filters

Bindings for protocols::denovo_design::filters namespace

class pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

static class_name() str

C++: protocols::denovo_design::filters::CavityVolumeFilter::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.denovo_design.filters.CavityVolumeFilter) pyrosetta.rosetta.protocols.filters.Filter

return a fresh instance of this class in an owning pointer

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

compute(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::CavityVolumeFilter::compute(const class core::pose::Pose &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter) pyrosetta.rosetta.protocols.filters.Filter

Apply the CavityVolumeFilter. Overloaded apply function from filter base class.

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

get_name(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter) str

Return the name of this mover.

C++: protocols::denovo_design::filters::CavityVolumeFilter::get_name() const –> std::string

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.denovo_design.filters.CavityVolumeFilter) str

C++: protocols::denovo_design::filters::CavityVolumeFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the CavityVolumeFilter tags

C++: protocols::denovo_design::filters::CavityVolumeFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::denovo_design::filters::CavityVolumeFilter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::CavityVolumeFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::filters::CavityVolumeFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::CavityVolumeFilter::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

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator, : pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator) pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator

C++: protocols::denovo_design::filters::CavityVolumeFilterCreator::operator=(const class protocols::denovo_design::filters::CavityVolumeFilterCreator &) –> class protocols::denovo_design::filters::CavityVolumeFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::CavityVolumeFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator) str

C++: protocols::denovo_design::filters::CavityVolumeFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::CavityVolumeFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

Apply the ExposedHydrophobicsFilter. Overloaded apply function from filter base class.

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

static class_name() str

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::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.denovo_design.filters.ExposedHydrophobicsFilter) pyrosetta.rosetta.protocols.filters.Filter

return a fresh instance of this class in an owning pointer

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

compute(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(const class core::pose::Pose &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter) pyrosetta.rosetta.protocols.filters.Filter

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

get_name(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter) str

Return the name of this mover.

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::get_name() const –> std::string

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.denovo_design.filters.ExposedHydrophobicsFilter) str

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the ExposedHydrophobicsFilter tags

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::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

set_sasa_cutoff(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, sasa_cutoff: float) None

Sets the SASA cutoff in order for a residue to be considered buried. If a residue has sasa <= sasa_cutoff, it is considered buried and will be ignored by the filter

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::set_sasa_cutoff(const double) –> void

set_threshold(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter, threshold: float) None

Sets the threshold; if the calculated filters core is <= threshold, the filter passes, otherwise it fails

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilter::set_threshold(const double) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator, : pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator) pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator::operator=(const class protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator &) –> class protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator) str

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::ExposedHydrophobicsFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

static class_name() str

C++: protocols::denovo_design::filters::PreProlineFilter::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.denovo_design.filters.PreProlineFilter) pyrosetta.rosetta.protocols.filters.Filter

return a fresh instance of this class in an owning pointer

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

compute(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::PreProlineFilter::compute(const class core::pose::Pose &) const –> double

compute_simple(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) float

C++: protocols::denovo_design::filters::PreProlineFilter::compute_simple(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> double

compute_spline(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool) float

C++: protocols::denovo_design::filters::PreProlineFilter::compute_spline(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter) pyrosetta.rosetta.protocols.filters.Filter

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

get_name(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter) str

Return the name of this mover.

C++: protocols::denovo_design::filters::PreProlineFilter::get_name() const –> std::string

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.denovo_design.filters.PreProlineFilter) str

C++: protocols::denovo_design::filters::PreProlineFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the PreProlineFilter tags

C++: protocols::denovo_design::filters::PreProlineFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::PreProlineFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::filters::PreProlineFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

Apply the PreProlineFilter. Overloaded apply function from filter base class.

C++: protocols::denovo_design::filters::PreProlineFilter::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

set_selector(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: protocols::denovo_design::filters::PreProlineFilter::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_threshold(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, threshold: float) None

C++: protocols::denovo_design::filters::PreProlineFilter::set_threshold(const double) –> void

set_use_statistical_potential(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter, use_stat: bool) None

C++: protocols::denovo_design::filters::PreProlineFilter::set_use_statistical_potential(const bool) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

setup_spline(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter) None

C++: protocols::denovo_design::filters::PreProlineFilter::setup_spline() –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator, : pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator) pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator

C++: protocols::denovo_design::filters::PreProlineFilterCreator::operator=(const class protocols::denovo_design::filters::PreProlineFilterCreator &) –> class protocols::denovo_design::filters::PreProlineFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::PreProlineFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator) str

C++: protocols::denovo_design::filters::PreProlineFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::PreProlineFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

static class_name() str

C++: protocols::denovo_design::filters::SSPredictionFilter::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.denovo_design.filters.SSPredictionFilter) pyrosetta.rosetta.protocols.filters.Filter

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

compute(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::SSPredictionFilter::compute(const class core::pose::Pose &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::SSPredictionFilter::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.denovo_design.filters.SSPredictionFilter) str

C++: protocols::denovo_design::filters::SSPredictionFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::filters::SSPredictionFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::SSPredictionFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::filters::SSPredictionFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::SSPredictionFilter::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

set_blueprint(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, blueprint: protocols::parser::BluePrint) None

