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.

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>

compute(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, pose: pyrosetta.rosetta.core.pose.Pose) → None

computes filter value

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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None

parse XML tag (to use this Filter in Rosetta Scripts)

C++: protocols::fldsgn::filters::HelixBendFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

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

set secondary structure

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

set_secstruct_from_bp(self: pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter, bp_file_path: str) → None

set secondary structure using a blueprint file

This triggers a read from disk; use with caution.

C++: protocols::fldsgn::filters::HelixBendFilter::set_secstruct_from_bp(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

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

parse_my_tag(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None

parse XML tag (to use this Filter in Rosetta Scripts)

C++: protocols::fldsgn::filters::StrandCurvatureByLevels::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> 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.

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

parse_my_tag(self: pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, filters: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, movers: pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, pose: pyrosetta.rosetta.core.pose.Pose) → None

parse XML tag (to use this Filter in Rosetta Scripts)

C++: protocols::fldsgn::filters::StrandHelixGeometryFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> 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