operation

Bindings for core::pack::task::operation namespace

class pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::AddBehaviorRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT, : pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT) → pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT

C++: core::pack::task::operation::AddBehaviorRLT::operator=(const class core::pack::task::operation::AddBehaviorRLT &) –> class core::pack::task::operation::AddBehaviorRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::AddBehaviorRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

static keyname() → str

C++: core::pack::task::operation::AddBehaviorRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::AddBehaviorRLT::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::AddBehaviorRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator

C++: core::pack::task::operation::AddBehaviorRLTCreator::operator=(const class core::pack::task::operation::AddBehaviorRLTCreator &) –> class core::pack::task::operation::AddBehaviorRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::AddBehaviorRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator) → str

C++: core::pack::task::operation::AddBehaviorRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AddBehaviorRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.AllResFilter

Bases: ResFilterComposition

assign(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilter, : pyrosetta.rosetta.core.pack.task.operation.AllResFilter) → pyrosetta.rosetta.core.pack.task.operation.AllResFilter

C++: core::pack::task::operation::AllResFilter::operator=(const class core::pack::task::operation::AllResFilter &) –> class core::pack::task::operation::AllResFilter &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::AllResFilter::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator

C++: core::pack::task::operation::ResFilterComposition::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

static keyname() → str

C++: core::pack::task::operation::AllResFilter::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResFilterComposition::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::AllResFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator, : pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator

C++: core::pack::task::operation::AllResFilterCreator::operator=(const class core::pack::task::operation::AllResFilterCreator &) –> class core::pack::task::operation::AllResFilterCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::AllResFilterCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator) → str

C++: core::pack::task::operation::AllResFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AllResFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.AnyResFilter

Bases: ResFilterComposition

assign(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilter, : pyrosetta.rosetta.core.pack.task.operation.AnyResFilter) → pyrosetta.rosetta.core.pack.task.operation.AnyResFilter

C++: core::pack::task::operation::AnyResFilter::operator=(const class core::pack::task::operation::AnyResFilter &) –> class core::pack::task::operation::AnyResFilter &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::AnyResFilter::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator

C++: core::pack::task::operation::ResFilterComposition::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

static keyname() → str

C++: core::pack::task::operation::AnyResFilter::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResFilterComposition::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::AnyResFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator, : pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator

C++: core::pack::task::operation::AnyResFilterCreator::operator=(const class core::pack::task::operation::AnyResFilterCreator &) –> class core::pack::task::operation::AnyResFilterCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::AnyResFilterCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator) → str

C++: core::pack::task::operation::AnyResFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AnyResFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet

Bases: TaskOperation

Apply rotamerSetOperation to only the rotamerSet for the given residue

Tim Jacobs (2011)

apply(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::AppendResidueRotamerSet::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet, : pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet) → pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet

C++: core::pack::task::operation::AppendResidueRotamerSet::operator=(const class core::pack::task::operation::AppendResidueRotamerSet &) –> class core::pack::task::operation::AppendResidueRotamerSet &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendResidueRotamerSet::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::AppendResidueRotamerSet::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::AppendResidueRotamerSet::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_resnum(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet, resnum: int) → None

C++: core::pack::task::operation::AppendResidueRotamerSet::set_resnum(unsigned long) –> void

set_rotamer_set_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet, rotamer_operation: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → None

C++: core::pack::task::operation::AppendResidueRotamerSet::set_rotamer_set_operation(class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>) –> void

class pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator, : pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator) → pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator

C++: core::pack::task::operation::AppendResidueRotamerSetCreator::operator=(const class core::pack::task::operation::AppendResidueRotamerSetCreator &) –> class core::pack::task::operation::AppendResidueRotamerSetCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendResidueRotamerSetCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator) → str

C++: core::pack::task::operation::AppendResidueRotamerSetCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AppendResidueRotamerSetCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.AppendRotamer

Bases: TaskOperation

when a PackerTask is created by the Factory, the RotamerOperation will be given to it

apply(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::AppendRotamer::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamer, : pyrosetta.rosetta.core.pack.task.operation.AppendRotamer) → pyrosetta.rosetta.core.pack.task.operation.AppendRotamer

C++: core::pack::task::operation::AppendRotamer::operator=(const class core::pack::task::operation::AppendRotamer &) –> class core::pack::task::operation::AppendRotamer &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamer) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendRotamer::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::AppendRotamer::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::AppendRotamer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_rotamer_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamer, rotamer_operation: pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation) → None

C++: core::pack::task::operation::AppendRotamer::set_rotamer_operation(class std::shared_ptr<class core::pack::rotamer_set::RotamerOperation>) –> void

class pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator, : pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator) → pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator

C++: core::pack::task::operation::AppendRotamerCreator::operator=(const class core::pack::task::operation::AppendRotamerCreator &) –> class core::pack::task::operation::AppendRotamerCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendRotamerCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator) → str

C++: core::pack::task::operation::AppendRotamerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AppendRotamerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet

Bases: TaskOperation

when a PackerTask is created by the Factory, the RotamerSetOperation will be given to it

Barak Raveh (Dec 2008)

apply(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::AppendRotamerSet::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet, : pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet) → pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet

C++: core::pack::task::operation::AppendRotamerSet::operator=(const class core::pack::task::operation::AppendRotamerSet &) –> class core::pack::task::operation::AppendRotamerSet &

clone(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendRotamerSet::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::AppendRotamerSet::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::AppendRotamerSet::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_rotamer_set_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet, rotamer_operation: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → None

C++: core::pack::task::operation::AppendRotamerSet::set_rotamer_set_operation(class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>) –> void

class pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator, : pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator) → pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator

C++: core::pack::task::operation::AppendRotamerSetCreator::operator=(const class core::pack::task::operation::AppendRotamerSetCreator &) –> class core::pack::task::operation::AppendRotamerSetCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::AppendRotamerSetCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator) → str

C++: core::pack::task::operation::AppendRotamerSetCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::AppendRotamerSetCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ChainIs

Bases: ResFilter

assign(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs, : pyrosetta.rosetta.core.pack.task.operation.ChainIs) → pyrosetta.rosetta.core.pack.task.operation.ChainIs

C++: core::pack::task::operation::ChainIs::operator=(const class core::pack::task::operation::ChainIs &) –> class core::pack::task::operation::ChainIs &

chain(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs) → str

C++: core::pack::task::operation::ChainIs::chain() const –> const char &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ChainIs::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes(xsd: utility::tag::XMLSchemaDefinition) → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ChainIs::get_xml_schema_attributes(class utility::tag::XMLSchemaDefinition &) –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ChainIs::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ChainIs::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::ChainIs::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator, : pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator) → pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator

C++: core::pack::task::operation::ChainIsCreator::operator=(const class core::pack::task::operation::ChainIsCreator &) –> class core::pack::task::operation::ChainIsCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ChainIsCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator) → str

C++: core::pack::task::operation::ChainIsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ChainIsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ChainIsnt

Bases: ChainIs

assign(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsnt, : pyrosetta.rosetta.core.pack.task.operation.ChainIsnt) → pyrosetta.rosetta.core.pack.task.operation.ChainIsnt

C++: core::pack::task::operation::ChainIsnt::operator=(const class core::pack::task::operation::ChainIsnt &) –> class core::pack::task::operation::ChainIsnt &

chain(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs) → str

C++: core::pack::task::operation::ChainIs::chain() const –> const char &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsnt) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ChainIsnt::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes(xsd: utility::tag::XMLSchemaDefinition) → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ChainIs::get_xml_schema_attributes(class utility::tag::XMLSchemaDefinition &) –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ChainIsnt::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ChainIs, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ChainIs::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::ChainIsnt::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator, : pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator) → pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator

C++: core::pack::task::operation::ChainIsntCreator::operator=(const class core::pack::task::operation::ChainIsntCreator &) –> class core::pack::task::operation::ChainIsntCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ChainIsntCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator) → str

C++: core::pack::task::operation::ChainIsntCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ChainIsntCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell

Bases: TaskOperation

Create a shell of residues that can repack around a smaller group of residues being repacked or designed.

More specifically, this task operation disables repacking for (i.e. freezes) any position that isn’t part of the aforementioned group or its shell. The most common use-case is to define a set of positions that you’re interested in designing (i.e. with a resfile), and limit the rest of the protein to repacking (e.g. NATAA). Then you can apply the ClashBasedRepackShell to limit the repacking to only the positions that really interact with the design positions. This keeps the simulations efficient and prevents the final scores from being affected by random changes in packing far away from the region being designed.

