task_operations¶

Bindings for protocols::task_operations namespace

class pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

alignment_file(*args, **kwargs)¶

Overloaded function.

alignment_file(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) -> str

C++: protocols::task_operations::AlignedThreadOperation::alignment_file() const –> std::string

alignment_file(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, s: str) -> None

C++: protocols::task_operations::AlignedThreadOperation::alignment_file(const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::AlignedThreadOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, : pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) → pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation¶: C++: protocols::task_operations::AlignedThreadOperation::operator=(const class protocols::task_operations::AlignedThreadOperation &) –> class protocols::task_operations::AlignedThreadOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::AlignedThreadOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::AlignedThreadOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::AlignedThreadOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::AlignedThreadOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

query_name(*args, **kwargs)¶

Overloaded function.

query_name(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) -> str

C++: protocols::task_operations::AlignedThreadOperation::query_name() const –> std::string

query_name(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, s: str) -> None

C++: protocols::task_operations::AlignedThreadOperation::query_name(const std::string &) –> void

start_res(*args, **kwargs)¶

Overloaded function.

start_res(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, s: int) -> None

C++: protocols::task_operations::AlignedThreadOperation::start_res(const unsigned long) –> void

start_res(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) -> int

C++: protocols::task_operations::AlignedThreadOperation::start_res() const –> unsigned long

template_name(*args, **kwargs)¶

Overloaded function.

template_name(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation) -> str

C++: protocols::task_operations::AlignedThreadOperation::template_name() const –> std::string

template_name(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation, s: str) -> None

C++: protocols::task_operations::AlignedThreadOperation::template_name(const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator, : pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator) → pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator¶: C++: protocols::task_operations::AlignedThreadOperationCreator::operator=(const class protocols::task_operations::AlignedThreadOperationCreator &) –> class protocols::task_operations::AlignedThreadOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::AlignedThreadOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator) → str¶: C++: protocols::task_operations::AlignedThreadOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::AlignedThreadOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation¶

Bases: TaskOperation

A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid’s conservative mutations.

Default is to act on all designable residues. Use limit_to_positions to limit this. Default is to replace the allowed_aas with these conservative mutations. Data is loaded from database/sequence/resinfo.db.

apply(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ConservativeDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, rhs: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation) → pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation¶: C++: protocols::task_operations::ConservativeDesignOperation::operator=(const class protocols::task_operations::ConservativeDesignOperation &) –> class protocols::task_operations::ConservativeDesignOperation &

clear_positions(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation) → None¶

Clear any set positions.

C++: protocols::task_operations::ConservativeDesignOperation::clear_positions() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ConservativeDesignOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

include_native_aa(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, setting: bool) → None¶

Include native amino acid in the allowed_aas list. Default true.

C++: protocols::task_operations::ConservativeDesignOperation::include_native_aa(bool) –> void

include_residue(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, resnum: int) → None¶: C++: protocols::task_operations::ConservativeDesignOperation::include_residue(unsigned long) –> void

static keyname() → str¶: C++: protocols::task_operations::ConservativeDesignOperation::keyname() –> std::string

limit_to_positions(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Limit to a subset of residue positions, already set to designable.

C++: protocols::task_operations::ConservativeDesignOperation::limit_to_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

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

C++: protocols::task_operations::ConservativeDesignOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ConservativeDesignOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_data_source(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, data_source: str) → None¶

Set the source of the data used to define what is conservative.: Options are: chothia_76 and the Blosum matrices from 30 to 100; designated as blosum30, 62, etc. Default is blosum62. The higher the number, the more conservative the set of mutations (numbers are sequence identity cutoffs)

C++: protocols::task_operations::ConservativeDesignOperation::set_data_source(const std::string &) –> void

set_native_sequence(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, seq: str) → None¶: C++: protocols::task_operations::ConservativeDesignOperation::set_native_sequence(const std::string &) –> void

use_pose_sequence_as_native(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Will use native residues from the this pose to determine conserved aa.

C++: protocols::task_operations::ConservativeDesignOperation::use_pose_sequence_as_native(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator¶: C++: protocols::task_operations::ConservativeDesignOperationCreator::operator=(const class protocols::task_operations::ConservativeDesignOperationCreator &) –> class protocols::task_operations::ConservativeDesignOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ConservativeDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator) → str¶: C++: protocols::task_operations::ConservativeDesignOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ConservativeDesignOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::CrystalContactsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation, : pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation) → pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation¶: C++: protocols::task_operations::CrystalContactsOperation::operator=(const class protocols::task_operations::CrystalContactsOperation &) –> class protocols::task_operations::CrystalContactsOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::CrystalContactsOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::CrystalContactsOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::CrystalContactsOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::CrystalContactsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator, : pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator) → pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator¶: C++: protocols::task_operations::CrystalContactsOperationCreator::operator=(const class protocols::task_operations::CrystalContactsOperationCreator &) –> class protocols::task_operations::CrystalContactsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::CrystalContactsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator) → str¶: C++: protocols::task_operations::CrystalContactsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::CrystalContactsOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.DatabaseThread¶

Bases: RestrictOperationsBase

this class is a TaskOperation to thread sequences from a database.

allow_design_around(*args, **kwargs)¶

Overloaded function.

allow_design_around(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> bool

C++: protocols::task_operations::DatabaseThread::allow_design_around() const –> bool

allow_design_around(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, b: bool) -> None

C++: protocols::task_operations::DatabaseThread::allow_design_around(const bool) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::DatabaseThread::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, : pyrosetta.rosetta.protocols.task_operations.DatabaseThread) → pyrosetta.rosetta.protocols.task_operations.DatabaseThread¶: C++: protocols::task_operations::DatabaseThread::operator=(const class protocols::task_operations::DatabaseThread &) –> class protocols::task_operations::DatabaseThread &

clone(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::DatabaseThread::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

database_fname(*args, **kwargs)¶

Overloaded function.

database_fname(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> str

C++: protocols::task_operations::DatabaseThread::database_fname() const –> std::string

database_fname(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, d: str) -> None

C++: protocols::task_operations::DatabaseThread::database_fname(const std::string &) –> void

designable(*args, **kwargs)¶

Overloaded function.

designable(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::task_operations::DatabaseThread::designable() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

designable(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, vector: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::DatabaseThread::designable(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

end_res(*args, **kwargs)¶

Overloaded function.

end_res(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> int

C++: protocols::task_operations::DatabaseThread::end_res() const –> unsigned long

end_res(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, s: int) -> None

C++: protocols::task_operations::DatabaseThread::end_res(const unsigned long) –> void

find_length(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::task_operations::DatabaseThread::find_length(const class core::pose::Pose &) const –> unsigned long

itterative(*args, **kwargs)¶

Overloaded function.

itterative(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> bool

C++: protocols::task_operations::DatabaseThread::itterative() const –> bool

itterative(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, b: bool) -> None

C++: protocols::task_operations::DatabaseThread::itterative(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::DatabaseThread::keyname() –> std::string

leave_as_is(*args, **kwargs)¶

Overloaded function.

leave_as_is(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::task_operations::DatabaseThread::leave_as_is() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

leave_as_is(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, vector: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::DatabaseThread::leave_as_is(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

mark_designable(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, sequence: str, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::task_operations::DatabaseThread::mark_designable(std::string &, const class core::pose::Pose &) const –> void

mark_leave_as_is(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, sequence: str, : pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::task_operations::DatabaseThread::mark_leave_as_is(std::string &, const class core::pose::Pose &) const –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::DatabaseThread::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pick_sequence_from_database(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, pose: pyrosetta.rosetta.core.pose.Pose) → str¶: C++: protocols::task_operations::DatabaseThread::pick_sequence_from_database(const class core::pose::Pose &) 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DatabaseThread::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

start_res(*args, **kwargs)¶

Overloaded function.

start_res(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> int

C++: protocols::task_operations::DatabaseThread::start_res() const –> unsigned long

start_res(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, s: int) -> None

C++: protocols::task_operations::DatabaseThread::start_res(const unsigned long) –> void

target_sequence(*args, **kwargs)¶

Overloaded function.

target_sequence(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, seq: str) -> None

C++: protocols::task_operations::DatabaseThread::target_sequence(const std::string &) –> void

target_sequence(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> str

C++: protocols::task_operations::DatabaseThread::target_sequence() const –> std::string

template_file(*args, **kwargs)¶

Overloaded function.

template_file(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread) -> str

C++: protocols::task_operations::DatabaseThread::template_file() const –> std::string

template_file(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThread, s: str) -> None

C++: protocols::task_operations::DatabaseThread::template_file(const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator, : pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator) → pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator¶: C++: protocols::task_operations::DatabaseThreadCreator::operator=(const class protocols::task_operations::DatabaseThreadCreator &) –> class protocols::task_operations::DatabaseThreadCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::DatabaseThreadCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator) → str¶: C++: protocols::task_operations::DatabaseThreadCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DatabaseThreadCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation¶

Bases: RestrictOperationsBase

allow_design(*args, **kwargs)¶

Overloaded function.

allow_design(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, a: bool) -> None

C++: protocols::task_operations::DesignAroundOperation::allow_design(const bool) –> void

allow_design(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) -> bool

C++: protocols::task_operations::DesignAroundOperation::allow_design() const –> bool

apply(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::DesignAroundOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, : pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) → pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation¶: C++: protocols::task_operations::DesignAroundOperation::operator=(const class protocols::task_operations::DesignAroundOperation &) –> class protocols::task_operations::DesignAroundOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::DesignAroundOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

design_shell(*args, **kwargs)¶

Overloaded function.

design_shell(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, radius: float) -> None

C++: protocols::task_operations::DesignAroundOperation::design_shell(const double) –> void

design_shell(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) -> float

C++: protocols::task_operations::DesignAroundOperation::design_shell() const –> double

get_designable_residues(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::task_operations::DesignAroundOperation::get_designable_residues() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

include_residue(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, resid: int) → None¶: C++: protocols::task_operations::DesignAroundOperation::include_residue(const unsigned long) –> void

static keyname() → str¶: C++: protocols::task_operations::DesignAroundOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::DesignAroundOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DesignAroundOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_shell(*args, **kwargs)¶

Overloaded function.

