residue_selector

Bindings for core::select::residue_selector namespace

class pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The AndResidueSelector combines the output of multiple ResidueSelectors using AND logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through %add_residue_selector.

__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.select.residue_selector.AndResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
4. __init__(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> 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_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

adds a ResidueSelector

C++: core::select::residue_selector::AndResidueSelector::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::AndResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_and_to_subset(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, newSubset: pyrosetta.rosetta.utility.vector1_bool, existingSubset: pyrosetta.rosetta.utility.vector1_bool) → None

applies newSubset to existingSubset and thereby modifies the latter

C++: core::select::residue_selector::AndResidueSelector::apply_and_to_subset(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector

C++: core::select::residue_selector::AndResidueSelector::operator=(const class core::select::residue_selector::AndResidueSelector &) –> class core::select::residue_selector::AndResidueSelector &

class_name() → str

C++: core::select::residue_selector::AndResidueSelector::class_name() –> std::string

clear(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → None

Clear the contained selectors.

C++: core::select::residue_selector::AndResidueSelector::clear() –> void

clone(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::AndResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → str

C++: core::select::residue_selector::AndResidueSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → int

Get the number of contained selectors.

C++: core::select::residue_selector::AndResidueSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::AndResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::AndResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.select.residue_selector.BinSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin).

__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.select.residue_selector.BinSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.BinSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::BinSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, : pyrosetta.rosetta.core.select.residue_selector.BinSelector) → pyrosetta.rosetta.core.select.residue_selector.BinSelector

C++: core::select::residue_selector::BinSelector::operator=(const class core::select::residue_selector::BinSelector &) –> class core::select::residue_selector::BinSelector &

bin_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str

Get the name of the bin that the residues that we will select must be in.

C++: core::select::residue_selector::BinSelector::bin_name() const –> const std::string &

bin_params_file_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str

Get the name of the bin params file that we’ll be using.

C++: core::select::residue_selector::BinSelector::bin_params_file_name() const –> const std::string &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::BinSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::BinSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str

Get the mover class name.

C++: core::select::residue_selector::BinSelector::get_name() const –> std::string

initialize_and_check(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → None

Load the bin params file and check that settings are consistent.

Must be called before apply() function.

C++: core::select::residue_selector::BinSelector::initialize_and_check() –> void

initialize_from_file_contents_and_check(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, filecontents: str) → None

Load the bin params file baed on a file contents string (instead of loading directly

from disk) and check that settings are consistent.

Must be called as an alternative to initialize_and_check() before apply() function.

C++: core::select::residue_selector::BinSelector::initialize_from_file_contents_and_check(const class std::basic_string<char> &) –> void

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::BinSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, allowing automatic evaluation of bad XML.

C++: core::select::residue_selector::BinSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

select_only_alpha_aas(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → bool

Get whether we’re selecting alpha-amino acids only.

C++: core::select::residue_selector::BinSelector::select_only_alpha_aas() const –> bool

set_bin_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, bin_name_in: str) → None

Set the name of the bin that the residues that we will select must be in.

C++: core::select::residue_selector::BinSelector::set_bin_name(const class std::basic_string<char> &) –> void

set_bin_params_file_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, filename_in: str) → None

Set the name of the bin params file that we’ll be using.

C++: core::select::residue_selector::BinSelector::set_bin_params_file_name(const class std::basic_string<char> &) –> void

set_select_only_alpha_aas(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, setting: bool) → None

Set whether we’re selecting alpha-amino acids only.

C++: core::select::residue_selector::BinSelector::set_select_only_alpha_aas(const bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector.

Residues in the input_set are included in the final selection.

__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.select.residue_selector.BondedResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, input_set: pyrosetta.rosetta.std.set_unsigned_long_t) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::BondedResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector

C++: core::select::residue_selector::BondedResidueSelector::operator=(const class core::select::residue_selector::BondedResidueSelector &) –> class core::select::residue_selector::BondedResidueSelector &

class_name() → str

C++: core::select::residue_selector::BondedResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::BondedResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → str

C++: core::select::residue_selector::BondedResidueSelector::get_name() const –> std::string

input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::select::residue_selector::BondedResidueSelector::input_set() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

input_set_defined(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → bool

C++: core::select::residue_selector::BondedResidueSelector::input_set_defined() const –> bool

input_set_selector(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::BondedResidueSelector::input_set_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

input_set_selector_defined(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → bool

C++: core::select::residue_selector::BondedResidueSelector::input_set_selector_defined() const –> bool

input_set_string(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → str

C++: core::select::residue_selector::BondedResidueSelector::input_set_string() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datacache: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::BondedResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::BondedResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_input_set(*args, **kwargs)

Overloaded function.