This task operation is a very thin wrapper around ClashBasedShellSelector. You can access and configure the selector in question via the selector() method.

apply(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

apply operations to PackerTask

C++: core::pack::task::operation::ClashBasedRepackShell::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell, : pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell) → pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell

C++: core::pack::task::operation::ClashBasedRepackShell::operator=(const class core::pack::task::operation::ClashBasedRepackShell &) –> class core::pack::task::operation::ClashBasedRepackShell &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Return a shallow copy of this object.

C++: core::pack::task::operation::ClashBasedRepackShell::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return “ClashBasedRepackShell”.

C++: core::pack::task::operation::ClashBasedRepackShell::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Initialize from an XML tag.

C++: core::pack::task::operation::ClashBasedRepackShell::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Define the expected XML options.

C++: core::pack::task::operation::ClashBasedRepackShell::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selector(*args, **kwargs)

Overloaded function.

1. selector(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell) -> core::pack::task::residue_selector::ClashBasedShellSelector

Get the ResidueSelector used to define the repack shell.

C++: core::pack::task::operation::ClashBasedRepackShell::selector() const –> class std::shared_ptr<class core::pack::task::residue_selector::ClashBasedShellSelector>

2. selector(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell, : core::pack::task::residue_selector::ClashBasedShellSelector) -> None

Set the ResidueSelector used to define the repack shell.

C++: core::pack::task::operation::ClashBasedRepackShell::selector(class std::shared_ptr<class core::pack::task::residue_selector::ClashBasedShellSelector>) –> void

class pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator, : pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator) → pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator

C++: core::pack::task::operation::ClashBasedRepackShellCreator::operator=(const class core::pack::task::operation::ClashBasedRepackShellCreator &) –> class core::pack::task::operation::ClashBasedRepackShellCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ClashBasedRepackShellCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator) → str

C++: core::pack::task::operation::ClashBasedRepackShellCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ClashBasedRepackShellCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions

Bases: TaskOperation

Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely

Basically, we want to be able to encode layer design as follows:

<RESIDUE_SELECTORS>

<Layer name=”surface” select_core=”false” select_boundary=”false” select_surface=”true” use_sidechain_neighbors=”true”/> <Layer name=”boundary” select_core=”false” select_boundary=”true” select_surface=”false” use_sidechain_neighbors=”true”/> <Layer name=”core” select_core=”true” select_boundary=”false” select_surface=”false” use_sidechain_neighbors=”true”/> <SecondaryStructure name=”helix” overlap=”0” minH=”3” include_terminal_loops=”false” use_dssp=”true” ss=”H” /> <SecondaryStructure name=”sheet” overlap=”0” minE=”3” include_terminal_loops=”false” use_dssp=”true” ss=”E” /> <SecondaryStructure name=”loop” overlap=”0” minH=”3” minE=”3” include_terminal_loops=”true” use_dssp=”true” ss=”L” />

</RESIDUE_SELECTORS> <TASKOPERATIONS>

<DesignRestrictions name=”layer_design”>

<Action selector_logic=”surface AND ( helix OR sheet) ” aas=”DEHKNQRST”/> <Action selector_logic=”surface AND loop” aas=”DEGHKNPQRST”/> <Action selector_logic=”boundary AND helix” aas=”ADEIKLMNQRSTVWY”/> <Action selector_logic=”boundary AND sheet” aas=”DEFIKLNQRSTVWY”/> <Action selector_logic=”boundary AND loop” aas=”ADEFGIKLMNPQRSTVWY”/> <Action selector_logic=”core AND helix” aas=”AFILMVWY”/> <Action selector_logic=”core AND sheet” aas=”FILVWY”/> <Action selector_logic=”core AND loop” aas=”AFILMPVWY”/>

</DesignRestrictions>

</TASKOPERATIONS>

So that it then becomes easy to adapt it to change the logic; e.g. if residues 19, 21, and 23 should keep their native amino acid, and still be allowed to pack, then it will look like this

<RESIDUE_SELECTORS>

… the surface, boundary, core, helix, sheet and loop selectors listed above … <ResidueIndexSelector name=”special_res” resnums=”19,21,23”/>

<RESIDUE_LEVEL_TASK_OPERATIONS>

<RestrictToRepackingRLT name=”rtr”/>

<RESIDUE_LEVEL_TASK_OPERATIONS> <TASKOPERATIONS>

<DesignRestrictions name=”custom_layer_design”>

<Action residue_selector=”special_res” residue_level_operations=”rtr”/> <Action selector_logic=”!special_res AND surface AND ( helix OR sheet) ” aas=”DEHKNQRST”/> <Action selector_logic=”!special_res AND surface AND loop” aas=”DEGHKNPQRST”/> <Action selector_logic=”!special_res AND boundary AND helix” aas=”ADEIKLMNQRSTVWY”/> <Action selector_logic=”!special_res AND boundary AND sheet” aas=”DEFIKLNQRSTVWY”/> <Action selector_logic=”!special_res AND boundary AND loop” aas=”ADEFGIKLMNPQRSTVWY”/> <Action selector_logic=”!special_res AND core AND helix” aas=”AFILMVWY”/> <Action selector_logic=”!special_res AND core AND sheet” aas=”FILVWY”/> <Action selector_logic=”!special_res AND core AND loop” aas=”AFILMPVWY”/>

</DesignRestrictions>

</TASKOPERATIONS>

Where the second “Action” above is saying “apply this to residues besides the special residues that are on surface loops”

add_selector_rlto_pair(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, rlto: core::pack::task::operation::ResLvlTaskOperation) → None

C++: core::pack::task::operation::DesignRestrictions::add_selector_rlto_pair(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::pack::task::operation::ResLvlTaskOperation>) –> void

apply(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::DesignRestrictions::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions, : pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions) → pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions

C++: core::pack::task::operation::DesignRestrictions::operator=(const class core::pack::task::operation::DesignRestrictions &) –> class core::pack::task::operation::DesignRestrictions &

clone(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::DesignRestrictions::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return the name used to construct this TaskOperation from an XML file

C++: core::pack::task::operation::DesignRestrictions::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts XML tag.

C++: core::pack::task::operation::DesignRestrictions::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Describe the format of XML file used to initialize this TaskOperation

C++: core::pack::task::operation::DesignRestrictions::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator, : pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator) → pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator

C++: core::pack::task::operation::DesignRestrictionsCreator::operator=(const class core::pack::task::operation::DesignRestrictionsCreator &) –> class core::pack::task::operation::DesignRestrictionsCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::DesignRestrictionsCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator) → str

C++: core::pack::task::operation::DesignRestrictionsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::DesignRestrictionsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative

Bases: TaskOperation

DisallowIfNonnative allows you to define what residues are NOT allowed in packing unless that residue is present in the input. Behaves like RestrictAbsentCanonicalAAS and NOTAA except will allow a resitricted residue at a position if it is there to begin with at the time of Task creation. Will do all residues unless otherwise defined by selection syntax below

apply(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::DisallowIfNonnative::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, : pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative) → pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative

C++: core::pack::task::operation::DisallowIfNonnative::operator=(const class core::pack::task::operation::DisallowIfNonnative &) –> class core::pack::task::operation::DisallowIfNonnative &

clear(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative) → None

C++: core::pack::task::operation::DisallowIfNonnative::clear() –> void

clone(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::DisallowIfNonnative::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

disallow_aas(*args, **kwargs)

Overloaded function.

1. disallow_aas(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, canonical_disallowed: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: core::pack::task::operation::DisallowIfNonnative::disallow_aas(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

2. disallow_aas(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, aa_string: str) -> None

C++: core::pack::task::operation::DisallowIfNonnative::disallow_aas(const std::string &) –> void

static keyname() → str

C++: core::pack::task::operation::DisallowIfNonnative::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::DisallowIfNonnative::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::DisallowIfNonnative::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

restrict_to_residue(*args, **kwargs)

Overloaded function.

1. restrict_to_residue(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, resid: int) -> None

C++: core::pack::task::operation::DisallowIfNonnative::restrict_to_residue(const unsigned long &) –> void

2. restrict_to_residue(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative, residues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::task::operation::DisallowIfNonnative::restrict_to_residue(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator, : pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator) → pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator

C++: core::pack::task::operation::DisallowIfNonnativeCreator::operator=(const class core::pack::task::operation::DisallowIfNonnativeCreator &) –> class core::pack::task::operation::DisallowIfNonnativeCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::DisallowIfNonnativeCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator) → str

C++: core::pack::task::operation::DisallowIfNonnativeCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::DisallowIfNonnativeCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT, rlt: pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::DisallowIfNonnativeRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT, : pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT) → pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT

C++: core::pack::task::operation::DisallowIfNonnativeRLT::operator=(const class core::pack::task::operation::DisallowIfNonnativeRLT &) –> class core::pack::task::operation::DisallowIfNonnativeRLT &

clear(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT) → None

C++: core::pack::task::operation::DisallowIfNonnativeRLT::clear() –> void

clone(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::DisallowIfNonnativeRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

disallow_aas(*args, **kwargs)

Overloaded function.

