filters¶

Bindings for protocols::fldsgn::filters namespace

class pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

Filter used in ‘Principles for designing proteins with cavities formed by curved b-sheets’ to control helix geometry.

__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.

__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, arg0: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter) -> 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.protocols.fldsgn.filters.HelixBendFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

returns true if the structure passes the filter, false otherwise

C++: protocols::fldsgn::filters::HelixBendFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::fldsgn::filters::HelixBendFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::HelixBendFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::HelixBendFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

helix_id(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, r: int) → None¶

Strand id number

C++: protocols::fldsgn::filters::HelixBendFilter::helix_id(const unsigned long) –> void

name(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter) → str¶: C++: protocols::fldsgn::filters::HelixBendFilter::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::fldsgn::filters::HelixBendFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

allows printing data to a stream

C++: protocols::fldsgn::filters::HelixBendFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

required for reporting score values

C++: protocols::fldsgn::filters::HelixBendFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

secstruct(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, ss: str) → None¶: C++: protocols::fldsgn::filters::HelixBendFilter::secstruct(const class std::basic_string<char> &) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

threshold(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, r: float) → None¶

minimum angle for filtering

C++: protocols::fldsgn::filters::HelixBendFilter::threshold(const double) –> void

class pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

Newer version of filter used in Marcos & Basanta et al. 2017

__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.

__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels) -> None
__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, arg0: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels) -> 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.protocols.fldsgn.filters.StrandCurvatureByLevels, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

returns true if the structure passes the filter, false otherwise

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::apply(const class core::pose::Pose &) const –> bool

bend_level(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: int) → None¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::bend_level(const unsigned long) –> void

class_name() → str¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::compute(const class core::pose::Pose &) const –> double

concavity_direction(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: bool) → None¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_direction(const bool &) –> void

concavity_reference_residue(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, ss: str) → None¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_reference_residue(const class std::basic_string<char> &) –> void

filter_max_bend(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: float) → None¶

maximum angle for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_bend(const double) –> void

filter_max_twist(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: float) → None¶

maximum twist for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_twist(const double) –> void

filter_min_bend(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: float) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_bend(const double) –> void

filter_min_twist(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: float) → None¶

miniimum twist for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_twist(const double) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels) → str¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::name() const –> std::string

output_type(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, s: str) → None¶

set output type

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::output_type(const class std::basic_string<char> &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

allows printing data to a stream

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

required for reporting score values

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

secstruct(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, ss: str) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::secstruct(const class std::basic_string<char> &) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

strand_id(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: int) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::strand_id(const unsigned long) –> void

twist_level(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, r: int) → None¶: C++: protocols::fldsgn::filters::StrandCurvatureByLevels::twist_level(const unsigned long) –> void

class pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

Another filter used in Marcos & Basanta et al. 2017 that needs to be updated.

__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.

__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, arg0: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter) -> 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.protocols.fldsgn.filters.StrandHelixGeometryFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

returns true if the structure passes the filter, false otherwise

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

filter_max_dist(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

maximum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_max_dist(const double) –> void

filter_max_orthoangle(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

maximum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_max_orthoangle(const double) –> void

filter_max_planeangle(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

maximum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_max_planeangle(const double) –> void

filter_min_dist(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_min_dist(const double) –> void

filter_min_orthoangle(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_min_orthoangle(const double) –> void

filter_min_planeangle(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: float) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::filter_min_planeangle(const double) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter) → pyrosetta.rosetta.protocols.filters.Filter¶

required in the context of the parser/scripting scheme

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

helix_id(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: int) → None¶

maximum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::helix_id(const unsigned long) –> void

name(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter) → str¶: C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::name() const –> std::string

output_type(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, s: str) → None¶

set output type

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::output_type(const class std::basic_string<char> &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, os: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

allows printing data to a stream

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

required for reporting score values

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

secstruct(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, ss: str) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::secstruct(const class std::basic_string<char> &) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

strand_id1(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: int) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::strand_id1(const unsigned long) –> void

strand_id2(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, r: int) → None¶

miniimum angle for filtering

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::strand_id2(const unsigned long) –> void

pyrosetta.rosetta.protocols.fldsgn.filters.find_pairing(spairset: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, s1: int, s2: int) → pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing¶

Searches the StrandPairingSet for a pairing containing s1 and s2. Returns OP to it

C++: protocols::fldsgn::filters::find_pairing(class protocols::fldsgn::topology::StrandPairingSet &, const unsigned long, const unsigned long) –> class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>

pyrosetta.rosetta.protocols.fldsgn.filters.find_pairing_idx(spairset: pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet, s1: int, s2: int) → int¶

Searches the StrandPairingSet for a pairing containing s1 and s2. Returns its 1-based index

C++: protocols::fldsgn::filters::find_pairing_idx(class protocols::fldsgn::topology::StrandPairingSet &, const unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.fldsgn.filters.remove_register_shifts(pair_str: str) → str¶

helper function for replacing register shift of all pairs with 99

C++: protocols::fldsgn::filters::remove_register_shifts(const class std::basic_string<char> &) –> std::string