1. set_input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, input_set: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

adds a ResidueSelector

C++: core::select::residue_selector::BondedResidueSelector::set_input_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

2. set_input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, input_set_str: str) -> None

C++: core::select::residue_selector::BondedResidueSelector::set_input_set(const class std::basic_string<char> &) –> void

set_input_set_selector(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::select::residue_selector::BondedResidueSelector::set_input_set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A class that finds the neighboring residues for a particular residue by looking at atom-atom distances

__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.select.residue_selector.CloseContactResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::CloseContactResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector

C++: core::select::residue_selector::CloseContactResidueSelector::operator=(const class core::select::residue_selector::CloseContactResidueSelector &) –> class core::select::residue_selector::CloseContactResidueSelector &

central_residue_group_selector(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::select::residue_selector::CloseContactResidueSelector::central_residue_group_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::CloseContactResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::CloseContactResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → str

Get the mover class name.

C++: core::select::residue_selector::CloseContactResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::CloseContactResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::CloseContactResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

threshold(*args, **kwargs)

Overloaded function.

1. threshold(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, contact_threshold: float) -> None

C++: core::select::residue_selector::CloseContactResidueSelector::threshold(double) –> void

2. threshold(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) -> float

C++: core::select::residue_selector::CloseContactResidueSelector::threshold() const –> double

class pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree. If no layer is set, will select all glycan residues.

__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.select.residue_selector.GlycanLayerSelector) → 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::GlycanLayerSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector

C++: core::select::residue_selector::GlycanLayerSelector::operator=(const class core::select::residue_selector::GlycanLayerSelector &) –> class core::select::residue_selector::GlycanLayerSelector &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::GlycanLayerSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanLayerSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → str

Get the mover class name.

C++: core::select::residue_selector::GlycanLayerSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanLayerSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanLayerSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_layer(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, start: int, end: int) → None

Set the layer we will be returning.

C++: core::select::residue_selector::GlycanLayerSelector::set_layer(unsigned long, unsigned long) –> void

set_layer_as_greater_than_or_equal_to(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, start: int) → None

Set the layer as all residues greater than or equal to this number (such as the end of the tree)

C++: core::select::residue_selector::GlycanLayerSelector::set_layer_as_greater_than_or_equal_to(unsigned long) –> void

set_layer_as_less_than_or_equal_to(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, end: int) → None

Set the layer as all residue less or equal to this number (the beginning of the tree).

C++: core::select::residue_selector::GlycanLayerSelector::set_layer_as_less_than_or_equal_to(unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc.

__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.select.residue_selector.GlycanResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, arg0: pyrosetta.rosetta.utility.vector1_bool) -> None

doc

3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residues: pyrosetta.rosetta.utility.vector1_bool, include_root: bool) -> None
4. __init__(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, arg0: int) -> None

doc

5. __init__(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residue: int, include_root: bool) -> None
6. __init__(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::GlycanResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector

C++: core::select::residue_selector::GlycanResidueSelector::operator=(const class core::select::residue_selector::GlycanResidueSelector &) –> class core::select::residue_selector::GlycanResidueSelector &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::GlycanResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → str

Get the mover class name.

C++: core::select::residue_selector::GlycanResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_include_root(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, include_root: bool) → None

Option to include the root(s) we are selecting from.

Default FALSE.

C++: core::select::residue_selector::GlycanResidueSelector::set_include_root(bool) –> void

set_select_from_branch_residue(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residue: int) → None

Set the residue to select from. These can be the branch points of the glycans or

carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

C++: core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residue(unsigned long) –> void

set_select_from_branch_residues(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residues: pyrosetta.rosetta.utility.vector1_bool) → None

Set the residue(s) to select from. These can be the branch points of the glycans or

carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

C++: core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

class pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The %InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset.

__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.select.residue_selector.InterGroupInterfaceByVectorSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, : pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::operator=(const class core::select::residue_selector::InterGroupInterfaceByVectorSelector &) –> class core::select::residue_selector::InterGroupInterfaceByVectorSelector &

cb_dist_cut(*args, **kwargs)

Overloaded function.