1. disallow_aas(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT, canonical_disallowed: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

2. disallow_aas(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT, aa_string: str) -> None

C++: core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(const std::string &) –> void

static keyname() → str

C++: core::pack::task::operation::DisallowIfNonnativeRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::DisallowIfNonnativeRLT::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::DisallowIfNonnativeRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator

C++: core::pack::task::operation::DisallowIfNonnativeRLTCreator::operator=(const class core::pack::task::operation::DisallowIfNonnativeRLTCreator &) –> class core::pack::task::operation::DisallowIfNonnativeRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::DisallowIfNonnativeRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator) → str

C++: core::pack::task::operation::DisallowIfNonnativeRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::DisallowIfNonnativeRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer

Bases: TaskOperation

Task Operation for turning on the multi-cool annealer

apply(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::EnableMultiCoolAnnealer::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer, : pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer) → pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer

C++: core::pack::task::operation::EnableMultiCoolAnnealer::operator=(const class core::pack::task::operation::EnableMultiCoolAnnealer &) –> class core::pack::task::operation::EnableMultiCoolAnnealer &

clone(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::EnableMultiCoolAnnealer::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return the name used to construct this TaskOperation from an XML file

C++: core::pack::task::operation::EnableMultiCoolAnnealer::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts XML tag.

C++: core::pack::task::operation::EnableMultiCoolAnnealer::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Describe the format of XML file used to initialize this TaskOperation

C++: core::pack::task::operation::EnableMultiCoolAnnealer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator, : pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator) → pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator

C++: core::pack::task::operation::EnableMultiCoolAnnealerCreator::operator=(const class core::pack::task::operation::EnableMultiCoolAnnealerCreator &) –> class core::pack::task::operation::EnableMultiCoolAnnealerCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::EnableMultiCoolAnnealerCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator) → str

C++: core::pack::task::operation::EnableMultiCoolAnnealerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::EnableMultiCoolAnnealerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer

Bases: TaskOperation

Task Operation for turning on the multi-cool annealer

apply(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::EnableSmartAnnealer::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, : pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer

C++: core::pack::task::operation::EnableSmartAnnealer::operator=(const class core::pack::task::operation::EnableSmartAnnealer &) –> class core::pack::task::operation::EnableSmartAnnealer &

clone(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::EnableSmartAnnealer::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return the name used to construct this TaskOperation from an XML file

C++: core::pack::task::operation::EnableSmartAnnealer::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts XML tag.

C++: core::pack::task::operation::EnableSmartAnnealer::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Describe the format of XML file used to initialize this TaskOperation

C++: core::pack::task::operation::EnableSmartAnnealer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_smart_annealer_cutoff(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, smart_annealer_cutoff: float) → None

C++: core::pack::task::operation::EnableSmartAnnealer::set_smart_annealer_cutoff(const double) –> void

set_smart_annealer_disable_during_quench(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, smart_annealer_disable_during_quench: bool) → None

C++: core::pack::task::operation::EnableSmartAnnealer::set_smart_annealer_disable_during_quench(const bool) –> void

set_smart_annealer_model(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, smart_annealer_model: str) → None

C++: core::pack::task::operation::EnableSmartAnnealer::set_smart_annealer_model(const std::string &) –> void

set_smart_annealer_pick_again(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer, smart_annealer_pick_again: bool) → None

C++: core::pack::task::operation::EnableSmartAnnealer::set_smart_annealer_pick_again(const bool) –> void

smart_annealer_cutoff(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → float

C++: core::pack::task::operation::EnableSmartAnnealer::smart_annealer_cutoff() const –> double

smart_annealer_disable_during_quench(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → bool

C++: core::pack::task::operation::EnableSmartAnnealer::smart_annealer_disable_during_quench() const –> bool

smart_annealer_model(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → str

C++: core::pack::task::operation::EnableSmartAnnealer::smart_annealer_model() const –> const std::string &

smart_annealer_pick_again(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer) → bool

C++: core::pack::task::operation::EnableSmartAnnealer::smart_annealer_pick_again() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator, : pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator) → pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator

C++: core::pack::task::operation::EnableSmartAnnealerCreator::operator=(const class core::pack::task::operation::EnableSmartAnnealerCreator &) –> class core::pack::task::operation::EnableSmartAnnealerCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::EnableSmartAnnealerCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator) → str

C++: core::pack::task::operation::EnableSmartAnnealerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::EnableSmartAnnealerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff(correponding to flag "-extrachi_cutoff <float>")

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ExtraChiCutoff::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff, : pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff) → pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff

C++: core::pack::task::operation::ExtraChiCutoff::operator=(const class core::pack::task::operation::ExtraChiCutoff &) –> class core::pack::task::operation::ExtraChiCutoff &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraChiCutoff::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::ExtraChiCutoff::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ExtraChiCutoff::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ExtraChiCutoff::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator, : pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator) → pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator

C++: core::pack::task::operation::ExtraChiCutoffCreator::operator=(const class core::pack::task::operation::ExtraChiCutoffCreator &) –> class core::pack::task::operation::ExtraChiCutoffCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraChiCutoffCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator) → str

C++: core::pack::task::operation::ExtraChiCutoffCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ExtraChiCutoffCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::ExtraChiCutoffRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT, : pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT) → pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT

C++: core::pack::task::operation::ExtraChiCutoffRLT::operator=(const class core::pack::task::operation::ExtraChiCutoffRLT &) –> class core::pack::task::operation::ExtraChiCutoffRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::ExtraChiCutoffRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

static keyname() → str

C++: core::pack::task::operation::ExtraChiCutoffRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ExtraChiCutoffRLT::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ExtraChiCutoffRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator

C++: core::pack::task::operation::ExtraChiCutoffRLTCreator::operator=(const class core::pack::task::operation::ExtraChiCutoffRLTCreator &) –> class core::pack::task::operation::ExtraChiCutoffRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::ExtraChiCutoffRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator) → str

C++: core::pack::task::operation::ExtraChiCutoffRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ExtraChiCutoffRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData

C++: core::pack::task::operation::ExtraRotamerSamplingData::operator=(const struct core::pack::task::operation::ExtraRotamerSamplingData &) –> struct core::pack::task::operation::ExtraRotamerSamplingData &

property ex1_

property ex1_sample_level_

property ex1aro_

property ex1aro_exposed_

property ex1aro_exposed_sample_level_

property ex1aro_sample_level_

property ex2_

property ex2_sample_level_

property ex2aro_

property ex2aro_exposed_

property ex2aro_exposed_sample_level_

property ex2aro_sample_level_

property ex3_

property ex3_sample_level_

property ex4_

property ex4_sample_level_

property exdna_sample_level_

property extrachi_cutoff_

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers

Bases: TaskOperation

ExtraRotamer for a residue. You know, -ex1, -ex2, all that.

apply(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ExtraRotamers::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers

C++: core::pack::task::operation::ExtraRotamers::operator=(const class core::pack::task::operation::ExtraRotamers &) –> class core::pack::task::operation::ExtraRotamers &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraRotamers::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::ExtraRotamers::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ExtraRotamers::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ExtraRotamers::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator

C++: core::pack::task::operation::ExtraRotamersCreator::operator=(const class core::pack::task::operation::ExtraRotamersCreator &) –> class core::pack::task::operation::ExtraRotamersCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraRotamersCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator) → str

C++: core::pack::task::operation::ExtraRotamersCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ExtraRotamersCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric

Bases: TaskOperation

control the extra chi rotamers for all residues

apply(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric

C++: core::pack::task::operation::ExtraRotamersGeneric::operator=(const class core::pack::task::operation::ExtraRotamersGeneric &) –> class core::pack::task::operation::ExtraRotamersGeneric &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraRotamersGeneric::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

ex1(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1(bool) –> void

ex1_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex1aro(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1aro(bool) –> void

ex1aro_exposed(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1aro_exposed(bool) –> void

ex1aro_exposed_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1aro_exposed_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex1aro_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex1aro_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2(bool) –> void

ex2_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2aro(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2aro(bool) –> void

ex2aro_exposed(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2aro_exposed(bool) –> void

ex2aro_exposed_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2aro_exposed_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2aro_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex2aro_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex3(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex3(bool) –> void

ex3_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex3_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex4(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex4(bool) –> void

ex4_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::ex4_sample_level(enum core::pack::task::ExtraRotSample) –> void

exdna_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::exdna_sample_level(enum core::pack::task::ExtraRotSample) –> void

extrachi_cutoff(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, value: int) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::extrachi_cutoff(unsigned long) –> void

static keyname() → str

C++: core::pack::task::operation::ExtraRotamersGeneric::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ExtraRotamersGeneric::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ExtraRotamersGeneric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sampling_data(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData

C++: core::pack::task::operation::ExtraRotamersGeneric::sampling_data() const –> const struct core::pack::task::operation::ExtraRotamerSamplingData &

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator

C++: core::pack::task::operation::ExtraRotamersGenericCreator::operator=(const class core::pack::task::operation::ExtraRotamersGenericCreator &) –> class core::pack::task::operation::ExtraRotamersGenericCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ExtraRotamersGenericCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator) → str

C++: core::pack::task::operation::ExtraRotamersGenericCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ExtraRotamersGenericCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT

C++: core::pack::task::operation::ExtraRotamersGenericRLT::operator=(const class core::pack::task::operation::ExtraRotamersGenericRLT &) –> class core::pack::task::operation::ExtraRotamersGenericRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::ExtraRotamersGenericRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

ex1(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1(bool) –> void

ex1_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex1aro(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1aro(bool) –> void

ex1aro_exposed(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1aro_exposed(bool) –> void

ex1aro_exposed_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1aro_exposed_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex1aro_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex1aro_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2(bool) –> void

ex2_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2aro(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2aro(bool) –> void

ex2aro_exposed(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2aro_exposed(bool) –> void

ex2aro_exposed_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2aro_exposed_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex2aro_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex2aro_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex3(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex3(bool) –> void

ex3_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex3_sample_level(enum core::pack::task::ExtraRotSample) –> void

ex4(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: bool) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex4(bool) –> void

ex4_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::ex4_sample_level(enum core::pack::task::ExtraRotSample) –> void

exdna_sample_level(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: pyrosetta.rosetta.core.pack.task.ExtraRotSample) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::exdna_sample_level(enum core::pack::task::ExtraRotSample) –> void

extrachi_cutoff(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, value: int) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::extrachi_cutoff(unsigned long) –> void

static keyname() → str

C++: core::pack::task::operation::ExtraRotamersGenericRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLT::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ExtraRotamersGenericRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sampling_data(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamerSamplingData

C++: core::pack::task::operation::ExtraRotamersGenericRLT::sampling_data() const –> const struct core::pack::task::operation::ExtraRotamerSamplingData &

class pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator

C++: core::pack::task::operation::ExtraRotamersGenericRLTCreator::operator=(const class core::pack::task::operation::ExtraRotamersGenericRLTCreator &) –> class core::pack::task::operation::ExtraRotamersGenericRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::ExtraRotamersGenericRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator) → str

C++: core::pack::task::operation::ExtraRotamersGenericRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ExtraRotamersGenericRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation

Bases: TaskOperation

fills the AUTO behavior for all residues in Task. Useful if a protocol expects AUTO-style resfile, but no resfile present.

apply(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::FillAUTOTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation, : pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation

C++: core::pack::task::operation::FillAUTOTaskOperation::operator=(const class core::pack::task::operation::FillAUTOTaskOperation &) –> class core::pack::task::operation::FillAUTOTaskOperation &

clone(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::FillAUTOTaskOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return the name used to construct this TaskOperation from an XML file

C++: core::pack::task::operation::FillAUTOTaskOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts XML tag.

C++: core::pack::task::operation::FillAUTOTaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Describe the format of XML file used to initialize this TaskOperation

C++: core::pack::task::operation::FillAUTOTaskOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator, : pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator

C++: core::pack::task::operation::FillAUTOTaskOperationCreator::operator=(const class core::pack::task::operation::FillAUTOTaskOperationCreator &) –> class core::pack::task::operation::FillAUTOTaskOperationCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::FillAUTOTaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator) → str

C++: core::pack::task::operation::FillAUTOTaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::FillAUTOTaskOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::IncludeCurrent::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent, : pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent) → pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent

C++: core::pack::task::operation::IncludeCurrent::operator=(const class core::pack::task::operation::IncludeCurrent &) –> class core::pack::task::operation::IncludeCurrent &

clone(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::IncludeCurrent::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::IncludeCurrent::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::IncludeCurrent::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator, : pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator) → pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator

C++: core::pack::task::operation::IncludeCurrentCreator::operator=(const class core::pack::task::operation::IncludeCurrentCreator &) –> class core::pack::task::operation::IncludeCurrentCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::IncludeCurrentCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator) → str

C++: core::pack::task::operation::IncludeCurrentCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::IncludeCurrentCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::IncludeCurrentRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT, : pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT) → pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT

C++: core::pack::task::operation::IncludeCurrentRLT::operator=(const class core::pack::task::operation::IncludeCurrentRLT &) –> class core::pack::task::operation::IncludeCurrentRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::IncludeCurrentRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

static keyname() → str

C++: core::pack::task::operation::IncludeCurrentRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.utility.tag.Tag) → None

parser xml-like tags to set class data/parameters

C++: core::pack::task::operation::ResLvlTaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::IncludeCurrentRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator

C++: core::pack::task::operation::IncludeCurrentRLTCreator::operator=(const class core::pack::task::operation::IncludeCurrentRLTCreator &) –> class core::pack::task::operation::IncludeCurrentRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::IncludeCurrentRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator) → str

C++: core::pack::task::operation::IncludeCurrentRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::IncludeCurrentRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::InitializeExtraRotsFromCommandline::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline, : pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline) → pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline

C++: core::pack::task::operation::InitializeExtraRotsFromCommandline::operator=(const class core::pack::task::operation::InitializeExtraRotsFromCommandline &) –> class core::pack::task::operation::InitializeExtraRotsFromCommandline &

clone(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeExtraRotsFromCommandline::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::InitializeExtraRotsFromCommandline::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::InitializeExtraRotsFromCommandline::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator, : pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator) → pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator

C++: core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator::operator=(const class core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator &) –> class core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator) → str

C++: core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::InitializeExtraRotsFromCommandlineCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::InitializeFromCommandline::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline, : pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline) → pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline

C++: core::pack::task::operation::InitializeFromCommandline::operator=(const class core::pack::task::operation::InitializeFromCommandline &) –> class core::pack::task::operation::InitializeFromCommandline &

clone(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeFromCommandline::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::InitializeFromCommandline::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::InitializeFromCommandline::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::InitializeFromCommandline::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator, : pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator) → pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator

C++: core::pack::task::operation::InitializeFromCommandlineCreator::operator=(const class core::pack::task::operation::InitializeFromCommandlineCreator &) –> class core::pack::task::operation::InitializeFromCommandlineCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeFromCommandlineCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator) → str

C++: core::pack::task::operation::InitializeFromCommandlineCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::InitializeFromCommandlineCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection

Bases: TaskOperation

retrieves an OptionCollection from the DataMap.

apply(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::InitializeFromOptionCollection::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection, : pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection) → pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection

C++: core::pack::task::operation::InitializeFromOptionCollection::operator=(const class core::pack::task::operation::InitializeFromOptionCollection &) –> class core::pack::task::operation::InitializeFromOptionCollection &

clone(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeFromOptionCollection::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::InitializeFromOptionCollection::keyname() –> std::string

options(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection, options: pyrosetta.rosetta.utility.options.OptionCollection) → None

C++: core::pack::task::operation::InitializeFromOptionCollection::options(class std::shared_ptr<const class utility::options::OptionCollection>) –> void

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::InitializeFromOptionCollection::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::InitializeFromOptionCollection::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator, : pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator) → pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator

C++: core::pack::task::operation::InitializeFromOptionCollectionCreator::operator=(const class core::pack::task::operation::InitializeFromOptionCollectionCreator &) –> class core::pack::task::operation::InitializeFromOptionCollectionCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::InitializeFromOptionCollectionCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator) → str

C++: core::pack::task::operation::InitializeFromOptionCollectionCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::InitializeFromOptionCollectionCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry

Bases: TaskOperation

Task Operation for turning on the multi-cool annealer

apply(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::KeepSequenceSymmetry::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry, : pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry) → pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry

C++: core::pack::task::operation::KeepSequenceSymmetry::operator=(const class core::pack::task::operation::KeepSequenceSymmetry &) –> class core::pack::task::operation::KeepSequenceSymmetry &

clone(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::KeepSequenceSymmetry::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

Return the name used to construct this TaskOperation from an XML file

C++: core::pack::task::operation::KeepSequenceSymmetry::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts XML tag.

C++: core::pack::task::operation::KeepSequenceSymmetry::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prefix_name(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry) → str

C++: core::pack::task::operation::KeepSequenceSymmetry::prefix_name() const –> std::string

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Describe the format of XML file used to initialize this TaskOperation

C++: core::pack::task::operation::KeepSequenceSymmetry::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_prefix_name(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry, setting: str) → None

Sets the name used for determining sequence symmetric selectors.