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, repack_shell: float) -> None

C++: protocols::task_operations::DesignAroundOperation::repack_shell(const double) –> void

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) -> float

C++: protocols::task_operations::DesignAroundOperation::repack_shell() const –> double

resnums_allow_design(*args, **kwargs)¶

Overloaded function.

resnums_allow_design(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation, a: bool) -> None

C++: protocols::task_operations::DesignAroundOperation::resnums_allow_design(const bool) –> void

resnums_allow_design(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation) -> bool

C++: protocols::task_operations::DesignAroundOperation::resnums_allow_design() const –> bool

class pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator, : pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator) → pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator¶: C++: protocols::task_operations::DesignAroundOperationCreator::operator=(const class protocols::task_operations::DesignAroundOperationCreator &) –> class protocols::task_operations::DesignAroundOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::DesignAroundOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator) → str¶: C++: protocols::task_operations::DesignAroundOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DesignAroundOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation¶

Bases: TaskOperation

TaskOperation that can be used to restrict AAs allowed at each position based on DSSP-assigned secondary structure

apply(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::DsspDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, : pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation) → pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation¶: C++: protocols::task_operations::DsspDesignOperation::operator=(const class protocols::task_operations::DsspDesignOperation &) –> class protocols::task_operations::DsspDesignOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

static keyname() → str¶: C++: protocols::task_operations::DsspDesignOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse RosettaScripts XML

C++: protocols::task_operations::DsspDesignOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DsspDesignOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_blueprint(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, bp: pyrosetta.rosetta.protocols.parser.BluePrint) → None¶

define secondary structure from a blueprint

C++: protocols::task_operations::DsspDesignOperation::set_blueprint(const class std::shared_ptr<class protocols::parser::BluePrint>) –> void

set_restrictions_aa(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, sse: str, aas: str) → None¶

define allowed residues for some SSE

C++: protocols::task_operations::DsspDesignOperation::set_restrictions_aa(const std::string &, const std::string &) –> void

set_restrictions_append(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, sse: str, aas: str) → None¶

append allowed residues for some SSE

C++: protocols::task_operations::DsspDesignOperation::set_restrictions_append(const std::string &, const std::string &) –> void

set_restrictions_exclude(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation, sse: str, aas: str) → None¶

exclude allowed residues for some SSE

C++: protocols::task_operations::DsspDesignOperation::set_restrictions_exclude(const std::string &, const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator, : pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator) → pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator¶: C++: protocols::task_operations::DsspDesignOperationCreator::operator=(const class protocols::task_operations::DsspDesignOperationCreator &) –> class protocols::task_operations::DsspDesignOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::DsspDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator) → str¶: C++: protocols::task_operations::DsspDesignOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::DsspDesignOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::ImportUnboundRotamersOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation, : pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation) → pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation¶: C++: protocols::task_operations::ImportUnboundRotamersOperation::operator=(const class protocols::task_operations::ImportUnboundRotamersOperation &) –> class protocols::task_operations::ImportUnboundRotamersOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

static keyname() → str¶: C++: protocols::task_operations::ImportUnboundRotamersOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ImportUnboundRotamersOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ImportUnboundRotamersOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator¶: C++: protocols::task_operations::ImportUnboundRotamersOperationCreator::operator=(const class protocols::task_operations::ImportUnboundRotamersOperationCreator &) –> class protocols::task_operations::ImportUnboundRotamersOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ImportUnboundRotamersOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator) → str¶: C++: protocols::task_operations::ImportUnboundRotamersOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ImportUnboundRotamersOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion¶

Bases: TaskOperation

: taskop to oversample rotamers that make good interactions with a (set of) specified target residue(s) similar to Rosetta 2.x rotamer explosion

apply(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::InteractingRotamerExplosion::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion, : pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion) → pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion¶: C++: protocols::task_operations::InteractingRotamerExplosion::operator=(const class protocols::task_operations::InteractingRotamerExplosion &) –> class protocols::task_operations::InteractingRotamerExplosion &

clone(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::InteractingRotamerExplosion::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::InteractingRotamerExplosion::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::InteractingRotamerExplosion::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::InteractingRotamerExplosion::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator, : pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator) → pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator¶: C++: protocols::task_operations::InteractingRotamerExplosionCreator::operator=(const class protocols::task_operations::InteractingRotamerExplosionCreator &) –> class protocols::task_operations::InteractingRotamerExplosionCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::InteractingRotamerExplosionCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator) → str¶: C++: protocols::task_operations::InteractingRotamerExplosionCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::InteractingRotamerExplosionCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation¶

Bases: TaskOperation

add_native_fasta(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, fasta_file: str) → None¶

Add the sequence from the given fasta filename to the set of allowed aas

C++: protocols::task_operations::JointSequenceOperation::add_native_fasta(std::string) –> void

add_native_pdb(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, filename: str) → None¶

Add the sequence from the given filename to the set of allowed aas: and add the rotamers to the set of possible rotamers

C++: protocols::task_operations::JointSequenceOperation::add_native_pdb(std::string) –> void

add_native_pose(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, posecop: pyrosetta.rosetta.core.pose.Pose) → None¶

Add the sequence from the given pose to the set of allowed aas: and add the rotamers to the set of possible rotamers

C++: protocols::task_operations::JointSequenceOperation::add_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

add_pdb(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, filename: str) → None¶

Add the sequence from the given filename to the set of allowed aas.

C++: protocols::task_operations::JointSequenceOperation::add_pdb(std::string) –> void

add_pose(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Add the sequence from the given pose to the set of allowed aas.

C++: protocols::task_operations::JointSequenceOperation::add_pose(const class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::JointSequenceOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, : pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation) → pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation¶: C++: protocols::task_operations::JointSequenceOperation::operator=(const class protocols::task_operations::JointSequenceOperation &) –> class protocols::task_operations::JointSequenceOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

static keyname() → str¶: C++: protocols::task_operations::JointSequenceOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::JointSequenceOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::JointSequenceOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_chain(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, chain: int) → None¶

Return which chain to operate on with 0 meaning all

C++: protocols::task_operations::JointSequenceOperation::set_chain(unsigned long) –> void

use_current_pose(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, ucp: bool) → None¶

Should the current pose (pose supplied to apply) be used in addition to the other ones?

C++: protocols::task_operations::JointSequenceOperation::use_current_pose(bool) –> void

use_natro(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation, unr: bool) → None¶

Should the rotamers for the native poses be used?

C++: protocols::task_operations::JointSequenceOperation::use_natro(bool) –> void

class pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator, : pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator) → pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator¶: C++: protocols::task_operations::JointSequenceOperationCreator::operator=(const class protocols::task_operations::JointSequenceOperationCreator &) –> class protocols::task_operations::JointSequenceOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::JointSequenceOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator) → str¶: C++: protocols::task_operations::JointSequenceOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::JointSequenceOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::LimitAromaChi2Operation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, : pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation) → pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation¶: C++: protocols::task_operations::LimitAromaChi2Operation::operator=(const class protocols::task_operations::LimitAromaChi2Operation &) –> class protocols::task_operations::LimitAromaChi2Operation &

chi2max(*args, **kwargs)¶

Overloaded function.

chi2max(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation) -> float

max chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2Operation::chi2max() const –> double

chi2max(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, r: float) -> None

max chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2Operation::chi2max(const double) –> void

chi2min(*args, **kwargs)¶

Overloaded function.

chi2min(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation) -> float

min chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2Operation::chi2min() const –> double

chi2min(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, r: float) -> None

min chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2Operation::chi2min(const double) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

C++: protocols::task_operations::LimitAromaChi2Operation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

include_trp(*args, **kwargs)¶

Overloaded function.

include_trp(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation) -> bool

include TRP ?

C++: protocols::task_operations::LimitAromaChi2Operation::include_trp() const –> bool

include_trp(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, b: bool) -> None

include TRP ?

C++: protocols::task_operations::LimitAromaChi2Operation::include_trp(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::LimitAromaChi2Operation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::LimitAromaChi2Operation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::LimitAromaChi2Operation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator, : pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator) → pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator¶: C++: protocols::task_operations::LimitAromaChi2OperationCreator::operator=(const class protocols::task_operations::LimitAromaChi2OperationCreator &) –> class protocols::task_operations::LimitAromaChi2OperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::LimitAromaChi2OperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator) → str¶: C++: protocols::task_operations::LimitAromaChi2OperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::LimitAromaChi2OperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation¶

Bases: RotamerSetOperation

alter_rotamer_set(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None¶: C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation, : pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation) → pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation¶: C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::operator=(const class protocols::task_operations::LimitAromaChi2_RotamerSetOperation &) –> class protocols::task_operations::LimitAromaChi2_RotamerSetOperation &

chi2max(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation, r: float) → None¶

max chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::chi2max(const double) –> void

chi2min(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation, r: float) → None¶

min chi2 for picking rotamers of YFH

C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::chi2min(const double) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation¶: C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

include_trp(self: pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation, b: bool) → None¶

include TRP ?

C++: protocols::task_operations::LimitAromaChi2_RotamerSetOperation::include_trp(const bool) –> void

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float¶: C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.protocols.task_operations.LinkResidues¶

Bases: TaskOperation

this class is a TaskOperation to prevent repacking of residues not near an interface.

add_group(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues, group: str) → None¶: C++: protocols::task_operations::LinkResidues::add_group(std::string) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::LinkResidues::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues, : pyrosetta.rosetta.protocols.task_operations.LinkResidues) → pyrosetta.rosetta.protocols.task_operations.LinkResidues¶: C++: protocols::task_operations::LinkResidues::operator=(const class protocols::task_operations::LinkResidues &) –> class protocols::task_operations::LinkResidues &

clone(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::LinkResidues::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::LinkResidues::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::LinkResidues::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::LinkResidues::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

remap_allowed_residues_to_template(self: pyrosetta.rosetta.protocols.task_operations.LinkResidues, pose: pyrosetta.rosetta.core.pose.Pose, links: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks) → None¶: C++: protocols::task_operations::LinkResidues::remap_allowed_residues_to_template(const class core::pose::Pose &, class std::shared_ptr<class core::pack::rotamer_set::RotamerLinks> &) const –> void

class pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator, : pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator) → pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator¶: C++: protocols::task_operations::LinkResiduesCreator::operator=(const class protocols::task_operations::LinkResiduesCreator &) –> class protocols::task_operations::LinkResiduesCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::LinkResiduesCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator) → str¶: C++: protocols::task_operations::LinkResiduesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::LinkResiduesCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ModifyAnnealer::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer, : pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer) → pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer¶: C++: protocols::task_operations::ModifyAnnealer::operator=(const class protocols::task_operations::ModifyAnnealer &) –> class protocols::task_operations::ModifyAnnealer &

clone(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ModifyAnnealer::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::ModifyAnnealer::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ModifyAnnealer::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ModifyAnnealer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator, : pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator) → pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator¶: C++: protocols::task_operations::ModifyAnnealerCreator::operator=(const class protocols::task_operations::ModifyAnnealerCreator &) –> class protocols::task_operations::ModifyAnnealerCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ModifyAnnealerCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator) → str¶: C++: protocols::task_operations::ModifyAnnealerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ModifyAnnealerCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation¶

Bases: TaskOperation

Sample a set of mutations each time packer is generated. A MutationSet is a simple map of resnum:aa. Each apply will sample a set either at random, or with a set of weights.

Does not enable/disable packing or design by default. Simply controls what the design set will be. Typically each set would be of the same resnums, but this is not necessary. Iterative Sampling can be achieved somewhat by setting the sample index with each pack.

apply(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::MutationSetDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, : pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation¶: C++: protocols::task_operations::MutationSetDesignOperation::operator=(const class protocols::task_operations::MutationSetDesignOperation &) –> class protocols::task_operations::MutationSetDesignOperation &

clear_mutation_sets(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → None¶

Clear any stored mutation sets and weights.

C++: protocols::task_operations::MutationSetDesignOperation::clear_mutation_sets() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::MutationSetDesignOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

get_sample_index(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → int¶: C++: protocols::task_operations::MutationSetDesignOperation::get_sample_index() const –> unsigned long

get_total_mutation_sets(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → int¶

Get the total number of mutation sets housed.

C++: protocols::task_operations::MutationSetDesignOperation::get_total_mutation_sets() const –> unsigned long

include_native_aa(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, setting: bool) → None¶

Include native amino acid in the allowed_aas list. Default False.