1. cb_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut() const –> double

2. cb_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut(double) –> void

class_name() → str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::get_name() const –> std::string

group1_resstring(*args, **kwargs)

Overloaded function.

1. group1_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring() const –> const std::string &

2. group1_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: str) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring(const class std::basic_string<char> &) –> void

group1_selector(*args, **kwargs)

Overloaded function.

1. group1_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. group1_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

group1_set(*args, **kwargs)

Overloaded function.

1. group1_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

2. group1_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

group2_resstring(*args, **kwargs)

Overloaded function.

1. group2_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring() const –> const std::string &

2. group2_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: str) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring(const class std::basic_string<char> &) –> void

group2_selector(*args, **kwargs)

Overloaded function.

1. group2_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. group2_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

group2_set(*args, **kwargs)

Overloaded function.

1. group2_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

2. group2_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

nearby_atom_cut(*args, **kwargs)

Overloaded function.

1. nearby_atom_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut() const –> double

2. nearby_atom_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut(double) –> void

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

vector_angle_cut(*args, **kwargs)

Overloaded function.

1. vector_angle_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut() const –> double

2. vector_angle_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut(double) –> void

vector_dist_cut(*args, **kwargs)

Overloaded function.

1. vector_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut() const –> double

2. vector_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut(double) –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which lie downstream of a given jump in the FoldTree. The jump is specified by an integer index.

__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.select.residue_selector.JumpDownstreamSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, jump: 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::JumpDownstreamSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, : pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector

C++: core::select::residue_selector::JumpDownstreamSelector::operator=(const class core::select::residue_selector::JumpDownstreamSelector &) –> class core::select::residue_selector::JumpDownstreamSelector &

class_name() → str

C++: core::select::residue_selector::JumpDownstreamSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::JumpDownstreamSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → str

C++: core::select::residue_selector::JumpDownstreamSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::JumpDownstreamSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::JumpDownstreamSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_jump(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, jump: int) → None

sets the string by which residues are selected

C++: core::select::residue_selector::JumpDownstreamSelector::set_jump(int) –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index.

__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.select.residue_selector.JumpUpstreamSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, jump: 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::JumpUpstreamSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, : pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector

C++: core::select::residue_selector::JumpUpstreamSelector::operator=(const class core::select::residue_selector::JumpUpstreamSelector &) –> class core::select::residue_selector::JumpUpstreamSelector &

class_name() → str

C++: core::select::residue_selector::JumpUpstreamSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::JumpUpstreamSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → str

C++: core::select::residue_selector::JumpUpstreamSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::JumpUpstreamSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::JumpUpstreamSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_jump(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, jump: int) → None

sets the string by which residues are selected

C++: core::select::residue_selector::JumpUpstreamSelector::set_jump(int) –> void

class pyrosetta.rosetta.core.select.residue_selector.LayerSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The LayerSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

__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.select.residue_selector.LayerSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

Apply function: generate a ResidueSubset given a Pose.

C++: core::select::residue_selector::LayerSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, : pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → pyrosetta.rosetta.core.select.residue_selector.LayerSelector

C++: core::select::residue_selector::LayerSelector::operator=(const class core::select::residue_selector::LayerSelector &) –> class core::select::residue_selector::LayerSelector &

class_name() → str

Get the class name.

C++: core::select::residue_selector::LayerSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::LayerSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → str

Get the class name.

Calls class_name().

C++: core::select::residue_selector::LayerSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Parse xml tag setting up this selector.

C++: core::select::residue_selector::LayerSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::LayerSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_angle_exponent(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None

Set the sidechain neighbor angle exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_angle_exponent(const double &) –> void

set_angle_shift_factor(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None

Set the sidechain neighbor angle shift value.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_angle_shift_factor(const double &) –> void

set_ball_radius(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, radius: float) → None

Set the radius for the rolling ball algorithm used to determine burial.

C++: core::select::residue_selector::LayerSelector::set_ball_radius(const double &) –> void

set_cache_selection(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: bool) → None

Set whether to cache versus recompute the layer selection whenever it is accessed.

C++: core::select::residue_selector::LayerSelector::set_cache_selection(const bool) –> void

set_cutoffs(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, core: float, surf: float) → None

Set the cutoffs for core and surface layers.

Boundary is defined implicitly. This can be a SASA cutoff or a neighbour count, depending on the algorithm.