C++: core::pack::task::operation::KeepSequenceSymmetry::set_prefix_name(const std::string &) –> void

set_setting(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry, setting: bool) → None

C++: core::pack::task::operation::KeepSequenceSymmetry::set_setting(const bool) –> void

setting(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry) → bool

C++: core::pack::task::operation::KeepSequenceSymmetry::setting() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator, : pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator) → pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator

C++: core::pack::task::operation::KeepSequenceSymmetryCreator::operator=(const class core::pack::task::operation::KeepSequenceSymmetryCreator &) –> class core::pack::task::operation::KeepSequenceSymmetryCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::KeepSequenceSymmetryCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator) → str

C++: core::pack::task::operation::KeepSequenceSymmetryCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::KeepSequenceSymmetryCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides

Bases: TaskOperation

prevent disulfides from being repacked; assume disulfides info in Pose is up-to-date

apply(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

apply operations to PackerTask

C++: core::pack::task::operation::NoRepackDisulfides::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides, : pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides) → pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides

C++: core::pack::task::operation::NoRepackDisulfides::operator=(const class core::pack::task::operation::NoRepackDisulfides &) –> class core::pack::task::operation::NoRepackDisulfides &

clone(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

clone this object

C++: core::pack::task::operation::NoRepackDisulfides::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::NoRepackDisulfides::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::NoRepackDisulfides::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator, : pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator) → pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator

C++: core::pack::task::operation::NoRepackDisulfidesCreator::operator=(const class core::pack::task::operation::NoRepackDisulfidesCreator &) –> class core::pack::task::operation::NoRepackDisulfidesCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::NoRepackDisulfidesCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator) → str

C++: core::pack::task::operation::NoRepackDisulfidesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::NoRepackDisulfidesCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.NoResFilter

Bases: ResFilterComposition

assign(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilter, : pyrosetta.rosetta.core.pack.task.operation.NoResFilter) → pyrosetta.rosetta.core.pack.task.operation.NoResFilter

C++: core::pack::task::operation::NoResFilter::operator=(const class core::pack::task::operation::NoResFilter &) –> class core::pack::task::operation::NoResFilter &

clone(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::NoResFilter::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator

C++: core::pack::task::operation::ResFilterComposition::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

static keyname() → str

C++: core::pack::task::operation::NoResFilter::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResFilterComposition::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::NoResFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator, : pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator

C++: core::pack::task::operation::NoResFilterCreator::operator=(const class core::pack::task::operation::NoResFilterCreator &) –> class core::pack::task::operation::NoResFilterCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::NoResFilterCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator) → str

C++: core::pack::task::operation::NoResFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::NoResFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::OperateOnCertainResidues::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues) → pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues

C++: core::pack::task::operation::OperateOnCertainResidues::operator=(const class core::pack::task::operation::OperateOnCertainResidues &) –> class core::pack::task::operation::OperateOnCertainResidues &

clone(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OperateOnCertainResidues::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

filter(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : core::pack::task::operation::ResFilter) → None

sets an optional filter that is applied to each individual residue

C++: core::pack::task::operation::OperateOnCertainResidues::filter(class std::shared_ptr<class core::pack::task::operation::ResFilter>) –> void

static keyname() → str

C++: core::pack::task::operation::OperateOnCertainResidues::keyname() –> std::string

op(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : core::pack::task::operation::ResLvlTaskOperation) → None

sets the ResLvlTaskOperation that will be applied to residues

C++: core::pack::task::operation::OperateOnCertainResidues::op(class std::shared_ptr<const class core::pack::task::operation::ResLvlTaskOperation>) –> void

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to construct the ResLvlTaskOperation and the ResFilter

C++: core::pack::task::operation::OperateOnCertainResidues::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::OperateOnCertainResidues::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_indices(*args, **kwargs)

Overloaded function.

1. residue_indices(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

supports direct limitation of residues to be affected, without the need for a filter

C++: core::pack::task::operation::OperateOnCertainResidues::residue_indices(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. residue_indices(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::task::operation::OperateOnCertainResidues::residue_indices() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

class pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator, : pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator) → pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator

C++: core::pack::task::operation::OperateOnCertainResiduesCreator::operator=(const class core::pack::task::operation::OperateOnCertainResiduesCreator &) –> class core::pack::task::operation::OperateOnCertainResiduesCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OperateOnCertainResiduesCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator) → str

C++: core::pack::task::operation::OperateOnCertainResiduesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::OperateOnCertainResiduesCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset

Bases: TaskOperation

Class, much like the OperateOnCertainResidues task operation, to apply a particular residue-level task operation on the residues identified by a ResidueSelector (Or a pre-selected subset).

append_op(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : core::pack::task::operation::ResLvlTaskOperation) → None

Add a ResLvlTaskOperation to the list of those that will be applied to the selected

residues

C++: core::pack::task::operation::OperateOnResidueSubset::append_op(class std::shared_ptr<const class core::pack::task::operation::ResLvlTaskOperation>) –> void

apply(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::OperateOnResidueSubset::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset) → pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset

C++: core::pack::task::operation::OperateOnResidueSubset::operator=(const class core::pack::task::operation::OperateOnResidueSubset &) –> class core::pack::task::operation::OperateOnResidueSubset &

clone(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OperateOnResidueSubset::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

flip_subset(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, flip: bool) → None

Flip the subset on apply. False becomes True, True becomes False. Easier to interact with certain RLTOP.

C++: core::pack::task::operation::OperateOnResidueSubset::flip_subset(bool) –> void

static keyname() → str

C++: core::pack::task::operation::OperateOnResidueSubset::keyname() –> std::string

op(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : core::pack::task::operation::ResLvlTaskOperation) → None

sets the ResLvlTaskOperation that will be applied to residues

C++: core::pack::task::operation::OperateOnResidueSubset::op(class std::shared_ptr<const class core::pack::task::operation::ResLvlTaskOperation>) –> void

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to construct the ResLvlTaskOperation and the ResFilter

C++: core::pack::task::operation::OperateOnResidueSubset::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::OperateOnResidueSubset::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selector(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

sets the ResidueSelector that will be used to determine which residues to apply the RLTOP to

C++: core::pack::task::operation::OperateOnResidueSubset::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

subset(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset, subset_residues: pyrosetta.rosetta.utility.vector1_bool) → None

sets a specific subset that will be operated on instead of a selector itself.

C++: core::pack::task::operation::OperateOnResidueSubset::subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

class pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator, : pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator) → pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator

C++: core::pack::task::operation::OperateOnResidueSubsetCreator::operator=(const class core::pack::task::operation::OperateOnResidueSubsetCreator &) –> class core::pack::task::operation::OperateOnResidueSubsetCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OperateOnResidueSubsetCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator) → str

C++: core::pack::task::operation::OperateOnResidueSubsetCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::OperateOnResidueSubsetCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.OptCysHG

Bases: TaskOperation

run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides()

apply(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHG, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

apply operations to PackerTask

C++: core::pack::task::operation::OptCysHG::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHG, : pyrosetta.rosetta.core.pack.task.operation.OptCysHG) → pyrosetta.rosetta.core.pack.task.operation.OptCysHG

C++: core::pack::task::operation::OptCysHG::operator=(const class core::pack::task::operation::OptCysHG &) –> class core::pack::task::operation::OptCysHG &

clone(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHG) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

clone this object

C++: core::pack::task::operation::OptCysHG::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::OptCysHG::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::OptCysHG::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator, : pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator) → pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator

C++: core::pack::task::operation::OptCysHGCreator::operator=(const class core::pack::task::operation::OptCysHGCreator &) –> class core::pack::task::operation::OptCysHGCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OptCysHGCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator) → str

C++: core::pack::task::operation::OptCysHGCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::OptCysHGCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.OptH

Bases: TaskOperation

run optH; disallowed positions may be set to prevent optimization for those residues

apply(self: pyrosetta.rosetta.core.pack.task.operation.OptH, : pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

apply operations to PackerTask

C++: core::pack::task::operation::OptH::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.OptH, : pyrosetta.rosetta.core.pack.task.operation.OptH) → pyrosetta.rosetta.core.pack.task.operation.OptH

C++: core::pack::task::operation::OptH::operator=(const class core::pack::task::operation::OptH &) –> class core::pack::task::operation::OptH &

clone(self: pyrosetta.rosetta.core.pack.task.operation.OptH) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

clone this object

C++: core::pack::task::operation::OptH::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

disallow_resid(self: pyrosetta.rosetta.core.pack.task.operation.OptH, resid: int) → None

prevent a position from being optimized

C++: core::pack::task::operation::OptH::disallow_resid(const unsigned long) –> void

flip_HNQ(self: pyrosetta.rosetta.core.pack.task.operation.OptH, flag: bool) → None

allow sidechain flips of HNQ? (default false)

