pose::ReferencePose>

reference_pose_cop(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, key_string: str) → pyrosetta.rosetta.core.pose.reference_pose.ReferencePose

Get a const owning pointer to a reference pose stored in the reference pose map, given a key string.

An error is thrown if the key string doesn’t associate with anything (i.e. if the reference pose doesn’t exist).

C++: core::pose::reference_pose::ReferencePoseSet::reference_pose_cop(const class std::basic_string<char> &) const –> class std::shared_ptr<const class core::pose::reference_pose::ReferencePose>

zero_reference_pose_mapping_at_seqpos(self: pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet, seqpos: int) → None

Find all mappings to indices in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal).

If there is no ReferencePose object, do nothing.

C++: core::pose::reference_pose::ReferencePoseSet::zero_reference_pose_mapping_at_seqpos(const unsigned long) –> void