C++: core::select::residue_selector::LayerSelector::set_cutoffs(const double &, const double &) –> void

set_dist_exponent(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None

Set the sidechain neighbor distance exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_dist_exponent(const double &) –> void

set_layers(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, pick_core: bool, pick_boundary: bool, pick_surface: bool) → None

Set the layers that this selector will choose.

C++: core::select::residue_selector::LayerSelector::set_layers(const bool, const bool, const bool) –> void

set_sc_neighbor_denominator(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None

Set the factor by which sidechain neighbor counts are divided if the sidechain

neighbors method is used to define layers.

C++: core::select::residue_selector::LayerSelector::set_sc_neighbor_denominator(const double &) –> void

set_sc_neighbor_dist_midpoint(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None

Set the midpoint of the distance falloff if the sidechain neighbors method is used

to define layers.

C++: core::select::residue_selector::LayerSelector::set_sc_neighbor_dist_midpoint(const double &) –> void

set_use_sc_neighbors(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: bool) → None

Set whether the sidechain neighbors algorithm is used to determine burial (as

opposed to the rolling ball algorithm).

C++: core::select::residue_selector::LayerSelector::set_use_sc_neighbors(const bool) –> void

use_sc_neighbors(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → bool

Get whether the sidechain neighbors algorithm is used to determine burial (as

opposed to the rolling ball algorithm).

C++: core::select::residue_selector::LayerSelector::use_sc_neighbors() const –> bool

class pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this!

Note: Uses the 10 A neighbor graph by default. If neighbor distance is great than this, we use slow-style double for loop.

__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.select.residue_selector.NeighborhoodResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, arg0: pyrosetta.rosetta.utility.vector1_bool, arg1: float) -> None

doc

4. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus: pyrosetta.rosetta.utility.vector1_bool, distance: float, include_focus_in_subset: bool) -> None
5. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, arg1: float) -> None

doc

6. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, distance: float, include_focus_in_subset: bool) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::NeighborhoodResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector

C++: core::select::residue_selector::NeighborhoodResidueSelector::operator=(const class core::select::residue_selector::NeighborhoodResidueSelector &) –> class core::select::residue_selector::NeighborhoodResidueSelector &

class_name() → str

C++: core::select::residue_selector::NeighborhoodResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::NeighborhoodResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → str

C++: core::select::residue_selector::NeighborhoodResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::NeighborhoodResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_atom_names_for_distance_measure(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, atom_names: pyrosetta.rosetta.utility.vector1_std_string) → None

Set atom names to be used for selecting instead of using neighbor atoms.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_atom_names_for_distance_measure(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

set_distance(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, distance: float) → None

Set the distance we will be measuring to get neighbors

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_distance(double) –> void

set_focus(*args, **kwargs)

Overloaded function.

1. set_focus(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus_str: str) -> None

Set the focus, which is the residues for which we will be getting neighbors of.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus(const class std::basic_string<char> &) –> void

2. set_focus(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus: pyrosetta.rosetta.utility.vector1_bool) -> None

Set the focus, which is the residues for which we will be getting neighbors of.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

set_focus_selector(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set a Residue Selector for the focus

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_include_focus_in_subset(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, include_focus: bool) → None

Setting to include the focus in the resulting subset or not. Default is TRUE

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_include_focus_in_subset(bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT - it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true. The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector. Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting the opposite of the passed in selector.

__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.select.residue_selector.NotResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::NotResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector

C++: core::select::residue_selector::NotResidueSelector::operator=(const class core::select::residue_selector::NotResidueSelector &) –> class core::select::residue_selector::NotResidueSelector &

class_name() → str

C++: core::select::residue_selector::NotResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::NotResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → str

C++: core::select::residue_selector::NotResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::NotResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::NotResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

sets a ResidueSelector

C++: core::select::residue_selector::NotResidueSelector::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The OrResidueSelector combines the output of multiple ResidueSelectors using OR logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through %add_residue_selector.

__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.select.residue_selector.OrResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, selector1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> 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_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

adds a ResidueSelector

C++: core::select::residue_selector::OrResidueSelector::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::OrResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_or_to_subset(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, newSubset: pyrosetta.rosetta.utility.vector1_bool, existingSubset: pyrosetta.rosetta.utility.vector1_bool) → None

applies newSubset to existingSubset and thereby modifies the latter

C++: core::select::residue_selector::OrResidueSelector::apply_or_to_subset(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector

C++: core::select::residue_selector::OrResidueSelector::operator=(const class core::select::residue_selector::OrResidueSelector &) –> class core::select::residue_selector::OrResidueSelector &

class_name() → str

C++: core::select::residue_selector::OrResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::OrResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → str

C++: core::select::residue_selector::OrResidueSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → int

C++: core::select::residue_selector::OrResidueSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::OrResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::OrResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.select.residue_selector.PhiSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences).

