task_operations

Bindings for protocols::denovo_design::task_operations namespace

class pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies, : pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies

C++: protocols::denovo_design::task_operations::AAFrequencies::operator=(const class protocols::denovo_design::task_operations::AAFrequencies &) –> class protocols::denovo_design::task_operations::AAFrequencies &

frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies, aa: str) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency

C++: protocols::denovo_design::task_operations::AAFrequencies::frequency(const char) const –> const class protocols::denovo_design::task_operations::AAFrequency &

has_frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies, aa: str) bool

C++: protocols::denovo_design::task_operations::AAFrequencies::has_frequency(const char) const –> bool

set_frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies, aa: str, frequency: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency) None

C++: protocols::denovo_design::task_operations::AAFrequencies::set_frequency(const char, class std::shared_ptr<const class protocols::denovo_design::task_operations::AAFrequency>) –> void

class pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency, : pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency

C++: protocols::denovo_design::task_operations::AAFrequency::operator=(const class protocols::denovo_design::task_operations::AAFrequency &) –> class protocols::denovo_design::task_operations::AAFrequency &

enrichment(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency) float

C++: protocols::denovo_design::task_operations::AAFrequency::enrichment() const –> double

frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency) float

C++: protocols::denovo_design::task_operations::AAFrequency::frequency() const –> double

class pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_task_operations_ConsensusLoopDatabase_t

frequencies(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str, loop_resid: int) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::frequencies(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &, const unsigned long) const –> const class protocols::denovo_design::task_operations::AAFrequencies &

frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str, loop_resid: int, aa: str) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::frequency(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &, const unsigned long, const char) const –> const class protocols::denovo_design::task_operations::AAFrequency &

static get_instance() protocols::denovo_design::task_operations::ConsensusLoopDatabase

C++: utility::SingletonBase<protocols::denovo_design::task_operations::ConsensusLoopDatabase>::get_instance() –> class protocols::denovo_design::task_operations::ConsensusLoopDatabase *

has_frequencies(*args, **kwargs)

Overloaded function.

  1. has_frequencies(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str) -> bool

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::has_frequencies(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &) const –> bool

  1. has_frequencies(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str, loop_resid: int) -> bool

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::has_frequencies(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &, const unsigned long) const –> bool

has_frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str, loop_resid: int, aa: str) bool

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::has_frequency(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &, const unsigned long, const char) const –> bool

set_frequency(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase, surrounding_ss: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, abego: str, loop_resid: int, aa: str, frequency: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency) None

C++: protocols::denovo_design::task_operations::ConsensusLoopDatabase::set_frequency(const struct protocols::denovo_design::task_operations::SurroundingSS &, const std::string &, const unsigned long, const char, const class std::shared_ptr<const class protocols::denovo_design::task_operations::AAFrequency>) –> void

class pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation

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

aa_frequencies(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, info: pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo, resid: int) pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::aa_frequencies(const struct protocols::denovo_design::task_operations::LoopInfo &, const unsigned long) const –> const class protocols::denovo_design::task_operations::AAFrequencies &

apply(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

apply

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

assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, : pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation) pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::operator=(const class protocols::denovo_design::task_operations::ConsensusLoopDesignOperation &) –> class protocols::denovo_design::task_operations::ConsensusLoopDesignOperation &

static class_name() str

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

make clone

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

disallow_aas(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, task: pyrosetta.rosetta.core.pack.task.PackerTask, info: pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo) None

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(class core::pack::task::PackerTask &, const struct protocols::denovo_design::task_operations::LoopInfo &) const –> void

forbidden_aas(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, frequencies: pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies) str

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::forbidden_aas(const class protocols::denovo_design::task_operations::AAFrequencies &) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation) str

Returns the name of the class

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::get_name() const –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) None

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

set_enrichment_threshold(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, threshold: float) None

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_enrichment_threshold(const double) –> void

set_include_adjacent_residues(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, include_res: bool) None

if true, residues adjacent to loops will be restricted. Otherwise, just the loop. (default=false)

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_include_adjacent_residues(const bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, selector_val: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None
Sets residue selector. If set, only selected residues will

be operated upon. (default = select by secondary structure type L)

Residue selector to be used. Cloned by this function and

set as selector_

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

set_secstruct(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, secstruct: str) None
Sets the secondary structure to be used for selection of loops.

If a residue selector is set, this is ignored.

Secondary structure to be used. Must match pose length

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct(const std::string &) –> void

set_secstruct_from_blueprint(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, bp_file: str) None
Reads/parses a blueprint file and calls set_secstruct() on the

resulting secondary structure. Length of blueprint file must match the length of the input pose.

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_secstruct_from_blueprint(const std::string &) –> void

set_use_dssp(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation, use_dssp: bool) None

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::set_use_dssp(const bool) –> void

class pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator

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

assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator, : pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator) pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator::operator=(const class protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator &) –> class protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator) str

C++: protocols::denovo_design::task_operations::ConsensusLoopDesignOperationCreator::keyname() const –> std::string

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

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

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

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

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

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

class pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo

Bases: pybind11_builtins.pybind11_object

property abego
assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo, : pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo) pyrosetta.rosetta.protocols.denovo_design.task_operations.LoopInfo

C++: protocols::denovo_design::task_operations::LoopInfo::operator=(const struct protocols::denovo_design::task_operations::LoopInfo &) –> struct protocols::denovo_design::task_operations::LoopInfo &

property ss_around
property startres
class pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS

Bases: pybind11_builtins.pybind11_object

property after
assign(self: pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS, : pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS) pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS

C++: protocols::denovo_design::task_operations::SurroundingSS::operator=(const struct protocols::denovo_design::task_operations::SurroundingSS &) –> struct protocols::denovo_design::task_operations::SurroundingSS &

property before