C++: protocols::task_operations::MutationSetDesignOperation::include_native_aa(const bool &) –> void

static keyname() → str¶: C++: protocols::task_operations::MutationSetDesignOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::MutationSetDesignOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reset_sample_index(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation) → None¶

Set the sample index back to zero - which means we will sample from all of them according to weights.

C++: protocols::task_operations::MutationSetDesignOperation::reset_sample_index() –> void

set_mutation_sets(*args, **kwargs)¶

Overloaded function.

set_mutation_sets(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, mutation_sets: pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t) -> None

Set the mutation sets.: Each MutationSet is a std::map of resnum:aa Will use a weight of 1 for each.

C++: protocols::task_operations::MutationSetDesignOperation::set_mutation_sets(class utility::vector1<class std::map<unsigned long, enum core::chemical::AA, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, enum core::chemical::AA> > >, class std::allocator<class std::map<unsigned long, enum core::chemical::AA, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, enum core::chemical::AA> > > > >) –> void

set_mutation_sets(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, mutation_sets: pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t, mutation_set_weights: pyrosetta.rosetta.utility.vector1_double) -> None

Set the mutation sets and corresponding weights: Each MutationSet is a std::map of resnum:aa

C++: protocols::task_operations::MutationSetDesignOperation::set_mutation_sets(class utility::vector1<class std::map<unsigned long, enum core::chemical::AA, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, enum core::chemical::AA> > >, class std::allocator<class std::map<unsigned long, enum core::chemical::AA, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, enum core::chemical::AA> > > > >, class utility::vector1<double, class std::allocator<double> >) –> void

set_picking_rounds(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, picking_rounds: int) → None¶

Number of times we sample from our sets. Default 1/apply.: The more rounds, the closer the final amino acid set for each position will be to the full profile for that position. If using weights for the residue sets, this would increase variability.

C++: protocols::task_operations::MutationSetDesignOperation::set_picking_rounds(unsigned long) –> void

set_sample_index(self: pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation, sample_index: int) → None¶

Used to sample particular indexes, since we can’t do this iteratively due to const apply. 1 through n: Set to 0 in order to sample from the weights.

C++: protocols::task_operations::MutationSetDesignOperation::set_sample_index(unsigned long) –> void

class pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation, : pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation) → pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::operator=(const class protocols::task_operations::PreventChainFromRepackingOperation &) –> class protocols::task_operations::PreventChainFromRepackingOperation &

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation, chain: int) -> None

C++: protocols::task_operations::PreventChainFromRepackingOperation::chain(const unsigned long) –> void

chain(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation) -> int

C++: protocols::task_operations::PreventChainFromRepackingOperation::chain() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PreventChainFromRepackingOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator, : pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator) → pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator¶: C++: protocols::task_operations::PreventChainFromRepackingOperationCreator::operator=(const class protocols::task_operations::PreventChainFromRepackingOperationCreator &) –> class protocols::task_operations::PreventChainFromRepackingOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::PreventChainFromRepackingOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator) → str¶: C++: protocols::task_operations::PreventChainFromRepackingOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PreventChainFromRepackingOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation, : pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation) → pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::operator=(const class protocols::task_operations::PreventResiduesFromRepackingOperation &) –> class protocols::task_operations::PreventResiduesFromRepackingOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

get_residues(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::get_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

static keyname() → str¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pdb_id(*args, **kwargs)¶

Overloaded function.

reference_pdb_id(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation) -> str

C++: protocols::task_operations::PreventResiduesFromRepackingOperation::reference_pdb_id() const –> std::string

reference_pdb_id(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation, s: str) -> None

C++: protocols::task_operations::PreventResiduesFromRepackingOperation::reference_pdb_id(const std::string &) –> void

set_residues(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation, residues_vec: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperation::set_residues(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

class pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator, : pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator) → pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperationCreator::operator=(const class protocols::task_operations::PreventResiduesFromRepackingOperationCreator &) –> class protocols::task_operations::PreventResiduesFromRepackingOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator) → str¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PreventResiduesFromRepackingOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ProteinCore¶

Bases: ResFilter

assign(self: pyrosetta.rosetta.protocols.task_operations.ProteinCore, : pyrosetta.rosetta.protocols.task_operations.ProteinCore) → pyrosetta.rosetta.protocols.task_operations.ProteinCore¶: C++: protocols::task_operations::ProteinCore::operator=(const class protocols::task_operations::ProteinCore &) –> class protocols::task_operations::ProteinCore &

clone(self: pyrosetta.rosetta.protocols.task_operations.ProteinCore) → pyrosetta.rosetta.core.pack.task.operation.ResFilter¶: C++: protocols::task_operations::ProteinCore::clone() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

static keyname() → str¶: C++: protocols::task_operations::ProteinCore::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ProteinCore, : pyrosetta.rosetta.utility.tag.Tag) → None¶: C++: protocols::task_operations::ProteinCore::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ProteinCore::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator¶

Bases: ResFilterCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator, : pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator) → pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator¶: C++: protocols::task_operations::ProteinCoreFilterCreator::operator=(const class protocols::task_operations::ProteinCoreFilterCreator &) –> class protocols::task_operations::ProteinCoreFilterCreator &

create_res_filter(self: pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator) → pyrosetta.rosetta.core.pack.task.operation.ResFilter¶: C++: protocols::task_operations::ProteinCoreFilterCreator::create_res_filter() const –> class std::shared_ptr<class core::pack::task::operation::ResFilter>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator) → str¶: C++: protocols::task_operations::ProteinCoreFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ProteinCoreFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

allow_all_aas(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, allow: bool) → None¶

allow all amino acids to be designed at all positions, do not exclude C, G, P

C++: protocols::task_operations::ProteinInterfaceDesignOperation::allow_all_aas(const bool) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, : pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) → pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::operator=(const class protocols::task_operations::ProteinInterfaceDesignOperation &) –> class protocols::task_operations::ProteinInterfaceDesignOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

design_all_aas(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, design_all: bool) → None¶

allow design of all residues on input pose, do not exclude G,P

C++: protocols::task_operations::ProteinInterfaceDesignOperation::design_all_aas(const bool) –> void

design_chain1(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, design: bool) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::design_chain1(const bool) –> void

design_chain2(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, design: bool) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2(const bool) –> void

interface_distance_cutoff(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, dist: float) → None¶

distance cutoff for atom distance in an interface.: All residues an atoms less than the distance cutoff from an atom in the other chain are defined as interface.

C++: protocols::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff(const double) –> void

jump(*args, **kwargs)¶

Overloaded function.

jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, j: int) -> None

C++: protocols::task_operations::ProteinInterfaceDesignOperation::jump(const unsigned long) –> void

jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) -> int

C++: protocols::task_operations::ProteinInterfaceDesignOperation::jump() const –> unsigned long

static keyname() → str¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::keyname() –> std::string

modify_after_jump(*args, **kwargs)¶

Overloaded function.

modify_after_jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) -> bool

C++: protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump() const –> bool

modify_after_jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, m: bool) -> None

C++: protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump(const bool) –> void

modify_before_jump(*args, **kwargs)¶

Overloaded function.

modify_before_jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) -> bool

C++: protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump() const –> bool

modify_before_jump(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, m: bool) -> None

C++: protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump(const bool) –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_chain1(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, repack: bool) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1(const bool) –> void

repack_chain2(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation, repack: bool) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain2(const bool) –> void

class pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator¶: C++: protocols::task_operations::ProteinInterfaceDesignOperationCreator::operator=(const class protocols::task_operations::ProteinInterfaceDesignOperationCreator &) –> class protocols::task_operations::ProteinInterfaceDesignOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ProteinInterfaceDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator) → str¶: C++: protocols::task_operations::ProteinInterfaceDesignOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ProteinInterfaceDesignOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation¶

Bases: TaskOperation

allow_even_trades(*args, **kwargs)¶

Overloaded function.

allow_even_trades(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) -> bool

C++: protocols::task_operations::PruneBuriedUnsatsOperation::allow_even_trades() const –> bool

allow_even_trades(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, allow_even_trades: bool) -> None

C++: protocols::task_operations::PruneBuriedUnsatsOperation::allow_even_trades(bool) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::PruneBuriedUnsatsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, other: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) → pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation¶: C++: protocols::task_operations::PruneBuriedUnsatsOperation::operator=(const class protocols::task_operations::PruneBuriedUnsatsOperation &) –> class protocols::task_operations::PruneBuriedUnsatsOperation &

atomic_depth_cutoff(*args, **kwargs)¶

Overloaded function.

atomic_depth_cutoff(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) -> float

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_cutoff() const –> double

atomic_depth_cutoff(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, atomic_depth_cutoff: float) -> None

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_cutoff(double) –> void

atomic_depth_probe_radius(*args, **kwargs)¶

Overloaded function.

atomic_depth_probe_radius(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) -> float

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_probe_radius() const –> double

atomic_depth_probe_radius(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, atomic_depth_probe_radius: float) -> None

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_probe_radius(double) –> void

atomic_depth_resolution(*args, **kwargs)¶

Overloaded function.

atomic_depth_resolution(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) -> float

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_resolution() const –> double

atomic_depth_resolution(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, atomic_depth_resolution: float) -> None

C++: protocols::task_operations::PruneBuriedUnsatsOperation::atomic_depth_resolution(double) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

static keyname() → str¶: C++: protocols::task_operations::PruneBuriedUnsatsOperation::keyname() –> std::string

minimum_hbond_energy(*args, **kwargs)¶

Overloaded function.

minimum_hbond_energy(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation) -> float

C++: protocols::task_operations::PruneBuriedUnsatsOperation::minimum_hbond_energy() const –> double

minimum_hbond_energy(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, minimum_hbond_energy: float) -> None

C++: protocols::task_operations::PruneBuriedUnsatsOperation::minimum_hbond_energy(double) –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::PruneBuriedUnsatsOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PruneBuriedUnsatsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator, : pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator) → pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator¶: C++: protocols::task_operations::PruneBuriedUnsatsOperationCreator::operator=(const class protocols::task_operations::PruneBuriedUnsatsOperationCreator &) –> class protocols::task_operations::PruneBuriedUnsatsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::PruneBuriedUnsatsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator) → str¶: C++: protocols::task_operations::PruneBuriedUnsatsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::PruneBuriedUnsatsOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation¶

Bases: RotamerSetsOperation

alter_rotamer_sets(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.utility.graph.Graph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None¶: C++: protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSets &) –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation, : pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation) → pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation¶: C++: protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::operator=(const class protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation &) –> class protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation¶: C++: protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetsOperation>

class pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ReadResfileFromDB::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, : pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB) → pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB¶: C++: protocols::task_operations::ReadResfileFromDB::operator=(const class protocols::task_operations::ReadResfileFromDB &) –> class protocols::task_operations::ReadResfileFromDB &

clone(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ReadResfileFromDB::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

database_table(*args, **kwargs)¶

Overloaded function.

database_table(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, database_table: str) -> None

C++: protocols::task_operations::ReadResfileFromDB::database_table(const std::string &) –> void

database_table(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB) -> str

C++: protocols::task_operations::ReadResfileFromDB::database_table() const –> const std::string &

db_session(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, db_session: pyrosetta.rosetta.utility.sql_database.session) → None¶: C++: protocols::task_operations::ReadResfileFromDB::db_session(class std::shared_ptr<class utility::sql_database::session>) –> void

static keyname() → str¶: C++: protocols::task_operations::ReadResfileFromDB::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ReadResfileFromDB::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ReadResfileFromDB::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

residue_selector(*args, **kwargs)¶

Overloaded function.

residue_selector(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::task_operations::ReadResfileFromDB::residue_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

residue_selector(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::task_operations::ReadResfileFromDB::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

selection_tag(*args, **kwargs)¶

Overloaded function.

selection_tag(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB, setting: str) -> None

C++: protocols::task_operations::ReadResfileFromDB::selection_tag(const std::string &) –> void

selection_tag(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB) -> str

C++: protocols::task_operations::ReadResfileFromDB::selection_tag() const –> const std::string &

class pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator, : pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator) → pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator¶: C++: protocols::task_operations::ReadResfileFromDBCreator::operator=(const class protocols::task_operations::ReadResfileFromDBCreator &) –> class protocols::task_operations::ReadResfileFromDBCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ReadResfileFromDBCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator) → str¶: C++: protocols::task_operations::ReadResfileFromDBCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ReadResfileFromDBCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation¶

Bases: TaskOperation

Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector.

apply(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ResfileCommandOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation, : pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation) → pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation¶: C++: protocols::task_operations::ResfileCommandOperation::operator=(const class protocols::task_operations::ResfileCommandOperation &) –> class protocols::task_operations::ResfileCommandOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ResfileCommandOperation::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++: protocols::task_operations::ResfileCommandOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure from a RosettaScripts XML tag.