__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.select.residue_selector.PhiSelector) → 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::PhiSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, : pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → pyrosetta.rosetta.core.select.residue_selector.PhiSelector

C++: core::select::residue_selector::PhiSelector::operator=(const class core::select::residue_selector::PhiSelector &) –> class core::select::residue_selector::PhiSelector &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::PhiSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone function.

Copy this object and return owning pointer to the copy (created on the heap).

C++: core::select::residue_selector::PhiSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → str

Get the mover class name.

C++: core::select::residue_selector::PhiSelector::get_name() const –> std::string

ignore_unconnected_upper(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → bool

Are we ignoring residues with no upper connection?

Default true.

C++: core::select::residue_selector::PhiSelector::ignore_unconnected_upper() const –> bool

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::PhiSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, allowing automatic evaluation of bad XML.

C++: core::select::residue_selector::PhiSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

select_positive_phi(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → bool

Are we selecting the residues in the positive phi region?

Default true.

C++: core::select::residue_selector::PhiSelector::select_positive_phi() const –> bool

set_ignore_unconnected_upper(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, setting: bool) → None

Set whether we’re ignoring residues with no upper connection.

C++: core::select::residue_selector::PhiSelector::set_ignore_unconnected_upper(const bool) –> void

set_select_positive_phi(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, setting: bool) → None

Set whether we’re selecting residues in the positive phi region.

C++: core::select::residue_selector::PhiSelector::set_select_positive_phi(const bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are located near the given selected residues in primary sequence space

__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.select.residue_selector.PrimarySequenceNeighborhoodSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, lower_residues: int, upper_residues: int, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, : pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::operator=(const class core::select::residue_selector::PrimarySequenceNeighborhoodSelector &) –> class core::select::residue_selector::PrimarySequenceNeighborhoodSelector &

class_name() → str

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → str

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_lower_residues(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres: int) → None

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_lower_residues(const unsigned long) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_upper_residues(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres: int) → None

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_upper_residues(const unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling.

__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.select.residue_selector.RandomGlycanFoliageSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, subset: pyrosetta.rosetta.utility.vector1_bool) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
4. __init__(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::RandomGlycanFoliageSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, : pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector

C++: core::select::residue_selector::RandomGlycanFoliageSelector::operator=(const class core::select::residue_selector::RandomGlycanFoliageSelector &) –> class core::select::residue_selector::RandomGlycanFoliageSelector &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → str

Get the mover class name.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set a selector to set the glycan root and subsequent foliage on.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_subset(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, subset: pyrosetta.rosetta.utility.vector1_bool) → None

Set a subset to select the glycan root and subsequent foliage on.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::set_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

class pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The RandomResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for N randomly selected residue positions, where N is a user-specified integer.

__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.select.residue_selector.RandomResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, num_residues: int) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, num_residues: int, select_res_cluster: bool, distance_cutoff: 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::RandomResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector

C++: core::select::residue_selector::RandomResidueSelector::operator=(const class core::select::residue_selector::RandomResidueSelector &) –> class core::select::residue_selector::RandomResidueSelector &

class_name() → str

C++: core::select::residue_selector::RandomResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::RandomResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → str

C++: core::select::residue_selector::RandomResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::RandomResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::RandomResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

__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.select.residue_selector.ResidueIndexSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_str: str) -> 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_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_in: int) → None

Append an additional index (in Rosetta numbering) to the list of indices.