Sets a blueprint object which can be used to determine the desired secondary structure

C++: protocols::denovo_design::filters::SSPredictionFilter::set_blueprint(class std::shared_ptr<class protocols::parser::BluePrint>) –> void

set_blueprint_file(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, blueprint_file: str) None

Sets a blueprint file which can be used to determine the desired secondary structure

C++: protocols::denovo_design::filters::SSPredictionFilter::set_blueprint_file(const std::string &) –> void

set_cmd(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, cmd: str) None

Sets the psipred executable (has no effect if “use_svm” is true)

C++: protocols::denovo_design::filters::SSPredictionFilter::set_cmd(const std::string &) –> void

set_mismatch_probability(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, mismatch_probability: bool) None

assumes use_probability, if set this will compute the cumulative probability of having correct secondary structure at all residues

C++: protocols::denovo_design::filters::SSPredictionFilter::set_mismatch_probability(const bool) –> void

set_psipred_interface(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, psipred: pyrosetta.rosetta.core.io.external.PsiPredInterface) None

Sets the psipred interface object that will be used to call psipred

C++: protocols::denovo_design::filters::SSPredictionFilter::set_psipred_interface(class std::shared_ptr<class core::io::external::PsiPredInterface>) –> void

set_secstruct(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, secstruct: str) None

Sets the secondary structure to be compared with the psipred result. If neither this nor the blueprint is set, DSSP will be used to determine the pose secondary structure

C++: protocols::denovo_design::filters::SSPredictionFilter::set_secstruct(const std::string) –> void

set_temperature(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, temp: float) None

Sets the temperature which is used to compute probability-based values

C++: protocols::denovo_design::filters::SSPredictionFilter::set_temperature(const double) –> void

set_threshold(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, threshold: float) None

Sets the threshold. If use_probablility is true, the filter will pass if the calculated value is <= threshold. If use_probability is false, the filter will pass if the calcualted value is >= threshold.

C++: protocols::denovo_design::filters::SSPredictionFilter::set_threshold(const double) –> void

set_use_confidence(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, use_confidence: bool) None

tells whether to use the psipred pass2 confidence values – overrrides use_probability.

C++: protocols::denovo_design::filters::SSPredictionFilter::set_use_confidence(const bool) –> void

set_use_probability(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, use_probability: bool) None

Sets whether or not to use the predicted SS probabilities to compute a value, or to use the predicted secondary structure (match or not matching) for each residue. Values are combined into a boltzmann sum-like-value using the provided temperature, so that poorly predicted residues have a larger impact on the score

C++: protocols::denovo_design::filters::SSPredictionFilter::set_use_probability(const bool) –> void

set_use_svm(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter, use_svm: bool) None

If set, a trained SVM will be used instead of psipred to predict the secondary structure

C++: protocols::denovo_design::filters::SSPredictionFilter::set_use_svm(const bool) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator, : pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator) pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator

C++: protocols::denovo_design::filters::SSPredictionFilterCreator::operator=(const class protocols::denovo_design::filters::SSPredictionFilterCreator &) –> class protocols::denovo_design::filters::SSPredictionFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::SSPredictionFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator) str

C++: protocols::denovo_design::filters::SSPredictionFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::SSPredictionFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

static class_name() str

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::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.denovo_design.filters.SSShapeComplementarityFilter) pyrosetta.rosetta.protocols.filters.Filter

return a fresh instance of this class in an owning pointer

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

compute(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::compute(const class core::pose::Pose &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter) pyrosetta.rosetta.protocols.filters.Filter

Apply the SSShapeComplementarityFilter. Overloaded apply function from filter base class.

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

get_name(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter) str

Return the name of this mover.

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::get_name() const –> std::string

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.denovo_design.filters.SSShapeComplementarityFilter) str

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parses the SSShapeComplementarityFilter tags

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

rejection_thresh(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter) float

Get the threshold below which structures are rejected.

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::rejection_thresh() const –> double

report(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::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

set_calc_helices(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, calc_helices: bool) None

Sets whether or not to include helices in the calculations

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_calc_helices(const bool) –> void

set_calc_loops(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, calc_loops: bool) None

Sets whether or not to include loops in the calculations

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_calc_loops(const bool) –> void

set_rejection_thresh(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, val: float) None

Set the threshold below which structures are rejected.

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_rejection_thresh(const double &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

Sets the residue selector to be used; clones the residue selector

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_residue_selector(const class core::select::residue_selector::ResidueSelector &) –> void

set_secstruct(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, secstruct: str) None

Set the secondary structure to be used for the pose. If unspecified, dssp will be used

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_secstruct(const std::string &) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

set_verbose(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter, verbose: bool) None

Sets the verbosity; if true, shape complementarity information will be printed out to the tracer when the filter is run. Not sure why the code can’t just use the Tracer system to do this, but that is how the code works right now

C++: protocols::denovo_design::filters::SSShapeComplementarityFilter::set_verbose(const bool) –> void

class pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator, : pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator) pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator

C++: protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::operator=(const class protocols::denovo_design::filters::SSShapeComplementarityFilterCreator &) –> class protocols::denovo_design::filters::SSShapeComplementarityFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator) str

C++: protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::filters::SSShapeComplementarityFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void