C++: protocols::task_operations::ResfileCommandOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶

Describe the format of XML file used to initialize this TaskOperation

C++: protocols::task_operations::ResfileCommandOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_command(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation, command: str) → None¶

A resfile command string without any numbers in the front. eg:

C++: protocols::task_operations::ResfileCommandOperation::set_command(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::task_operations::ResfileCommandOperation::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator¶: C++: protocols::task_operations::ResfileCommandOperationCreator::operator=(const class protocols::task_operations::ResfileCommandOperationCreator &) –> class protocols::task_operations::ResfileCommandOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ResfileCommandOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator) → str¶: C++: protocols::task_operations::ResfileCommandOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ResfileCommandOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation¶

Bases: TaskOperation

A TaskOperation that allows amino acids at designable positions through a set of aa probabilities (aa profile).

Default is for the TaskOp to control the allowed amino acids only if the class has probabilities to use for that resnum. If no probabilities were set in general, it will not do anything. Probabilities should add to one, but if not, they will act as weights. Does NOT control which positions are set to design or repack, only what can be designed into.

If probabilities/weights for a particular residue are not present in the map, will not modify that residues task.

apply(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ResidueProbDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, : pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation¶: C++: protocols::task_operations::ResidueProbDesignOperation::operator=(const class protocols::task_operations::ResidueProbDesignOperation &) –> class protocols::task_operations::ResidueProbDesignOperation &

clear_overall_prob_set(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → None¶

Clears the overall probabilities if any are set.

C++: protocols::task_operations::ResidueProbDesignOperation::clear_overall_prob_set() –> void

clear_prob_set(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → None¶

Clears the probability matrix

C++: protocols::task_operations::ResidueProbDesignOperation::clear_prob_set() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ResidueProbDesignOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

include_native_restype(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → bool¶: C++: protocols::task_operations::ResidueProbDesignOperation::include_native_restype() const –> bool

static keyname() → str¶: C++: protocols::task_operations::ResidueProbDesignOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ResidueProbDesignOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

picking_rounds(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → int¶: C++: protocols::task_operations::ResidueProbDesignOperation::picking_rounds() const –> unsigned long

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ResidueProbDesignOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

resnum_exists_in_set(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, resnum: int) → bool¶: C++: protocols::task_operations::ResidueProbDesignOperation::resnum_exists_in_set(const unsigned long) const –> bool

sample_zero_probs_at(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → float¶: C++: protocols::task_operations::ResidueProbDesignOperation::sample_zero_probs_at() const –> double

set_aa_probabilities(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, resnum: int, aa_probs: pyrosetta.rosetta.std.map_core_chemical_AA_double) → None¶

Sets aa probabilities for a particular resnum

C++: protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities(const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >) –> void

set_aa_probabilities_from_file(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, weights_file: str) → None¶

Reads weights for each posenum and residue type. Format for each line in the file is: POSENUM RESIDUETYPE WEIGHT. With weight as a real between 0 and 1

C++: protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(const std::string &) –> void

set_aa_probability_set(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, per_res_aa_probs: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t) → None¶

Sets the whole aa probability set.

C++: protocols::task_operations::ResidueProbDesignOperation::set_aa_probability_set(class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > >) –> void

set_defaults(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation) → None¶: C++: protocols::task_operations::ResidueProbDesignOperation::set_defaults() –> void

set_include_native_restype(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, include: bool) → None¶

Include current residuetype in packer in addition to selected mutation. Default is true.

C++: protocols::task_operations::ResidueProbDesignOperation::set_include_native_restype(bool) –> void

set_no_probability(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, no_probability: bool) → None¶

Set to sample all available AAs per position instead of sampling based on weights: Used to increase diversity and for testing purposes.

C++: protocols::task_operations::ResidueProbDesignOperation::set_no_probability(bool) –> void

set_overall_aa_probabilities(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, aa_probs: pyrosetta.rosetta.std.map_core_chemical_AA_double) → None¶

Sets aa probabilities for all positions not given specifically. All designable residues will use these probabilities this if not specified through other functions.

C++: protocols::task_operations::ResidueProbDesignOperation::set_overall_aa_probabilities(class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >) –> void

set_picking_rounds(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, picking_rounds: int) → None¶

Max number of times to sample from the probability distribution. Default is once.

C++: protocols::task_operations::ResidueProbDesignOperation::set_picking_rounds(unsigned long) –> void

set_sample_zero_probs_at(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation, probability: float) → None¶

Sample any zero probabilities at this probability instead of not using them.

C++: protocols::task_operations::ResidueProbDesignOperation::set_sample_zero_probs_at(const double) –> void

class pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator¶: C++: protocols::task_operations::ResidueProbDesignOperationCreator::operator=(const class protocols::task_operations::ResidueProbDesignOperationCreator &) –> class protocols::task_operations::ResidueProbDesignOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ResidueProbDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator) → str¶: C++: protocols::task_operations::ResidueProbDesignOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ResidueProbDesignOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities¶

Bases: TaskOperation

A class to restrict designable amino acids depending on the probabilities from a PerResidueProbabilitiesMetric

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictAAsFromProbabilities::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, : pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities) → pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities¶: C++: protocols::task_operations::RestrictAAsFromProbabilities::operator=(const class protocols::task_operations::RestrictAAsFromProbabilities &) –> class protocols::task_operations::RestrictAAsFromProbabilities &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictAAsFromProbabilities::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

disable_AAs(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, probabilities: pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

disable all amino acids that do not meet user provided probability cutoffs

C++: protocols::task_operations::RestrictAAsFromProbabilities::disable_AAs(class std::map<unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::map<enum core::chemical::AA, double, struct std::less<enum core::chemical::AA>, class std::allocator<struct std::pair<const enum core::chemical::AA, double> > > > > > &, const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

static keyname() → str¶

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

C++: protocols::task_operations::RestrictAAsFromProbabilities::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure from a RosettaScripts XML tag.

C++: protocols::task_operations::RestrictAAsFromProbabilities::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶

Describe the format of XML file used to initialize this TaskOperation

C++: protocols::task_operations::RestrictAAsFromProbabilities::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_delta_prob_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, delta_prob_cutoff: float) → None¶

Set the delta probability cutoff option

C++: protocols::task_operations::RestrictAAsFromProbabilities::set_delta_prob_cutoff(double) –> void

set_fail_on_missing_cache(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, fail: bool) → None¶

If use_cache is set to false, do we fail if no data is found in the pose?: Default True

C++: protocols::task_operations::RestrictAAsFromProbabilities::set_fail_on_missing_cache(bool) –> void

set_metric(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric) → None¶

Set the PerResidueProbabilitiesMetric that will be used to calculate the pseudo-perplexity.

C++: protocols::task_operations::RestrictAAsFromProbabilities::set_metric(class std::shared_ptr<const class core::simple_metrics::PerResidueProbabilitiesMetric>) –> void

set_prob_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, prob_cutoff: float) → None¶

Set the probability cutoff option

C++: protocols::task_operations::RestrictAAsFromProbabilities::set_prob_cutoff(double) –> void

set_use_cached_data(*args, **kwargs)¶

Overloaded function.

set_use_cached_data(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, use_cache: bool) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, use_cache: bool, prefix: str) -> None
set_use_cached_data(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities, use_cache: bool, prefix: str, suffix: str) -> None

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric.

Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

C++: protocols::task_operations::RestrictAAsFromProbabilities::set_use_cached_data(bool, const std::string &, const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator¶: C++: protocols::task_operations::RestrictAAsFromProbabilitiesCreator::operator=(const class protocols::task_operations::RestrictAAsFromProbabilitiesCreator &) –> class protocols::task_operations::RestrictAAsFromProbabilitiesCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictAAsFromProbabilitiesCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator) → str¶: C++: protocols::task_operations::RestrictAAsFromProbabilitiesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictAAsFromProbabilitiesCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues according to std::set< core::Size >-returning PoseMetricCalculators

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictByCalculatorsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase, : pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase) → pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase¶: C++: protocols::task_operations::RestrictOperationsBase::operator=(const class protocols::task_operations::RestrictOperationsBase &) –> class protocols::task_operations::RestrictOperationsBase &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictByCalculatorsOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictByCalculatorsOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictByCalculatorsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator¶: C++: protocols::task_operations::RestrictByCalculatorsOperationCreator::operator=(const class protocols::task_operations::RestrictByCalculatorsOperationCreator &) –> class protocols::task_operations::RestrictByCalculatorsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictByCalculatorsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator) → str¶: C++: protocols::task_operations::RestrictByCalculatorsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictByCalculatorsOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::operator=(const class protocols::task_operations::RestrictChainToRepackingOperation &) –> class protocols::task_operations::RestrictChainToRepackingOperation &

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation, chain: int) -> None

C++: protocols::task_operations::RestrictChainToRepackingOperation::chain(const unsigned long) –> void

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation) -> int

C++: protocols::task_operations::RestrictChainToRepackingOperation::chain() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictChainToRepackingOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator¶: C++: protocols::task_operations::RestrictChainToRepackingOperationCreator::operator=(const class protocols::task_operations::RestrictChainToRepackingOperationCreator &) –> class protocols::task_operations::RestrictChainToRepackingOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictChainToRepackingOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator) → str¶: C++: protocols::task_operations::RestrictChainToRepackingOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictChainToRepackingOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation¶

Bases: SeqprofConsensusOperation

a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking.

wt ala positions are set to repacking based on seqprof criterion only. If the input pose contains a forbidden (i.e. non wildtype ) residue at an untouchable position, the residue currently in the pose is also allowed.