Vikram K. Mulligan (vmullig.edu)

C++: core::select::residue_selector::ResidueIndexSelector::append_index(const unsigned long) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::ResidueIndexSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector

C++: core::select::residue_selector::ResidueIndexSelector::operator=(const class core::select::residue_selector::ResidueIndexSelector &) –> class core::select::residue_selector::ResidueIndexSelector &

class_name() → str

C++: core::select::residue_selector::ResidueIndexSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueIndexSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → str

C++: core::select::residue_selector::ResidueIndexSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::ResidueIndexSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::ResidueIndexSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_str: str) → None

sets the string by which residues are selected

C++: core::select::residue_selector::ResidueIndexSelector::set_index(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The ResidueNameSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

__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.select.residue_selector.ResidueNameSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, res_name_str: str) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::ResidueNameSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector

C++: core::select::residue_selector::ResidueNameSelector::operator=(const class core::select::residue_selector::ResidueNameSelector &) –> class core::select::residue_selector::ResidueNameSelector &

class_name() → str

C++: core::select::residue_selector::ResidueNameSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueNameSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → str

C++: core::select::residue_selector::ResidueNameSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::ResidueNameSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::ResidueNameSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_residue_name3(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, res_name3_str: str) → None

sets the comma-separated string of 3-character residue names to be selected

C++: core::select::residue_selector::ResidueNameSelector::set_residue_name3(const class std::basic_string<char> &) –> void

set_residue_names(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, res_name_str: str) → None

sets the comma-separated string of residue names to be selected

C++: core::select::residue_selector::ResidueNameSelector::set_residue_names(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The ResiduePDBInfoHasLabelSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions with the given label in pose PDB info for that residue.

__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.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, label_str: str) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, : pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::operator=(const class core::select::residue_selector::ResiduePDBInfoHasLabelSelector &) –> class core::select::residue_selector::ResiduePDBInfoHasLabelSelector &

class_name() → str

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → str

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_label(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, label_str: str) → None

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::set_label(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueRange

Bases: pybind11_builtins.pybind11_object

Class for storing a range of resids

__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.select.residue_selector.ResidueRange) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange, startval: int, stopval: 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).

set_start(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange, start_res: int) → None

Sets starting residue of the range

C++: core::select::residue_selector::ResidueRange::set_start(const unsigned long) –> void

set_stop(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange, stop_res: int) → None

Sets stopping residue of the range

C++: core::select::residue_selector::ResidueRange::set_stop(const unsigned long) –> void

start(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → int

Returns the starting residue of the range

C++: core::select::residue_selector::ResidueRange::start() const –> unsigned long

stop(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → int

Returns the stopping residue of the range

C++: core::select::residue_selector::ResidueRange::stop() const –> unsigned long

to_string(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → str

String representation of the range

C++: core::select::residue_selector::ResidueRange::to_string() const –> std::string

class pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The ResidueSpanSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are within a given span. A span is defined by start and end point, each as either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. (The span is defined based on Rosetta indicies, even if residues are given by PDB numbers.)

__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.select.residue_selector.ResidueSpanSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, start_str: str, end_str: str) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::ResidueSpanSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector

C++: core::select::residue_selector::ResidueSpanSelector::operator=(const class core::select::residue_selector::ResidueSpanSelector &) –> class core::select::residue_selector::ResidueSpanSelector &

class_name() → str

C++: core::select::residue_selector::ResidueSpanSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueSpanSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → str

C++: core::select::residue_selector::ResidueSpanSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::ResidueSpanSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::ResidueSpanSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_span(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, start: str, end: str) → None

C++: core::select::residue_selector::ResidueSpanSelector::set_span(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

A simple selector that returns the set subset.

This is to enable simplification of code-based interfaces to residue selectors, so that one may accept only selectors, but using this selector, we can set subsets.

This greatly reduces the c++ interface complexity and

private variable - complexity arising from accepting BOTH ResidueSubsets and ResidueSelectors (Which I’m terribly sick of doing at this point).

__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.select.residue_selector.ReturnResidueSubsetSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, subset: pyrosetta.rosetta.utility.vector1_bool) -> None
3. __init__(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, arg0: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

“Apply” function.

Return the set subset.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, : pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector

C++: core::select::residue_selector::ReturnResidueSubsetSelector::operator=(const class core::select::residue_selector::ReturnResidueSubsetSelector &) –> class core::select::residue_selector::ReturnResidueSubsetSelector &

class_name() → str

Get the mover class name.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → str

Get the mover class name.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_residue_subset(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, subset: pyrosetta.rosetta.utility.vector1_bool) → None

Set the ResidueSubset, which will be returned at apply-time.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::set_residue_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

class pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector

Bases: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

The SymmetricalResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are symmetrically generated residues of the input list. (IE Union)

If the Pose is not symmetrical, returns the generated subset from the passed residue selector.