C++: core::pack::task::operation::OptH::flip_HNQ(const bool) –> void

include_current(self: pyrosetta.rosetta.core.pack.task.operation.OptH, flag: bool) → None

include current sidechain rotamers? (default true)

C++: core::pack::task::operation::OptH::include_current(const bool) –> void

init_from_comand_line(self: pyrosetta.rosetta.core.pack.task.operation.OptH, flag: bool) → None

init flags from command line? (default true)

C++: core::pack::task::operation::OptH::init_from_comand_line(const bool) –> void

static keyname() → str

C++: core::pack::task::operation::OptH::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::OptH::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

use_multicool_annealer(self: pyrosetta.rosetta.core.pack.task.operation.OptH, flag: bool) → None

use multicool annealer? (default false)

C++: core::pack::task::operation::OptH::use_multicool_annealer(const bool) –> void

class pyrosetta.rosetta.core.pack.task.operation.OptHCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.OptHCreator, : pyrosetta.rosetta.core.pack.task.operation.OptHCreator) → pyrosetta.rosetta.core.pack.task.operation.OptHCreator

C++: core::pack::task::operation::OptHCreator::operator=(const class core::pack::task::operation::OptHCreator &) –> class core::pack::task::operation::OptHCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.OptHCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::OptHCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.OptHCreator) → str

C++: core::pack::task::operation::OptHCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.OptHCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::OptHCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::PreserveCBeta::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta, : pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta) → pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta

C++: core::pack::task::operation::PreserveCBeta::operator=(const class core::pack::task::operation::PreserveCBeta &) –> class core::pack::task::operation::PreserveCBeta &

clone(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::PreserveCBeta::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::PreserveCBeta::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::PreserveCBeta::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator, : pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator) → pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator

C++: core::pack::task::operation::PreserveCBetaCreator::operator=(const class core::pack::task::operation::PreserveCBetaCreator &) –> class core::pack::task::operation::PreserveCBetaCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::PreserveCBetaCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator) → str

C++: core::pack::task::operation::PreserveCBetaCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::PreserveCBetaCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::PreserveCBetaRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT, : pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT) → pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT

C++: core::pack::task::operation::PreserveCBetaRLT::operator=(const class core::pack::task::operation::PreserveCBetaRLT &) –> class core::pack::task::operation::PreserveCBetaRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::PreserveCBetaRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

static keyname() → str

C++: core::pack::task::operation::PreserveCBetaRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.utility.tag.Tag) → None

parser xml-like tags to set class data/parameters

C++: core::pack::task::operation::ResLvlTaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::PreserveCBetaRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator

C++: core::pack::task::operation::PreserveCBetaRLTCreator::operator=(const class core::pack::task::operation::PreserveCBetaRLTCreator &) –> class core::pack::task::operation::PreserveCBetaRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::PreserveCBetaRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator) → str

C++: core::pack::task::operation::PreserveCBetaRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::PreserveCBetaRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.PreventRepacking

Bases: TaskOperation

PreventRepacking allows you to prevent repacking (NATRO behavior) through the Factory. Useful if you do not know the residue numbers when the resfile is created. Note that this is unlike RestrictToRepacking; you have to specify which residues. If PreventRepacking worked on the entire Task you’d have a do-nothing task.

apply(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::PreventRepacking::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking, : pyrosetta.rosetta.core.pack.task.operation.PreventRepacking) → pyrosetta.rosetta.core.pack.task.operation.PreventRepacking

C++: core::pack::task::operation::PreventRepacking::operator=(const class core::pack::task::operation::PreventRepacking &) –> class core::pack::task::operation::PreventRepacking &

clear(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking) → None

C++: core::pack::task::operation::PreventRepacking::clear() –> void

clone(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::PreventRepacking::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

include_residue(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking, resid: int) → None

C++: core::pack::task::operation::PreventRepacking::include_residue(unsigned long) –> void

static keyname() → str

C++: core::pack::task::operation::PreventRepacking::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepacking, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::PreventRepacking::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::PreventRepacking::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator, : pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator) → pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator

C++: core::pack::task::operation::PreventRepackingCreator::operator=(const class core::pack::task::operation::PreventRepackingCreator &) –> class core::pack::task::operation::PreventRepackingCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::PreventRepackingCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator) → str

C++: core::pack::task::operation::PreventRepackingCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::PreventRepackingCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT

Bases: ResLvlTaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

C++: core::pack::task::operation::PreventRepackingRLT::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT, : pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT) → pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT

C++: core::pack::task::operation::PreventRepackingRLT::operator=(const class core::pack::task::operation::PreventRepackingRLT &) –> class core::pack::task::operation::PreventRepackingRLT &

clone(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::PreventRepackingRLT::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

static keyname() → str

C++: core::pack::task::operation::PreventRepackingRLT::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.utility.tag.Tag) → None

parser xml-like tags to set class data/parameters

C++: core::pack::task::operation::ResLvlTaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::PreventRepackingRLT::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator

Bases: ResLvlTaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator, : pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator

C++: core::pack::task::operation::PreventRepackingRLTCreator::operator=(const class core::pack::task::operation::PreventRepackingRLTCreator &) –> class core::pack::task::operation::PreventRepackingRLTCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::PreventRepackingRLTCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator) → str

C++: core::pack::task::operation::PreventRepackingRLTCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::PreventRepackingRLTCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties

Bases: TaskOperation

Restrict the palette of ResidueTypes to those with the given properties.

Labonte <JWLabonte.edu>

apply(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ProhibitResidueProperties::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties, : pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties) → pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties

C++: core::pack::task::operation::ProhibitResidueProperties::operator=(const class core::pack::task::operation::ProhibitResidueProperties &) –> class core::pack::task::operation::ProhibitResidueProperties &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ProhibitResidueProperties::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::ProhibitResidueProperties::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties, tag: pyrosetta.rosetta.utility.tag.Tag, map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ProhibitResidueProperties::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

properties(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties) → pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty

C++: core::pack::task::operation::ProhibitResidueProperties::properties() const –> const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ProhibitResidueProperties::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selector(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::pack::task::operation::ProhibitResidueProperties::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_properties(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties, properties: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → None

C++: core::pack::task::operation::ProhibitResidueProperties::set_properties(const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &) –> void

set_selector(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::pack::task::operation::ProhibitResidueProperties::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

static xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ProhibitResidueProperties::xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

class pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator, : pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator) → pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator

C++: core::pack::task::operation::ProhibitResiduePropertiesCreator::operator=(const class core::pack::task::operation::ProhibitResiduePropertiesCreator &) –> class core::pack::task::operation::ProhibitResiduePropertiesCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Instantiate a new TaskOperation

C++: core::pack::task::operation::TaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → str

C++: core::pack::task::operation::TaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::TaskOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes

Bases: TaskOperation

Prohibit the base ResidueTypes provided by name from the palette of ResidueTypes.

Labonte <JWLabonte.edu>

apply(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes, : pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes) → pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::operator=(const class core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes &) –> class core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes &

base_types(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::base_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes, tag: pyrosetta.rosetta.utility.tag.Tag, map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selector(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_base_types(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes, base_types: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::set_base_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_selector(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

static xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

class pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator, : pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator) → pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator

C++: core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator::operator=(const class core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator &) –> class core::pack::task::operation::ProhibitSpecifiedBaseResidueTypesCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

Instantiate a new TaskOperation

C++: core::pack::task::operation::TaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → str

C++: core::pack::task::operation::TaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::TaskOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ReadResfile

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ReadResfile::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, : pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → pyrosetta.rosetta.core.pack.task.operation.ReadResfile

C++: core::pack::task::operation::ReadResfile::operator=(const class core::pack::task::operation::ReadResfile &) –> class core::pack::task::operation::ReadResfile &

cache_resfile(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → None

Read in the resfile and store it, so that it

doesn’t have to be read over and over again at apply time.

C++: core::pack::task::operation::ReadResfile::cache_resfile() –> void

clone(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ReadResfile::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

default_filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → None

queries options system for resfile name

C++: core::pack::task::operation::ReadResfile::default_filename() –> void

filename(*args, **kwargs)

Overloaded function.

1. filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, filename: str) -> None

C++: core::pack::task::operation::ReadResfile::filename(const std::string &) –> void

2. filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) -> str

C++: core::pack::task::operation::ReadResfile::filename() const –> const std::string &

static keyname() → str

C++: core::pack::task::operation::ReadResfile::keyname() –> std::string

static list_options_read(options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None

C++: core::pack::task::operation::ReadResfile::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ReadResfile::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ReadResfile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_selector(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector, if one exists. (Const-access owning pointer).

Returns NULL pointer if one does not.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::task::operation::ReadResfile::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_cached_resfile(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, file_contents: str) → None

Allows code to provide resfile contents, so that this TaskOperation doesn’t directly have to

handle file i/o. Handly on large systems (e.g. Blue Gene), where one might only want the master process to read a file.