static aa_occurrence_filter(pos_occurance: pyrosetta.rosetta.utility.vector1_double, pos_min_occurance: float, keep_aas: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::aa_occurrence_filter(const class utility::vector1<double, class std::allocator<double> > &, const double, class utility::vector1<bool, class std::allocator<bool> > &) –> void

aa_probability_filter(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pose: pyrosetta.rosetta.core.pose.Pose, pos_profile: pyrosetta.rosetta.utility.vector1_double, position_min_prob: float, aa_idx: int, keep_aas: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::aa_probability_filter(const class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const double, const unsigned long, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::operator=(const class protocols::task_operations::RestrictConservedLowDdgOperation &) –> class protocols::task_operations::RestrictConservedLowDdgOperation &

chain_num(*args, **kwargs)¶

Overloaded function.

chain_num(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> int

C++: protocols::task_operations::SeqprofConsensusOperation::chain_num() const –> unsigned long

chain_num(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, d: int) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::chain_num(const unsigned long) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

conservation_cutoff_aligned_segments(*args, **kwargs)¶

Overloaded function.

conservation_cutoff_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> float

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments() const –> double

conservation_cutoff_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: float) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments(const double) –> void

conservation_cutoff_protein_interface_design(*args, **kwargs)¶

Overloaded function.

conservation_cutoff_protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> float

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design() const –> double

conservation_cutoff_protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: float) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design(const double) –> void

convert_scores_to_probabilities(*args, **kwargs)¶

Overloaded function.

convert_scores_to_probabilities(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities(const bool) –> void

convert_scores_to_probabilities(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities() const –> bool

static create_complex_type_generator(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::create_complex_type_generator(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

debug(*args, **kwargs)¶

Overloaded function.

debug(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::debug(const bool) –> void

debug(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::debug() const –> bool

keep_native(*args, **kwargs)¶

Overloaded function.

keep_native(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::keep_native() const –> bool

keep_native(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::keep_native(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::keyname() –> std::string

parse_profile_from_pose(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.sequence.SequenceProfile¶: C++: protocols::task_operations::SeqprofConsensusOperation::parse_profile_from_pose(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceProfile>

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

position_ala_ddG(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, seqpos: int) → float¶

convenience function to query: what the ddG is for a to ala mutation at a certain position

C++: protocols::task_operations::RestrictConservedLowDdgOperation::position_ala_ddG(unsigned long) const –> double

position_untouchable(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, seqpos: int, seqprof_wt: pyrosetta.rosetta.core.chemical.AA) → bool¶

returns true if seqpos has a sequence profile: frequency > conservation_cutoff_ and an X->A ddG of > ddG_cutoff_

C++: protocols::task_operations::RestrictConservedLowDdgOperation::position_untouchable(unsigned long, enum core::chemical::AA) const –> bool

protein_interface_design(*args, **kwargs)¶

Overloaded function.

protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation

C++: protocols::task_operations::SeqprofConsensusOperation::protein_interface_design() const –> class std::shared_ptr<class protocols::task_operations::ProteinInterfaceDesignOperation>

protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pido: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::protein_interface_design(class std::shared_ptr<class protocols::task_operations::ProteinInterfaceDesignOperation>) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

restrict_to_aligned_segments(*args, **kwargs)¶

Overloaded function.

restrict_to_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation

C++: protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments() const –> class std::shared_ptr<class protocols::task_operations::RestrictToAlignedSegmentsOperation>

restrict_to_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, rtas: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments(class std::shared_ptr<class protocols::task_operations::RestrictToAlignedSegmentsOperation>) –> void

seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) → pyrosetta.rosetta.core.sequence.SequenceProfile¶: C++: protocols::task_operations::SeqprofConsensusOperation::seqprof() const –> class std::shared_ptr<const class core::sequence::SequenceProfile>

seqprof_wt_aa(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation, seqpos: int) → pyrosetta.rosetta.core.chemical.AA¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(unsigned long) const –> enum core::chemical::AA

set_ignore_pose_profile_length_mismatch(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, setting: bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::set_ignore_pose_profile_length_mismatch(const bool) –> void

set_seqprof(*args, **kwargs)¶

Overloaded function.

set_seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, seqprof: pyrosetta.rosetta.core.sequence.SequenceProfile) -> None
set_seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, seqprof: pyrosetta.rosetta.core.sequence.SequenceProfile, reweight: bool) -> None

Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first

C++: protocols::task_operations::SeqprofConsensusOperation::set_seqprof(class std::shared_ptr<class core::sequence::SequenceProfile>, bool) –> void

use_occurrence_data(*args, **kwargs)¶

Overloaded function.

use_occurrence_data(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data() const –> bool

use_occurrence_data(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation) → bool¶: C++: protocols::task_operations::RestrictConservedLowDdgOperation::verbose() const –> bool

class pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator¶: C++: protocols::task_operations::RestrictConservedLowDdgOperationCreator::operator=(const class protocols::task_operations::RestrictConservedLowDdgOperationCreator &) –> class protocols::task_operations::RestrictConservedLowDdgOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictConservedLowDdgOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator) → str¶: C++: protocols::task_operations::RestrictConservedLowDdgOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictConservedLowDdgOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::operator=(const class protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation &) –> class protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation &

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, c: int) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::chain(const unsigned long) –> void

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> int

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::chain() const –> unsigned long

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

design_only_target_residues(*args, **kwargs)¶

Overloaded function.

design_only_target_residues(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b: bool) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_only_target_residues(const bool) –> void

design_only_target_residues(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_only_target_residues() const –> bool

design_shell(*args, **kwargs)¶

Overloaded function.

design_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> float

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_shell() –> double

design_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, r: float) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_shell(double) –> void

keep_aas(*args, **kwargs)¶

Overloaded function.

keep_aas(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s: str) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::keep_aas(const std::string &) –> void

keep_aas(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> str

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::keep_aas() const –> std::string

static keyname() → str¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prevent_repacking(*args, **kwargs)¶

Overloaded function.

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::prevent_repacking() const –> bool

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b: bool) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::prevent_repacking(const bool) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_shell(*args, **kwargs)¶

Overloaded function.

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, r: float) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::repack_shell(double) –> void

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> float

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::repack_shell() –> double

res_ids(*args, **kwargs)¶

Overloaded function.

res_ids(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::res_ids() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

res_ids(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::res_ids(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

restrict_identities(*args, **kwargs)¶

Overloaded function.

restrict_identities(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, b: bool) -> None

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::restrict_identities(const bool) –> void

restrict_identities(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation) -> bool

C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::restrict_identities() const –> bool

source_pose(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation, s: str) → None¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::source_pose(const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator::operator=(const class protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator &) –> class protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator) → str¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation¶

Bases: TaskOperation

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictIdentitiesOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation¶: C++: protocols::task_operations::RestrictIdentitiesOperation::operator=(const class protocols::task_operations::RestrictIdentitiesOperation &) –> class protocols::task_operations::RestrictIdentitiesOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictIdentitiesOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

identities(*args, **kwargs)¶

Overloaded function.

identities(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::task_operations::RestrictIdentitiesOperation::identities() const –> class utility::vector1<std::string, class std::allocator<std::string > >

identities(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation, residues_vec: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::task_operations::RestrictIdentitiesOperation::identities(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

static keyname() → str¶: C++: protocols::task_operations::RestrictIdentitiesOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictIdentitiesOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prevent_repacking(*args, **kwargs)¶

Overloaded function.

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation) -> bool

C++: protocols::task_operations::RestrictIdentitiesOperation::prevent_repacking() const –> bool

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation, prevent_repacking: bool) -> None

C++: protocols::task_operations::RestrictIdentitiesOperation::prevent_repacking(const bool) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictIdentitiesOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator¶: C++: protocols::task_operations::RestrictIdentitiesOperationCreator::operator=(const class protocols::task_operations::RestrictIdentitiesOperationCreator &) –> class protocols::task_operations::RestrictIdentitiesOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictIdentitiesOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator) → str¶: C++: protocols::task_operations::RestrictIdentitiesOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictIdentitiesOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation¶

Bases: TaskOperation

CB_dist_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, CB_dist_cutoff: float) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::CB_dist_cutoff(double) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::RestrictInterGroupVectorOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::operator=(const class protocols::task_operations::RestrictInterGroupVectorOperation &) –> class protocols::task_operations::RestrictInterGroupVectorOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

insert_pair(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, pair: Tuple[pyrosetta.rosetta.std.set_unsigned_long_t, pyrosetta.rosetta.std.set_unsigned_long_t]) → None¶

setters for member data

C++: protocols::task_operations::RestrictInterGroupVectorOperation::insert_pair(struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > >) –> void

static keyname() → str¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::keyname() –> std::string

nearby_atom_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, nearby_atom_cutoff: float) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::nearby_atom_cutoff(double) –> void

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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

vector_angle_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, vector_angle_cutoff: float) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::vector_angle_cutoff(double) –> void

vector_dist_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation, vector_dist_cutoff: float) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperation::vector_dist_cutoff(double) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator¶: C++: protocols::task_operations::RestrictInterGroupVectorOperationCreator::operator=(const class protocols::task_operations::RestrictInterGroupVectorOperationCreator &) –> class protocols::task_operations::RestrictInterGroupVectorOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictInterGroupVectorOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator) → str¶: C++: protocols::task_operations::RestrictInterGroupVectorOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictInterGroupVectorOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::RestrictNativeResiduesOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation¶: C++: protocols::task_operations::RestrictNativeResiduesOperation::operator=(const class protocols::task_operations::RestrictNativeResiduesOperation &) –> class protocols::task_operations::RestrictNativeResiduesOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

static keyname() → str¶: C++: protocols::task_operations::RestrictNativeResiduesOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictNativeResiduesOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prevent_repacking(*args, **kwargs)¶

Overloaded function.

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation) -> bool

C++: protocols::task_operations::RestrictNativeResiduesOperation::prevent_repacking() const –> bool

prevent_repacking(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, prev: bool) -> None

C++: protocols::task_operations::RestrictNativeResiduesOperation::prevent_repacking(const bool) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictNativeResiduesOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::task_operations::RestrictNativeResiduesOperation::reference_pose() const –> class std::shared_ptr<const class core::pose::Pose>

reference_pose(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::task_operations::RestrictNativeResiduesOperation::reference_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

reference_pose(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::task_operations::RestrictNativeResiduesOperation::reference_pose(const class core::pose::Pose &) –> void

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation) -> bool

C++: protocols::task_operations::RestrictNativeResiduesOperation::verbose() const –> bool

verbose(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation, verb: bool) -> None

C++: protocols::task_operations::RestrictNativeResiduesOperation::verbose(const bool) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator¶: C++: protocols::task_operations::RestrictNativeResiduesOperationCreator::operator=(const class protocols::task_operations::RestrictNativeResiduesOperationCreator &) –> class protocols::task_operations::RestrictNativeResiduesOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictNativeResiduesOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator) → str¶: C++: protocols::task_operations::RestrictNativeResiduesOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictNativeResiduesOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation¶

Bases: TaskOperation

this class is a TaskOperation to allow design of only surface exposed positions

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::operator=(const class protocols::task_operations::RestrictNonSurfaceToRepackingOperation &) –> class protocols::task_operations::RestrictNonSurfaceToRepackingOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation, tag: pyrosetta.rosetta.utility.tag.Tag, dm: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

surface_exposed_nb_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation, nb_count: int) → None¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperation::surface_exposed_nb_cutoff(const unsigned long) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator::operator=(const class protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator &) –> class protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator) → str¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictNonSurfaceToRepackingOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase¶

Bases: TaskOperation

This base class defines an interface for TaskOperations which use PoseMetricCalculators to pick out certain residues in a pose. The apply function takes a vector of PoseMetricCalculators and a vector of calculation queries, and uses those queries to shape the PackerTask. This was designed to work with NeighborsByDistanceCalculator, NeighborhoodByDistanceCalculator, and InterfaceNeighborDefinitionCalculator; in general it works when the calculators can return MetricValue< std::set< core::Size > > (a std::set of resids).