__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.select.residue_selector.SymmetricalResidueSelector) -> None
2. __init__(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> 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).

apply(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool

C++: core::select::residue_selector::SymmetricalResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector

C++: core::select::residue_selector::SymmetricalResidueSelector::operator=(const class core::select::residue_selector::SymmetricalResidueSelector &) –> class core::select::residue_selector::SymmetricalResidueSelector &

class_name() → str

C++: core::select::residue_selector::SymmetricalResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SymmetricalResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → str

C++: core::select::residue_selector::SymmetricalResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::residue_selector::SymmetricalResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::select::residue_selector::SymmetricalResidueSelector::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

pyrosetta.rosetta.core.select.residue_selector.all_false_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool

Returns True if all the positions in the ResidueSubset are False

C++: core::select::residue_selector::all_false_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.all_true_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool

Returns True if all the positions in the ResidueSubset are True

C++: core::select::residue_selector::all_true_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector(*args, **kwargs)

Overloaded function.

1. attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
2. attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
3. attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_residue_selector

C++: core::select::residue_selector::attributes_for_parse_residue_selector(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector_default_option_name(*args, **kwargs)

Overloaded function.

1. attributes_for_parse_residue_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
2. attributes_for_parse_residue_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, documentation_string: str) -> None

Companion function for parse_residue_selector

This assumes the default residue selector option name (“residue_selector”).

C++: core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector_when_required(*args, **kwargs)

Overloaded function.

1. attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
2. attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
3. attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_residue_selector to be used when it is unacceptible

for the parse_residue_selector function to return a null pointer

C++: core::select::residue_selector::attributes_for_parse_residue_selector_when_required(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.select.residue_selector.complex_type_name_for_residue_selector(rs_type: str) → str

Used to name the xs:complexType for a residue selector that is

created with the “rs_type” tag-name. Does so by prepending “rs_” and appending “Type” to the “rs_type”. E.g., “rs_AndType” would be the name given to the complexType to describe the format of the AndResidueSelector.

C++: core::select::residue_selector::complex_type_name_for_residue_selector(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.select.residue_selector.count_selected(selection: pyrosetta.rosetta.utility.vector1_bool) → int

Returns the number of selected residues in the ResidueSubset

C++: core::select::residue_selector::count_selected(const class utility::vector1<bool, class std::allocator<bool> > &) –> unsigned long

pyrosetta.rosetta.core.select.residue_selector.get_embedded_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

utility::excn::EXCN_Msg_Exception if selector is not embedded ( ! tag->size() > 1)

C++: core::select::residue_selector::get_embedded_residue_selector(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.get_residue_selector(selector_name: str, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns a residue selector given a selector’s name and datamap

Looks for selector in the datamap

Returns a const ptr to the selector

utility::excn::EXCN_Msg_Exception if selector is not found in datamap

C++: core::select::residue_selector::get_residue_selector(const class std::basic_string<char> &, const class basic::datacache::DataMap &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.has_any_false_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool

Returns True if at least one position in the ResidueSubset is False

C++: core::select::residue_selector::has_any_false_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.has_any_true_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool

Returns True if at least one position in the ResidueSubset is True

C++: core::select::residue_selector::has_any_true_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.parse_residue_selector(*args, **kwargs)

Overloaded function.

1. parse_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
2. parse_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, option_name: str) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns a residue selector given a tag and datamap

Looks for “residue_selector” (or whatever option_name is set to)

option in tag.

If that option isn’t found, returns NULL ptr If that option is found, calls get_residue_selector()

C++: core::select::residue_selector::parse_residue_selector(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const class std::basic_string<char> &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.selection_positions(selection: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the Rosetta Numbering corresponding to the selected residues

C++: core::select::residue_selector::selection_positions(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Define the XML schema definition for a ResidueSelector that

contains no other ResidueSelectors but may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes_and_optional_subselector(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

Define the XML schema definition for a ResidueSelector that

contains a single ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselector(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes_and_optional_subselectors(*args, **kwargs)

Overloaded function.

1. xsd_type_definition_w_attributes_and_optional_subselectors(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

Define the XML schema definition for a ResidueSelector that

contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

2. xsd_type_definition_w_attributes_and_optional_subselectors(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition, rs_type: str, rs_description: str, min_occurrence: int, max_occurrence: int, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

Define the XML schema definition for a ResidueSelector that

contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors(class utility::tag::XMLSchemaDefinition &, const class std::basic_string<char> &, const class std::basic_string<char> &, unsigned long, unsigned long, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void