C++: core::pack::task::operation::ReadResfile::set_cached_resfile(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the residue selector.

The input selector is cloned and the clone is stored.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::task::operation::ReadResfile::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

static xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ReadResfile::xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

class pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents

Bases: ReadResfile

written by flo, feb 2011 class that can apply a resfile to a pose that had its length changed at some point in a protocol. A LengthEventCollector must be set in the pose’s observer cache for this to work properly

apply(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents, pose: pyrosetta.rosetta.core.pose.Pose, ptask: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents, : pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents) → pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::operator=(const class core::pack::task::operation::ReadResfileAndObeyLengthEvents &) –> class core::pack::task::operation::ReadResfileAndObeyLengthEvents &

cache_resfile(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → None

Read in the resfile and store it, so that it

doesn’t have to be read over and over again at apply time.

C++: core::pack::task::operation::ReadResfile::cache_resfile() –> void

clone(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

default_filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → None

queries options system for resfile name

C++: core::pack::task::operation::ReadResfile::default_filename() –> void

filename(*args, **kwargs)

Overloaded function.

1. filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, filename: str) -> None

C++: core::pack::task::operation::ReadResfile::filename(const std::string &) –> void

2. filename(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) -> str

C++: core::pack::task::operation::ReadResfile::filename() const –> const std::string &

static keyname() → str

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::keyname() –> std::string

static list_options_read(options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None

C++: core::pack::task::operation::ReadResfile::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

resfile_commands(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents, resfile_seqpos: int, contents: pyrosetta.rosetta.core.pack.task.ResfileContents, ptask: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t

C++: core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands(const unsigned long, const class core::pack::task::ResfileContents &, const class core::pack::task::PackerTask &) const –> const class std::list<class std::shared_ptr<const class core::pack::task::ResfileCommand>, class std::allocator<class std::shared_ptr<const class core::pack::task::ResfileCommand> > > &

residue_selector(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the residue selector, if one exists. (Const-access owning pointer).

Returns NULL pointer if one does not.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::task::operation::ReadResfile::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_cached_resfile(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, file_contents: str) → None

Allows code to provide resfile contents, so that this TaskOperation doesn’t directly have to

handle file i/o. Handly on large systems (e.g. Blue Gene), where one might only want the master process to read a file.

C++: core::pack::task::operation::ReadResfile::set_cached_resfile(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfile, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the residue selector.

The input selector is cloned and the clone is stored.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::task::operation::ReadResfile::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

static xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ReadResfile::xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

class pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator, : pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator) → pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator

C++: core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::operator=(const class core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator &) –> class core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator) → str

C++: core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ReadResfileAndObeyLengthEventsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator, : pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator) → pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator

C++: core::pack::task::operation::ReadResfileCreator::operator=(const class core::pack::task::operation::ReadResfileCreator &) –> class core::pack::task::operation::ReadResfileCreator &

create_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ReadResfileCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator) → str

C++: core::pack::task::operation::ReadResfileCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ReadResfileCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real task operation. True only for dummy task operations created for unit tests.

C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ReplicateTask

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.task.operation.ReplicateTask, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ReplicateTask::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ReplicateTask, : pyrosetta.rosetta.core.pack.task.operation.ReplicateTask) → pyrosetta.rosetta.core.pack.task.operation.ReplicateTask

C++: core::pack::task::operation::ReplicateTask::operator=(const class core::pack::task::operation::ReplicateTask &) –> class core::pack::task::operation::ReplicateTask &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ReplicateTask) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::task::operation::ReplicateTask::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

set_native_task(self: pyrosetta.rosetta.core.pack.task.operation.ReplicateTask, native_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::task::operation::ReplicateTask::set_native_task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResFilter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResFilter, : pyrosetta.rosetta.core.pack.task.operation.ResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResFilter::operator=(const class core::pack::task::operation::ResFilter &) –> class core::pack::task::operation::ResFilter &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResFilter::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResFilter, : pyrosetta.rosetta.utility.tag.Tag) → None

parser xml-like tags to set class data/parameters

C++: core::pack::task::operation::ResFilter::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition

Bases: ResFilter

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition, : pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition) → pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition

C++: core::pack::task::operation::ResFilterComposition::operator=(const class core::pack::task::operation::ResFilterComposition &) –> class core::pack::task::operation::ResFilterComposition &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResFilter) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResFilter::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator

C++: core::pack::task::operation::ResFilterComposition::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResFilterComposition::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator

Bases: pybind11_object

The ResFilterCreator class’s responsibilities are to create on demand a new ResFilter class. The ResFilterCreator must register itself with the ResFilterFactory at load time (before main() begins) so that the ResFilterFactory is ready to start creating ResFilters by the time any protocol requests one.

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator, : pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator

C++: core::pack::task::operation::ResFilterCreator::operator=(const class core::pack::task::operation::ResFilterCreator &) –> class core::pack::task::operation::ResFilterCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

Instantiate a new ResFilter

C++: core::pack::task::operation::ResFilterCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator) → str

C++: core::pack::task::operation::ResFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory

Bases: SingletonBase_core_pack_task_operation_ResFilterFactory_t

add_creator(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, : pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator) → None

add a prototype, using its default type name as the map key

C++: core::pack::task::operation::ResFilterFactory::add_creator(class std::shared_ptr<class core::pack::task::operation::ResFilterCreator>) –> void

define_res_filter_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, xsd: utility::tag::XMLSchemaDefinition) → None

The %ResFilterFactory is the point of entry for the definition of the XML Schemas

for every ResFilter that may be instantiated from a file. It is responsible for defining an xs:group named “res_filter” listing each of the residue-filter-complex types that may be initialized using the %ResFilterFactory and to iterate across each of the ResFilterCreator it contains asking them for the XML schema of the ResFilter they are responsible for creating.

C++: core::pack::task::operation::ResFilterFactory::define_res_filter_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, : pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator) → None

C++: core::pack::task::operation::ResFilterFactory::factory_register(class std::shared_ptr<class core::pack::task::operation::ResFilterCreator>) –> void

static get_instance() → core::pack::task::operation::ResFilterFactory

C++: utility::SingletonBase<core::pack::task::operation::ResFilterFactory>::get_instance() –> class core::pack::task::operation::ResFilterFactory *

has_type(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, : str) → bool

C++: core::pack::task::operation::ResFilterFactory::has_type(const std::string &) const –> bool

newResFilter(*args, **kwargs)

Overloaded function.

1. newResFilter(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, : str) -> pyrosetta.rosetta.core.pack.task.operation.ResFilter

return new ResFilter by key lookup in filter_map_; new ResFilter does not parse an input Tag

C++: core::pack::task::operation::ResFilterFactory::newResFilter(const std::string &) const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

2. newResFilter(self: pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory, : str, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.core.pack.task.operation.ResFilter

return new ResFilter by key lookup in filter_map_ new ResFilter parses Tag if provided

C++: core::pack::task::operation::ResFilterFactory::newResFilter(const std::string &, class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static res_filter_xml_schema_group_name() → str

The name given to the XML schema group of all ResFilter s.

C++: core::pack::task::operation::ResFilterFactory::res_filter_xml_schema_group_name() –> std::string

class pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

Bases: pybind11_object

apply(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.core.pack.task.ResidueLevelTask) → None

Change a ResidueLevelTask in some way. The input pose is the one to which the input

task will be later applied.

C++: core::pack::task::operation::ResLvlTaskOperation::apply(class core::pack::task::ResidueLevelTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

C++: core::pack::task::operation::ResLvlTaskOperation::operator=(const class core::pack::task::operation::ResLvlTaskOperation &) –> class core::pack::task::operation::ResLvlTaskOperation &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

Create another task operation of the type matching the most-derived

version of the class.

C++: core::pack::task::operation::ResLvlTaskOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : pyrosetta.rosetta.utility.tag.Tag) → None

parser xml-like tags to set class data/parameters

C++: core::pack::task::operation::ResLvlTaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::ResLvlTaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator

Bases: pybind11_object

The ResLvlTaskOperationCreator class’s responsibilities are to create on demand a new ResLvlTaskOperation class. The ResLvlTaskOperationCreator must register itself with the ResLvlTaskOperationFactory at load time (before main() begins) so that the ResLvlTaskOperationFactory is ready to start creating ResLvlTaskOperations by the time any protocol requests one.

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator, : pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator

C++: core::pack::task::operation::ResLvlTaskOperationCreator::operator=(const class core::pack::task::operation::ResLvlTaskOperationCreator &) –> class core::pack::task::operation::ResLvlTaskOperationCreator &

create_res_level_task_operation(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

Instantiate a new ResLvlTaskOperation

C++: core::pack::task::operation::ResLvlTaskOperationCreator::create_res_level_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → str

C++: core::pack::task::operation::ResLvlTaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResLvlTaskOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → bool

Indicate whether we skip adding citation information to the XML schema.

