task_operations

Bindings for protocols::task_operations namespace

class pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation

Bases: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

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

alignment_file(*args, **kwargs)

Overloaded function.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

query_name(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.DatabaseThread

Bases: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

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

allow_design_around(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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.

  1. 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> >

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

  1. 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> >

  1. 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: utility::tag::XMLSchemaDefinition) None

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

start_res(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation

Bases: pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

allow_design(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

repack_shell(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation

Bases: pyrosetta.rosetta.core.pack.task.operation.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.

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

max chi2 for picking rotamers of YFH

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

  1. 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.

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

min chi2 for picking rotamers of YFH

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

  1. 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.

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

include TRP ?

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

C++: protocols::task_operations::LimitAromaChi2OperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation

Bases: pyrosetta.rosetta.core.pack.rotamer_set.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: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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.

Does not touch any resnums not in a sampled mutation set.

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: 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.

  1. 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

  1. 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: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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: utility::tag::XMLSchemaDefinition) None

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

reference_pdb_id(*args, **kwargs)

Overloaded function.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ProteinCore

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

allow_even_trades(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsats_RotamerSetsOperation

Bases: pyrosetta.rosetta.core.pack.rotamer_set.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: pyrosetta.rosetta.core.pack.task.operation.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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

residue_selector(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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:

POLAR PIKAA X[R2]X[T6]X[OP5]

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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

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

Each time a task is generated, it will choose one amino acid from the set for that position and add it to (or replace)

the set of packable residues chosen for that position. Decreases number of rotamers for packing and the space for design. Instead of using energy for profiles, we use selection of residues through probabilities at each task generation. If picking rounds is higher can result in more than one additional residue in the task from the native.

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: 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) 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.

This is to increase variability. Too many rounds will even out the distribution. Can also run the PackRotamers mover or equivalent multiple times for sampling.

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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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.

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

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

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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: utility::tag::XMLSchemaDefinition) 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.

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

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

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

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

keep_native(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

  1. 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>

  1. 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: 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.

  1. 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>

  1. 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.

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

  2. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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.

  1. 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

  1. 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.

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

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

  1. 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.

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

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

  1. 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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

repack_shell(*args, **kwargs)

Overloaded function.

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

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

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

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

res_ids(*args, **kwargs)

Overloaded function.

  1. 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> >

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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.

  1. 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 > >

  1. 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.

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

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

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

reference_pose(*args, **kwargs)

Overloaded function.

  1. 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>

  1. 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

  1. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase

Bases: pyrosetta.rosetta.core.pack.task.operation.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: pyrosetta.rosetta.protocols.task_operations.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: utility::tag::XMLSchemaDefinition) None

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

reference_pdb_id(*args, **kwargs)

Overloaded function.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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.

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

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

  1. 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: utility::tag::XMLSchemaDefinition) None

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

repack_shell(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

  1. 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> >

  1. 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.

  1. 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> >

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

C++: protocols::task_operations::RestrictToCDRH3LoopCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation

Bases: pyrosetta.rosetta.protocols.simple_task_operations.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.

  1. lower_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, lower_chain: int) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::lower_chain(unsigned long) –> void

  1. 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: 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.

  1. upper_chain(self: pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation, upper_chain: int) -> None

C++: protocols::task_operations::RestrictToInterfaceVectorOperation::upper_chain(unsigned long) –> void

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.protocols.task_operations.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: 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.

  1. 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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.STMStoredTask

Bases: pyrosetta.rosetta.basic.datacache.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: pyrosetta.rosetta.core.pack.task.operation.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.

  1. individual_hbonds(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> bool

C++: protocols::task_operations::SelectByDeltaScoreOperation::individual_hbonds() const –> bool

  1. 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.

  1. lower(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> bool

C++: protocols::task_operations::SelectByDeltaScoreOperation::lower() const –> bool

  1. 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: utility::tag::XMLSchemaDefinition) None

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

reference_pose(*args, **kwargs)

Overloaded function.

  1. 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>

  1. 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.

  1. 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

  1. 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.

  1. score_type_name(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> str

C++: protocols::task_operations::SelectByDeltaScoreOperation::score_type_name() const –> std::string

  1. 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.

  1. 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>

  1. 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.

  1. threshold(self: pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation) -> float

C++: protocols::task_operations::SelectByDeltaScoreOperation::threshold() const –> double

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation

Bases: pyrosetta.rosetta.protocols.task_operations.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.

  1. allow_design(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

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

  1. 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.

  1. allow_repacking(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::allow_repacking(const bool) –> void

  1. 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.

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

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

  1. 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.

  1. modify_unselected_residues(self: pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation, b: bool) -> None

C++: protocols::task_operations::SelectResiduesWithinChainOperation::modify_unselected_residues(const bool) –> void

  1. 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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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.

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

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

  1. 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.

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

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

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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: utility::tag::XMLSchemaDefinition) 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.

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

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

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

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

keep_native(*args, **kwargs)

Overloaded function.

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

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

  1. 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.

  1. 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>

  1. 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: 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.

  1. 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>

  1. 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.

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

  2. 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.

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

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

  1. 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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.

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.

  • An X indicates it can be anything, and that we are designing here.

  • An AA Letter, like V, indicates that that position will be designed to a V.

  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.

  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine

  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.

  • RESFILE commands are accepted as well. Resfile commands need a % in front of the whole set.

    FOr example [%POLAR] is totally cool.

EXAMPLE:

Glycosylation N-Linked motif design: N[^P][ST]

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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.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: 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: pyrosetta.rosetta.core.pack.task.operation.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: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover

Bases: pyrosetta.rosetta.protocols.moves.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.

clear_info is called by jd2 before calling apply

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)