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictOperationsBase::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase, : pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase) → pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase¶: C++: protocols::task_operations::RestrictOperationsBase::operator=(const class protocols::task_operations::RestrictOperationsBase &) –> class protocols::task_operations::RestrictOperationsBase &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictOperationsBase::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

class pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::operator=(const class protocols::task_operations::RestrictResiduesToRepackingOperation &) –> class protocols::task_operations::RestrictResiduesToRepackingOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

get_residues(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::get_residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

static keyname() → str¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pdb_id(*args, **kwargs)¶

Overloaded function.

reference_pdb_id(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation) -> str

C++: protocols::task_operations::RestrictResiduesToRepackingOperation::reference_pdb_id() const –> std::string

reference_pdb_id(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation, s: str) -> None

C++: protocols::task_operations::RestrictResiduesToRepackingOperation::reference_pdb_id(const std::string &) –> void

set_residues(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation, residues_vec: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperation::set_residues(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperationCreator::operator=(const class protocols::task_operations::RestrictResiduesToRepackingOperationCreator &) –> class protocols::task_operations::RestrictResiduesToRepackingOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator) → str¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictResiduesToRepackingOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::operator=(const class protocols::task_operations::RestrictToAlignedSegmentsOperation &) –> class protocols::task_operations::RestrictToAlignedSegmentsOperation &

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> int

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::chain() const –> unsigned long

chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, c: int) -> None

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::chain(const unsigned long) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

repack_shell(*args, **kwargs)¶

Overloaded function.

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> float

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::repack_shell() const –> double

repack_shell(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, r: float) -> None

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::repack_shell(const double) –> void

start_res(*args, **kwargs)¶

Overloaded function.

start_res(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::start_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

start_res(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, s: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::start_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

stop_res(*args, **kwargs)¶

Overloaded function.

stop_res(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::stop_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

stop_res(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation, s: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::RestrictToAlignedSegmentsOperation::stop_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperationCreator::operator=(const class protocols::task_operations::RestrictToAlignedSegmentsOperationCreator &) –> class protocols::task_operations::RestrictToAlignedSegmentsOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator) → str¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToAlignedSegmentsOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToCDRH3Loop::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop, : pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop) → pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop¶: C++: protocols::task_operations::RestrictToCDRH3Loop::operator=(const class protocols::task_operations::RestrictToCDRH3Loop &) –> class protocols::task_operations::RestrictToCDRH3Loop &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToCDRH3Loop::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictToCDRH3Loop::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToCDRH3Loop::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator¶: C++: protocols::task_operations::RestrictToCDRH3LoopCreator::operator=(const class protocols::task_operations::RestrictToCDRH3LoopCreator &) –> class protocols::task_operations::RestrictToCDRH3LoopCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToCDRH3LoopCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator) → str¶: C++: protocols::task_operations::RestrictToCDRH3LoopCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToCDRH3LoopCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToInterfaceOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation¶: C++: protocols::task_operations::RestrictToInterfaceOperation::operator=(const class protocols::task_operations::RestrictToInterfaceOperation &) –> class protocols::task_operations::RestrictToInterfaceOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToInterfaceOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictToInterfaceOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToInterfaceOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator¶: C++: protocols::task_operations::RestrictToInterfaceOperationCreator::operator=(const class protocols::task_operations::RestrictToInterfaceOperationCreator &) –> class protocols::task_operations::RestrictToInterfaceOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToInterfaceOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator) → str¶: C++: protocols::task_operations::RestrictToInterfaceOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToInterfaceOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation¶

Bases: InterfaceTaskOperation

this class is a TaskOperation to prevent repacking of residues not near an interface.

CB_dist_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, CB_dist_cutoff: float) → None¶

Commenting out to fix PyRosetta build void jump_num( int jump_num);

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::CB_dist_cutoff(double) –> void

add_movable_chain(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation, additional_chain: int) → None¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::add_movable_chain(const int) –> void

add_movable_jump(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation, additional_jump: int) → None¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::add_movable_jump(const int) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::operator=(const class protocols::task_operations::RestrictToInterfaceVectorOperation &) –> class protocols::task_operations::RestrictToInterfaceVectorOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

include_all_water(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, include_all_water: bool) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::include_all_water(bool) –> void

static keyname() → str¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::keyname() –> std::string

lower_chain(*args, **kwargs)¶

Overloaded function.

lower_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, lower_chain: int) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::lower_chain(unsigned long) –> void

lower_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, lower_chain: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::lower_chain(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

movable_chains(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation) → pyrosetta.rosetta.utility.vector1_int¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::movable_chains() const –> const class utility::vector1<int, class std::allocator<int> > &

movable_jumps(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation) → pyrosetta.rosetta.utility.vector1_int¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::movable_jumps() const –> const class utility::vector1<int, class std::allocator<int> > &

nearby_atom_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, nearby_atom_cutoff: float) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::nearby_atom_cutoff(double) –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

parse_tag function for rosetta scripts

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_movable_chains(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation, movable_chains: pyrosetta.rosetta.utility.vector1_int) → None¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::set_movable_chains(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_movable_jumps(self: pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation, movable_jumps: pyrosetta.rosetta.utility.vector1_int) → None¶: C++: protocols::simple_task_operations::InterfaceTaskOperation::set_movable_jumps(const class utility::vector1<int, class std::allocator<int> > &) –> void

upper_chain(*args, **kwargs)¶

Overloaded function.

upper_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, upper_chain: int) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::upper_chain(unsigned long) –> void

upper_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, upper_chain: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::upper_chain(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

vector_angle_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, vector_angle_cutoff: float) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::vector_angle_cutoff(double) –> void

vector_dist_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, vector_dist_cutoff: float) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperation::vector_dist_cutoff(double) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperationCreator::operator=(const class protocols::task_operations::RestrictToInterfaceVectorOperationCreator &) –> class protocols::task_operations::RestrictToInterfaceVectorOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator) → str¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToInterfaceVectorOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation¶

Bases: TaskOperation

A TaskOperation that accepts a movemap and restricts chi that are false to either packing or design. Does not turn anything on, just like the rest of the RestrictTo operations.

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::operator=(const class protocols::task_operations::RestrictToMoveMapChiOperation &) –> class protocols::task_operations::RestrictToMoveMapChiOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_cutoff_distance(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, cutoff: float) → None¶

Cutoff distance for neighbor detection. Default is 10 A.

C++: protocols::task_operations::RestrictToMoveMapChiOperation::set_cutoff_distance(double) –> void

set_design(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, setting: bool) → None¶

Set residues from movemap to designable. Default false.

C++: protocols::task_operations::RestrictToMoveMapChiOperation::set_design(bool) –> void

set_include_neighbors(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, setting: bool) → None¶

Set to use neighbor residues in vacinity of movemap chi residues for packing. Default False.

C++: protocols::task_operations::RestrictToMoveMapChiOperation::set_include_neighbors(bool) –> void

set_movemap(self: pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None¶: C++: protocols::task_operations::RestrictToMoveMapChiOperation::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near a neighborhood. Internally it just user NeighborhoodByDistanceCalculator to do all the work. You are allowed a “calculator name” interface to tell it which you-constructed calculator to use, or you can give it a set of residues and a desired distance cutoff to have it define the calculator itself. (There is no need to use both interfaces).

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToNeighborhoodOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation, rhs: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation¶

assignment operator

C++: protocols::task_operations::RestrictToNeighborhoodOperation::operator=(const class protocols::task_operations::RestrictToNeighborhoodOperation &) –> class protocols::task_operations::RestrictToNeighborhoodOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToNeighborhoodOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

get_calculator(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → pyrosetta.rosetta.protocols.pose_metric_calculators.NeighborhoodByDistanceCalculator¶

look up actual calculator object

C++: protocols::task_operations::RestrictToNeighborhoodOperation::get_calculator() const –> class std::shared_ptr<const class protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator>

get_calculator_name(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → str¶

trivially returns underlying calculator string name

C++: protocols::task_operations::RestrictToNeighborhoodOperation::get_calculator_name() const –> const std::string &

get_central_residues(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → pyrosetta.rosetta.std.set_unsigned_long_t¶

this nontrivially checks the underlying calculator

C++: protocols::task_operations::RestrictToNeighborhoodOperation::get_central_residues() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

get_distance_cutoff(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation) → float¶

this nontrivially checks the underlying calculator

C++: protocols::task_operations::RestrictToNeighborhoodOperation::get_distance_cutoff() const –> double

static keyname() → str¶: C++: protocols::task_operations::RestrictToNeighborhoodOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToNeighborhoodOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_calculator_by_name(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation, calculator_name: str) → None¶: C++: protocols::task_operations::RestrictToNeighborhoodOperation::set_calculator_by_name(const std::string &) –> void

set_neighborhood_parameters(*args, **kwargs)¶

Overloaded function.

set_neighborhood_parameters(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation, central_residues: pyrosetta.rosetta.std.set_unsigned_long_t, dist_cutoff: float) -> None

reskin of normal make_calculator

C++: protocols::task_operations::RestrictToNeighborhoodOperation::set_neighborhood_parameters(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, double) –> void

set_neighborhood_parameters(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation, central_residues: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

reskin of normal make_calculator

C++: protocols::task_operations::RestrictToNeighborhoodOperation::set_neighborhood_parameters(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator¶: C++: protocols::task_operations::RestrictToNeighborhoodOperationCreator::operator=(const class protocols::task_operations::RestrictToNeighborhoodOperationCreator &) –> class protocols::task_operations::RestrictToNeighborhoodOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToNeighborhoodOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator) → str¶: C++: protocols::task_operations::RestrictToNeighborhoodOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToNeighborhoodOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RestrictToTerminiOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation, : pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation) → pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation¶: C++: protocols::task_operations::RestrictToTerminiOperation::operator=(const class protocols::task_operations::RestrictToTerminiOperation &) –> class protocols::task_operations::RestrictToTerminiOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToTerminiOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RestrictToTerminiOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RestrictToTerminiOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToTerminiOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator¶: C++: protocols::task_operations::RestrictToTerminiOperationCreator::operator=(const class protocols::task_operations::RestrictToTerminiOperationCreator &) –> class protocols::task_operations::RestrictToTerminiOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RestrictToTerminiOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator) → str¶: C++: protocols::task_operations::RestrictToTerminiOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RestrictToTerminiOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation¶

Bases: TaskOperation

this class is a TaskOperation to prevent repacking of residues not near an interface.

apply(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation, : pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation) → pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::operator=(const class protocols::task_operations::RetrieveStoredTaskOperation &) –> class protocols::task_operations::RetrieveStoredTaskOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RetrieveStoredTaskOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator, : pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator) → pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator¶: C++: protocols::task_operations::RetrieveStoredTaskOperationCreator::operator=(const class protocols::task_operations::RetrieveStoredTaskOperationCreator &) –> class protocols::task_operations::RetrieveStoredTaskOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::RetrieveStoredTaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator) → str¶: C++: protocols::task_operations::RetrieveStoredTaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::RetrieveStoredTaskOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.STMStoredTask¶

Bases: CacheableData

assign(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask, : pyrosetta.rosetta.protocols.task_operations.STMStoredTask) → pyrosetta.rosetta.protocols.task_operations.STMStoredTask¶: C++: protocols::task_operations::STMStoredTask::operator=(const class protocols::task_operations::STMStoredTask &) –> class protocols::task_operations::STMStoredTask &

clone(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: protocols::task_operations::STMStoredTask::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

fresh_instance(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: protocols::task_operations::STMStoredTask::fresh_instance() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

get_task(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask, task_name: str) → pyrosetta.rosetta.core.pack.task.PackerTask¶: C++: protocols::task_operations::STMStoredTask::get_task(const std::string &) const –> class std::shared_ptr<class core::pack::task::PackerTask>

has_task(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask, task_name: str) → bool¶: C++: protocols::task_operations::STMStoredTask::has_task(const std::string &) const –> bool

set_task(self: pyrosetta.rosetta.protocols.task_operations.STMStoredTask, task: pyrosetta.rosetta.core.pack.task.PackerTask, task_name: str) → None¶: C++: protocols::task_operations::STMStoredTask::set_task(const class std::shared_ptr<class core::pack::task::PackerTask>, const std::string &) –> void

class pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SelectByDeltaScoreOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, : pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) → pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation¶: C++: protocols::task_operations::SelectByDeltaScoreOperation::operator=(const class protocols::task_operations::SelectByDeltaScoreOperation &) –> class protocols::task_operations::SelectByDeltaScoreOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

individual_hbonds(*args, **kwargs)¶

Overloaded function.

individual_hbonds(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> bool

C++: protocols::task_operations::SelectByDeltaScoreOperation::individual_hbonds() const –> bool

individual_hbonds(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, individual_hbonds: bool) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::individual_hbonds(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::SelectByDeltaScoreOperation::keyname() –> std::string

lower(*args, **kwargs)¶

Overloaded function.

lower(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> bool

C++: protocols::task_operations::SelectByDeltaScoreOperation::lower() const –> bool

lower(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, lower: bool) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::lower(const bool) –> void

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SelectByDeltaScoreOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectByDeltaScoreOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::task_operations::SelectByDeltaScoreOperation::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

reference_pose(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::reference_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

score_type(*args, **kwargs)¶

Overloaded function.

score_type(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> pyrosetta.rosetta.core.scoring.ScoreType

C++: protocols::task_operations::SelectByDeltaScoreOperation::score_type() const –> enum core::scoring::ScoreType

score_type(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, st: pyrosetta.rosetta.core.scoring.ScoreType) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::score_type(const enum core::scoring::ScoreType) –> void

score_type_name(*args, **kwargs)¶

Overloaded function.

score_type_name(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> str

C++: protocols::task_operations::SelectByDeltaScoreOperation::score_type_name() const –> std::string

score_type_name(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, name: str) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::score_type_name(const std::string &) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::task_operations::SelectByDeltaScoreOperation::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> float

C++: protocols::task_operations::SelectByDeltaScoreOperation::threshold() const –> double

threshold(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation, threshold: float) -> None

C++: protocols::task_operations::SelectByDeltaScoreOperation::threshold(const double) –> void

class pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator¶: C++: protocols::task_operations::SelectByDeltaScoreOperationCreator::operator=(const class protocols::task_operations::SelectByDeltaScoreOperationCreator &) –> class protocols::task_operations::SelectByDeltaScoreOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectByDeltaScoreOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator) → str¶: C++: protocols::task_operations::SelectByDeltaScoreOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectByDeltaScoreOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SelectByDensityFitOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation, : pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation) → pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation¶: C++: protocols::task_operations::SelectByDensityFitOperation::operator=(const class protocols::task_operations::SelectByDensityFitOperation &) –> class protocols::task_operations::SelectByDensityFitOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectByDensityFitOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::SelectByDensityFitOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SelectByDensityFitOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectByDensityFitOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator¶: C++: protocols::task_operations::SelectByDensityFitOperationCreator::operator=(const class protocols::task_operations::SelectByDensityFitOperationCreator &) –> class protocols::task_operations::SelectByDensityFitOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectByDensityFitOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator) → str¶: C++: protocols::task_operations::SelectByDensityFitOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectByDensityFitOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SelectBySASAOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation, : pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation) → pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation¶: C++: protocols::task_operations::SelectBySASAOperation::operator=(const class protocols::task_operations::SelectBySASAOperation &) –> class protocols::task_operations::SelectBySASAOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectBySASAOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::SelectBySASAOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SelectBySASAOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectBySASAOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator¶: C++: protocols::task_operations::SelectBySASAOperationCreator::operator=(const class protocols::task_operations::SelectBySASAOperationCreator &) –> class protocols::task_operations::SelectBySASAOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectBySASAOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator) → str¶: C++: protocols::task_operations::SelectBySASAOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectBySASAOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

add_res(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, resid: int) → None¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::add_res(const unsigned long) –> void

allow_design(*args, **kwargs)¶

Overloaded function.

allow_design(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::allow_design(const bool) –> void

allow_design(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) -> bool

C++: protocols::task_operations::SelectResiduesWithinChainOperation::allow_design() const –> bool

allow_repacking(*args, **kwargs)¶

Overloaded function.

allow_repacking(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::allow_repacking(const bool) –> void

allow_repacking(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) -> bool

C++: protocols::task_operations::SelectResiduesWithinChainOperation::allow_repacking() const –> bool

apply(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, : pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) → pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::operator=(const class protocols::task_operations::SelectResiduesWithinChainOperation &) –> class protocols::task_operations::SelectResiduesWithinChainOperation &

chain(*args, **kwargs)¶

Overloaded function.

chain(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) -> int

C++: protocols::task_operations::SelectResiduesWithinChainOperation::chain() const –> unsigned long

chain(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, c: int) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::chain(const unsigned long) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::keyname() –> std::string

modify_unselected_residues(*args, **kwargs)¶

Overloaded function.

modify_unselected_residues(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::modify_unselected_residues(const bool) –> void

modify_unselected_residues(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) -> bool

C++: protocols::task_operations::SelectResiduesWithinChainOperation::modify_unselected_residues() const –> bool

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

resid(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::task_operations::SelectResiduesWithinChainOperation::resid() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator¶: C++: protocols::task_operations::SelectResiduesWithinChainOperationCreator::operator=(const class protocols::task_operations::SelectResiduesWithinChainOperationCreator &) –> class protocols::task_operations::SelectResiduesWithinChainOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SelectResiduesWithinChainOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator) → str¶: C++: protocols::task_operations::SelectResiduesWithinChainOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SelectResiduesWithinChainOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation¶

Bases: TaskOperation

static aa_occurrence_filter(pos_occurance: pyrosetta.rosetta.utility.vector1_double, pos_min_occurance: float, keep_aas: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::aa_occurrence_filter(const class utility::vector1<double, class std::allocator<double> > &, const double, class utility::vector1<bool, class std::allocator<bool> > &) –> void

aa_probability_filter(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pose: pyrosetta.rosetta.core.pose.Pose, pos_profile: pyrosetta.rosetta.utility.vector1_double, position_min_prob: float, aa_idx: int, keep_aas: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::aa_probability_filter(const class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const double, const unsigned long, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

apply

C++: protocols::task_operations::SeqprofConsensusOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, : pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) → pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation¶: C++: protocols::task_operations::SeqprofConsensusOperation::operator=(const class protocols::task_operations::SeqprofConsensusOperation &) –> class protocols::task_operations::SeqprofConsensusOperation &

chain_num(*args, **kwargs)¶

Overloaded function.

chain_num(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> int

C++: protocols::task_operations::SeqprofConsensusOperation::chain_num() const –> unsigned long

chain_num(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, d: int) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::chain_num(const unsigned long) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶

make clone

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

conservation_cutoff_aligned_segments(*args, **kwargs)¶

Overloaded function.

conservation_cutoff_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> float

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments() const –> double

conservation_cutoff_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: float) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_aligned_segments(const double) –> void

conservation_cutoff_protein_interface_design(*args, **kwargs)¶

Overloaded function.

conservation_cutoff_protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> float

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design() const –> double

conservation_cutoff_protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: float) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::conservation_cutoff_protein_interface_design(const double) –> void

convert_scores_to_probabilities(*args, **kwargs)¶

Overloaded function.

convert_scores_to_probabilities(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, c: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities(const bool) –> void

convert_scores_to_probabilities(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::convert_scores_to_probabilities() const –> bool

static create_complex_type_generator(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator¶: C++: protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

debug(*args, **kwargs)¶

Overloaded function.

debug(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::debug(const bool) –> void

debug(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::debug() const –> bool

keep_native(*args, **kwargs)¶

Overloaded function.

keep_native(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::keep_native() const –> bool

keep_native(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::keep_native(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::SeqprofConsensusOperation::keyname() –> std::string

parse_profile_from_pose(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.sequence.SequenceProfile¶: C++: protocols::task_operations::SeqprofConsensusOperation::parse_profile_from_pose(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceProfile>

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

protein_interface_design(*args, **kwargs)¶

Overloaded function.

protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation

C++: protocols::task_operations::SeqprofConsensusOperation::protein_interface_design() const –> class std::shared_ptr<class protocols::task_operations::ProteinInterfaceDesignOperation>

protein_interface_design(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, pido: pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::protein_interface_design(class std::shared_ptr<class protocols::task_operations::ProteinInterfaceDesignOperation>) –> 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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

restrict_to_aligned_segments(*args, **kwargs)¶

Overloaded function.

restrict_to_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation

C++: protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments() const –> class std::shared_ptr<class protocols::task_operations::RestrictToAlignedSegmentsOperation>

restrict_to_aligned_segments(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, rtas: pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::restrict_to_aligned_segments(class std::shared_ptr<class protocols::task_operations::RestrictToAlignedSegmentsOperation>) –> void

seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) → pyrosetta.rosetta.core.sequence.SequenceProfile¶: C++: protocols::task_operations::SeqprofConsensusOperation::seqprof() const –> class std::shared_ptr<const class core::sequence::SequenceProfile>

set_ignore_pose_profile_length_mismatch(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, setting: bool) → None¶: C++: protocols::task_operations::SeqprofConsensusOperation::set_ignore_pose_profile_length_mismatch(const bool) –> void

set_seqprof(*args, **kwargs)¶

Overloaded function.

set_seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, seqprof: pyrosetta.rosetta.core.sequence.SequenceProfile) -> None
set_seqprof(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, seqprof: pyrosetta.rosetta.core.sequence.SequenceProfile, reweight: bool) -> None

Set the sequence profile. If reweight is true, convert the profile into per-residue probabilities first

C++: protocols::task_operations::SeqprofConsensusOperation::set_seqprof(class std::shared_ptr<class core::sequence::SequenceProfile>, bool) –> void

use_occurrence_data(*args, **kwargs)¶

Overloaded function.

use_occurrence_data(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation) -> bool

C++: protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data() const –> bool

use_occurrence_data(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation, b: bool) -> None

C++: protocols::task_operations::SeqprofConsensusOperation::use_occurrence_data(const bool) –> void

class pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator¶: C++: protocols::task_operations::SeqprofConsensusOperationCreator::operator=(const class protocols::task_operations::SeqprofConsensusOperationCreator &) –> class protocols::task_operations::SeqprofConsensusOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SeqprofConsensusOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator) → str¶: C++: protocols::task_operations::SeqprofConsensusOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SeqprofConsensusOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation¶

Bases: TaskOperation

A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position.

See the MOTIF option for a description of the syntax used to define a motif.

apply(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SequenceMotifTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation, : pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation) → pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation¶: C++: protocols::task_operations::SequenceMotifTaskOperation::operator=(const class protocols::task_operations::SequenceMotifTaskOperation &) –> class protocols::task_operations::SequenceMotifTaskOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SequenceMotifTaskOperation::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++: protocols::task_operations::SequenceMotifTaskOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure from a RosettaScripts XML tag.

C++: protocols::task_operations::SequenceMotifTaskOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶

Describe the format of XML file used to initialize this TaskOperation

C++: protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_motif(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation, motif: str) → None¶

Set a string that tells this operation how to design.

C++: protocols::task_operations::SequenceMotifTaskOperation::set_motif(const std::string &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: protocols::task_operations::SequenceMotifTaskOperation::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator¶: C++: protocols::task_operations::SequenceMotifTaskOperationCreator::operator=(const class protocols::task_operations::SequenceMotifTaskOperationCreator &) –> class protocols::task_operations::SequenceMotifTaskOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SequenceMotifTaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator) → str¶: C++: protocols::task_operations::SequenceMotifTaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SequenceMotifTaskOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::SetIGTypeOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation, : pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation) → pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation¶: C++: protocols::task_operations::SetIGTypeOperation::operator=(const class protocols::task_operations::SetIGTypeOperation &) –> class protocols::task_operations::SetIGTypeOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SetIGTypeOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::task_operations::SetIGTypeOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::SetIGTypeOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SetIGTypeOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator, : pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator) → pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator¶: C++: protocols::task_operations::SetIGTypeOperationCreator::operator=(const class protocols::task_operations::SetIGTypeOperationCreator &) –> class protocols::task_operations::SetIGTypeOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::SetIGTypeOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator) → str¶: C++: protocols::task_operations::SetIGTypeOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::SetIGTypeOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover¶

Bases: Mover

mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls.

apply(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover, : pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover) → pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::operator=(const class protocols::task_operations::StoreCombinedStoredTasksMover &) –> class protocols::task_operations::StoreCombinedStoredTasksMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover) → str¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : 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 movers wishing to provide citation information.

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

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreCombinedStoredTasksMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator, : pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator) → pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator¶: C++: protocols::task_operations::StoreCombinedStoredTasksMoverCreator::operator=(const class protocols::task_operations::StoreCombinedStoredTasksMoverCreator &) –> class protocols::task_operations::StoreCombinedStoredTasksMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCombinedStoredTasksMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator) → str¶: C++: protocols::task_operations::StoreCombinedStoredTasksMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreCombinedStoredTasksMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover¶

Bases: Mover

CompoundDesignableTask(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, pose: pyrosetta.rosetta.core.pose.Pose, total_residue: int, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::CompoundDesignableTask(const class core::pose::Pose &, unsigned long &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

CompoundPackableTask(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, pose: pyrosetta.rosetta.core.pose.Pose, total_residue: int, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::CompoundPackableTask(const class core::pose::Pose &, unsigned long &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, : pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover¶: C++: protocols::task_operations::StoreCompoundTaskMover::operator=(const class protocols::task_operations::StoreCompoundTaskMover &) –> class protocols::task_operations::StoreCompoundTaskMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCompoundTaskMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

factory_clear(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::factory_clear() –> void

false_behavior(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, fb: str) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::false_behavior(const std::string &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCompoundTaskMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → str¶: C++: protocols::task_operations::StoreCompoundTaskMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

invert(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, inv: bool) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::invert(const bool) –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mode(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, md: str) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::mode(const std::string &) –> void

static mover_name() → str¶: C++: protocols::task_operations::StoreCompoundTaskMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

overwrite(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, ow: bool) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::overwrite(const bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : 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 movers wishing to provide citation information.

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

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

task_clear(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::task_clear() –> void

task_name(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, tn: str) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::task_name(const std::string &) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

true_behavior(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, tb: str) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::true_behavior(const std::string &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

verbose(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover, verb: bool) → None¶: C++: protocols::task_operations::StoreCompoundTaskMover::verbose(const bool) –> void

class pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator, : pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator) → pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator¶: C++: protocols::task_operations::StoreCompoundTaskMoverCreator::operator=(const class protocols::task_operations::StoreCompoundTaskMoverCreator &) –> class protocols::task_operations::StoreCompoundTaskMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreCompoundTaskMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator) → str¶: C++: protocols::task_operations::StoreCompoundTaskMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreCompoundTaskMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.StoreTaskMover¶

Bases: Mover

mover that can be used to save or restore a task at an arbitrary point during a rosetta scripts protocol. other task operations, movers, or filters can be set up to access tasks saved by this mover during their apply calls.

apply(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::task_operations::StoreTaskMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover, : pyrosetta.rosetta.protocols.task_operations.StoreTaskMover) → pyrosetta.rosetta.protocols.task_operations.StoreTaskMover¶: C++: protocols::task_operations::StoreTaskMover::operator=(const class protocols::task_operations::StoreTaskMover &) –> class protocols::task_operations::StoreTaskMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreTaskMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreTaskMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶

fpd

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob¶: C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str¶

A tag is a unique identifier used to identify structures produced: by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus¶

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover) → str¶: C++: protocols::task_operations::StoreTaskMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t¶: C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t¶

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str¶: C++: protocols::task_operations::StoreTaskMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMover, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::StoreTaskMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : 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 movers wishing to provide citation information.

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

static provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreTaskMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None¶

Overload this static method if you access options within the mover.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on: each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool¶

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None¶

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None¶: C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

: Unit test support function. Apply one move to a given pose.: Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)¶

Overloaded function.

type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator, : pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator) → pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator¶: C++: protocols::task_operations::StoreTaskMoverCreator::operator=(const class protocols::task_operations::StoreTaskMoverCreator &) –> class protocols::task_operations::StoreTaskMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::task_operations::StoreTaskMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator) → str¶: C++: protocols::task_operations::StoreTaskMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::StoreTaskMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation¶

Bases: RestrictOperationsBase

this class is a TaskOperation to prevent repacking of residues not near an interface.

allow_design_around(*args, **kwargs)¶

Overloaded function.

allow_design_around(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) -> bool

C++: protocols::task_operations::ThreadSequenceOperation::allow_design_around() const –> bool

allow_design_around(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, b: bool) -> None

C++: protocols::task_operations::ThreadSequenceOperation::allow_design_around(const bool) –> void

apply(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ThreadSequenceOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, : pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) → pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation¶: C++: protocols::task_operations::ThreadSequenceOperation::operator=(const class protocols::task_operations::ThreadSequenceOperation &) –> class protocols::task_operations::ThreadSequenceOperation &

chain_num(*args, **kwargs)¶

Overloaded function.

chain_num(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) -> int

C++: protocols::task_operations::ThreadSequenceOperation::chain_num() const –> unsigned long

chain_num(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, s: int) -> None

C++: protocols::task_operations::ThreadSequenceOperation::chain_num(const unsigned long) –> void

clone(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ThreadSequenceOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

filter_non_aas(*args, **kwargs)¶

Overloaded function.

filter_non_aas(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) -> bool

C++: protocols::task_operations::ThreadSequenceOperation::filter_non_aas() const –> bool

filter_non_aas(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, b: bool) -> None

C++: protocols::task_operations::ThreadSequenceOperation::filter_non_aas(const bool) –> void

static keyname() → str¶: C++: protocols::task_operations::ThreadSequenceOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::task_operations::ThreadSequenceOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ThreadSequenceOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static restrict_aas(resi: int, aa: str, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::task_operations::ThreadSequenceOperation::restrict_aas(const unsigned long, const char, const class core::pose::Pose &, class core::pack::task::PackerTask &) –> void

start_res(*args, **kwargs)¶

Overloaded function.

start_res(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) -> int

C++: protocols::task_operations::ThreadSequenceOperation::start_res() const –> unsigned long

start_res(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, s: int) -> None

C++: protocols::task_operations::ThreadSequenceOperation::start_res(const unsigned long) –> void

target_sequence(*args, **kwargs)¶

Overloaded function.

target_sequence(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation, seq: str) -> None

C++: protocols::task_operations::ThreadSequenceOperation::target_sequence(const std::string &) –> void

target_sequence(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation) -> str

C++: protocols::task_operations::ThreadSequenceOperation::target_sequence() const –> std::string

class pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator, : pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator) → pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator¶: C++: protocols::task_operations::ThreadSequenceOperationCreator::operator=(const class protocols::task_operations::ThreadSequenceOperationCreator &) –> class protocols::task_operations::ThreadSequenceOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::ThreadSequenceOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator) → str¶: C++: protocols::task_operations::ThreadSequenceOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::ThreadSequenceOperationCreator::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.

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

class pyrosetta.rosetta.protocols.task_operations.boolean_operations¶

Bases: pybind11_object

Members:

AND = <boolean_operations.AND: 1>¶

ANDNOT = <boolean_operations.ANDNOT: 7>¶

NAND = <boolean_operations.NAND: 5>¶

NOR = <boolean_operations.NOR: 4>¶

NOT = <boolean_operations.NOT: 8>¶

OR = <boolean_operations.OR: 2>¶

ORNOT = <boolean_operations.ORNOT: 6>¶

XOR = <boolean_operations.XOR: 3>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation¶

Bases: TaskOperation

During repacking, allow interchangeability of protonated and deprotonated variants

apply(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶

A TaskOp that enables sampling of protonation variants during repacking. The ionizable sidechains considered are ASP, GLU, LYS, TYR, and HIS. All other posiitons are restricted to repacking. The -pH_mode commandline option is still currently required to initially read the variants into the database.

C++: protocols::task_operations::pHVariantTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation, : pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation) → pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation¶: C++: protocols::task_operations::pHVariantTaskOperation::operator=(const class protocols::task_operations::pHVariantTaskOperation &) –> class protocols::task_operations::pHVariantTaskOperation &

clone(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::pHVariantTaskOperation::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++: protocols::task_operations::pHVariantTaskOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Configure from a RosettaScripts XML tag.

C++: protocols::task_operations::pHVariantTaskOperation::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: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶

Describe the format of XML file used to initialize this TaskOperation

C++: protocols::task_operations::pHVariantTaskOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator, : pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator) → pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator¶: C++: protocols::task_operations::pHVariantTaskOperationCreator::operator=(const class protocols::task_operations::pHVariantTaskOperationCreator &) –> class protocols::task_operations::pHVariantTaskOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::task_operations::pHVariantTaskOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator) → str¶: C++: protocols::task_operations::pHVariantTaskOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::task_operations::pHVariantTaskOperationCreator::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.

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