False for any real residue-level task operation. True only for dummy residue-level task operations created for unit tests.

C++: core::pack::task::operation::ResLvlTaskOperationCreator::skip_citation_info_in_schema() const –> bool

class pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory

Bases: SingletonBase_core_pack_task_operation_ResLvlTaskOperationFactory_t

add_creator(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, : pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → None

add a prototype, using its default type name as the map key

C++: core::pack::task::operation::ResLvlTaskOperationFactory::add_creator(class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperationCreator>) –> void

creator_map(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t

Access the creator map (for unit testing).

C++: core::pack::task::operation::ResLvlTaskOperationFactory::creator_map() const –> const class std::map<std::string, class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperationCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperationCreator> > > > &

define_res_lvl_task_op_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, xsd: utility::tag::XMLSchemaDefinition) → None

The %ResLvlTaskOperationFactory is the point of entry for the definition of the XML Schemas

for every ResLvlTaskOperation that may be instantiated from a file. It is responsible for defining an xs:group named “res_lvl_task_op” listing each of the residue-level-task-operation-complex types that may be initialized using the %ResLvlTaskOperationFactory and to iterate across each of the ResLvlTaskOperationCreator it contains asking them for the XML schema of the ResLvlTaskOperation they are responsible for creating.

C++: core::pack::task::operation::ResLvlTaskOperationFactory::define_res_lvl_task_op_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, : pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator) → None

C++: core::pack::task::operation::ResLvlTaskOperationFactory::factory_register(class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperationCreator>) –> void

get_citation_humanreadable(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, taskop_name: str) → str

Get a human-readable listing of the citations for a given residue level task operation, by taskop name.

Returns an empty string if there are no citations.

Vikram K. Mulligan (vmulligan.org).

C++: core::pack::task::operation::ResLvlTaskOperationFactory::get_citation_humanreadable(const std::string &) const –> std::string

static get_instance() → core::pack::task::operation::ResLvlTaskOperationFactory

C++: utility::SingletonBase<core::pack::task::operation::ResLvlTaskOperationFactory>::get_instance() –> class core::pack::task::operation::ResLvlTaskOperationFactory *

has_type(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, : str) → bool

C++: core::pack::task::operation::ResLvlTaskOperationFactory::has_type(const std::string &) const –> bool

newRLTO(*args, **kwargs)

Overloaded function.

1. newRLTO(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, : str) -> pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

return new ResLvlTaskOperation by key lookup in rlto_map_

C++: core::pack::task::operation::ResLvlTaskOperationFactory::newRLTO(const std::string &) const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

2. newRLTO(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, class_keyname: str, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation

return new ResLvlTaskOperation by key lookup in rlto_map_ (with the

new ResLvlTaskOperation parsing the input Tag)

C++: core::pack::task::operation::ResLvlTaskOperationFactory::newRLTO(const std::string &, class std::shared_ptr<const class utility::tag::Tag>) const –> class std::shared_ptr<class core::pack::task::operation::ResLvlTaskOperation>

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory, task_operation_name: str, xsd: utility::tag::XMLSchemaDefinition) → None

Get the XML schema for a given ResLvlTaskOperation.

Throws an error if the ResLvlTaskOperation is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: core::pack::task::operation::ResLvlTaskOperationFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

static res_lvl_task_op_xml_schema_group_name() → str

The name given to the XML schema group of all ResLvlTaskOperation s.

C++: core::pack::task::operation::ResLvlTaskOperationFactory::res_lvl_task_op_xml_schema_group_name() –> std::string

class pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty

Bases: ResFilter

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty, : pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty) → pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty

C++: core::pack::task::operation::ResidueHasProperty::operator=(const class core::pack::task::operation::ResidueHasProperty &) –> class core::pack::task::operation::ResidueHasProperty &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueHasProperty::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueHasProperty::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ResidueHasProperty::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResidueHasProperty::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

property(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty) → str

C++: core::pack::task::operation::ResidueHasProperty::property() const –> const std::string &

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

C++: core::pack::task::operation::ResidueHasProperty::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator, : pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator) → pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator

C++: core::pack::task::operation::ResidueHasPropertyCreator::operator=(const class core::pack::task::operation::ResidueHasPropertyCreator &) –> class core::pack::task::operation::ResidueHasPropertyCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueHasPropertyCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator) → str

C++: core::pack::task::operation::ResidueHasPropertyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResidueHasPropertyCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs

Bases: ResFilter

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs, : pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs) → pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs

C++: core::pack::task::operation::ResidueIndexIs::operator=(const class core::pack::task::operation::ResidueIndexIs &) –> class core::pack::task::operation::ResidueIndexIs &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueIndexIs::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueIndexIs::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

indices(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::task::operation::ResidueIndexIs::indices() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

static keyname() → str

C++: core::pack::task::operation::ResidueIndexIs::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResidueIndexIs::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::ResidueIndexIs::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator, : pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator) → pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator

C++: core::pack::task::operation::ResidueIndexIsCreator::operator=(const class core::pack::task::operation::ResidueIndexIsCreator &) –> class core::pack::task::operation::ResidueIndexIsCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueIndexIsCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator) → str

C++: core::pack::task::operation::ResidueIndexIsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResidueIndexIsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt

Bases: ResidueIndexIs

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt, : pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt) → pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt

C++: core::pack::task::operation::ResidueIndexIsnt::operator=(const class core::pack::task::operation::ResidueIndexIsnt &) –> class core::pack::task::operation::ResidueIndexIsnt &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueIndexIsnt::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueIndexIs::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

indices(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::task::operation::ResidueIndexIs::indices() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

static keyname() → str

C++: core::pack::task::operation::ResidueIndexIsnt::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResidueIndexIs::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::ResidueIndexIsnt::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator, : pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator) → pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator

C++: core::pack::task::operation::ResidueIndexIsntCreator::operator=(const class core::pack::task::operation::ResidueIndexIsntCreator &) –> class core::pack::task::operation::ResidueIndexIsntCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueIndexIsntCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator) → str

C++: core::pack::task::operation::ResidueIndexIsntCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResidueIndexIsntCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty

Bases: ResidueHasProperty

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty, : pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty) → pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty

C++: core::pack::task::operation::ResidueLacksProperty::operator=(const class core::pack::task::operation::ResidueLacksProperty &) –> class core::pack::task::operation::ResidueLacksProperty &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueLacksProperty::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueHasProperty::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ResidueLacksProperty::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResidueHasProperty::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

property(self: pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty) → str

C++: core::pack::task::operation::ResidueHasProperty::property() const –> const std::string &

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

C++: core::pack::task::operation::ResidueLacksProperty::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator, : pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator) → pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator

C++: core::pack::task::operation::ResidueLacksPropertyCreator::operator=(const class core::pack::task::operation::ResidueLacksPropertyCreator &) –> class core::pack::task::operation::ResidueLacksPropertyCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueLacksPropertyCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator) → str

C++: core::pack::task::operation::ResidueLacksPropertyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResidueLacksPropertyCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is

Bases: ResFilter

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is, : pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is) → pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is

C++: core::pack::task::operation::ResidueName3Is::operator=(const class core::pack::task::operation::ResidueName3Is &) –> class core::pack::task::operation::ResidueName3Is &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueName3Is::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueName3Is::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ResidueName3Is::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is, : pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::pack::task::operation::ResidueName3Is::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: core::pack::task::operation::ResidueName3Is::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator, : pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator) → pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator

C++: core::pack::task::operation::ResidueName3IsCreator::operator=(const class core::pack::task::operation::ResidueName3IsCreator &) –> class core::pack::task::operation::ResidueName3IsCreator &

create_res_filter(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueName3IsCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator) → str

C++: core::pack::task::operation::ResidueName3IsCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: core::pack::task::operation::ResidueName3IsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt

Bases: ResidueName3Is

assign(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt, : pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt) → pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt

C++: core::pack::task::operation::ResidueName3Isnt::operator=(const class core::pack::task::operation::ResidueName3Isnt &) –> class core::pack::task::operation::ResidueName3Isnt &

clone(self: pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt) → pyrosetta.rosetta.core.pack.task.operation.ResFilter

C++: core::pack::task::operation::ResidueName3Isnt::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static get_xml_schema_attributes() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: core::pack::task::operation::ResidueName3Is::get_xml_schema_attributes() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

static keyname() → str

C++: core::pack::task::operation::ResidueName3Isnt::keyname() –> std::string

parse_tag(self: