task_operations¶

Bindings for protocols::antibody::task_operations namespace

class pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation¶

Bases: TaskOperation

Add Cluster-based sets of mutations as a TaskOperation. Essentially samples full sequences of CDRs within a particular CDR cluster randomly each time the packer is called. Does this for each CDR.

See protocols/task_operations/MutationSetDesignOperation for more info. If a CDR has an unknown cluster or there are no data for that particular CDR, will skip that CDR.

CDR definitions used are North/Dunbrack as the clusters are defined using it.

Note that by default, a data cutoff of 10 is set. If the cluster has less than 10 sequences it will be skipped. Use the set_cutoff function to change this.

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

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

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

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

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

Configure from a RosettaScripts XML tag.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pre_load_data(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

Pre load the data according to options instead of at each apply.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::pre_load_data(const class core::pose::Pose &) –> class utility::vector1<bool, class std::allocator<bool> >

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::antibody::task_operations::AddCDRProfileSetsOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_cdr_only(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → None¶

Set a single CDR with which to use this task op on.: Default is all of them.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_cdr_only(enum protocols::antibody::CDRNameEnum) –> void

set_cdrs(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cdrs: pyrosetta.rosetta.utility.vector1_bool) → None¶

Set the CDRs with which to use this task op on.: Default is all of them.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

set_cutoff(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, cutoff: int) → None¶

Set the cutoff. Will not add the profile set if the total is less than or equal to this number.: Default is 10.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_cutoff(unsigned long) –> void

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

set_force_north_paper_db(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, force_north_db: bool) → None¶

Force the use of the antibody database that houses only the North data.: This is the db distributed with Rosetta. If a current one is present in the database, it will use that instead. Default False.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_force_north_paper_db(bool) –> void

set_ignore_light_chain(*args, **kwargs)¶

Overloaded function.

set_ignore_light_chain(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation) -> None
set_ignore_light_chain(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, ignore_light_chain: bool) -> None

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_ignore_light_chain(const bool) –> void

set_include_native_type(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, use_native: bool) → None¶

Include the poses current residue type in the allowed amino acids.: Default True.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_include_native_type(bool) –> void

set_limit_only_to_length(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, limit_only_to_length: bool) → None¶

Set the class to sample all CDR sequences within a particular length,: instead of by cluster, which is the default. Default False.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_limit_only_to_length(bool) –> void

set_picking_rounds(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, rounds: int) → None¶

Set the number of times a sequence each chosen. Increase this number to increase variability of design.: Default 1 round

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

set_use_outliers(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation, use_outliers: bool) → None¶

Use cluster outliers as defined using DihedralDistance and RMSD.: Default false.

C++: protocols::antibody::task_operations::AddCDRProfileSetsOperation::set_use_outliers(bool) –> void

class pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator¶

Bases: TaskOperationCreator

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

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

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

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

Bases: TaskOperation

Add Cluster-based CDR Profiles as the task operation for the set of CDRs by default. See protocols/task_operations/ResidueProbTaskOperation for more.

CDR definitions used are North/Dunbrack as the clusters are defined using it.

If Cluster-based profiles cannot be used, will use the fallback strategy. This can happen if the the CDR is of an unknown cluster or there is too little data about the cluster to use profiles.

See protocols/antibody/design/AntibodyDesignEnum; SeqDesignStrategyEnum for possible fallback strategies. Right now, only conservative or basic/none are implemented.

FALLBACK STRATEGIES:: seq_design_conservative adds a conservative mutation set to the possible residue types (blosum62 default), seq_design_basic will do nothing (as the default for design is to allow all residue positions); seq_design_none will disable design for that CDR (essentially your saying that if it doesn’t have profiles, don’t design it)

Due to constness of the apply method, cannot store which CDRs used the fall back strategy. Functions in antibody/database/util can be used to query the database for the number of datapoints Functions in AntibodyInfo can query what the CDR cluster is (NA for unknown clusters)

This TaskOperation is not currently recommended for H3 as it does not cluster well.

Optionally sample whole CDR sequences via the primary strategy of: seq_design_profile_sets (use sets instead of profile probability)

seq_design_profile_sets_combined (use profile sets and profile probability)

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

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

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

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

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

Configure from a RosettaScripts XML tag.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pre_load_data(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Pre load the profile data with this function instead of loading it when we apply.: Use this function after all settings are ready to save time with each apply. This is needed due to const apply for TaskOps

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::pre_load_data(const class core::pose::Pose &) –> 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::antibody::task_operations::AddCDRProfilesOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_cdr_only(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → None¶: C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_cdr_only(enum protocols::antibody::CDRNameEnum) –> void

set_cdrs(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, cdrs: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

set_cons_design_data_source(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, data_source: str) → None¶

Set the data source for conservative design. Default is blosum62. Increased blosum are more stringent, more conservative design.

legal = ‘chothia_1976’, ‘BLOSUM30’, ‘blosum30’, ‘BLOSUM35’, ‘blosum35’, ‘BLOSUM40’, ‘blosum40’,: ‘BLOSUM45’, ‘blosum45’, ‘BLOSUM50’, ‘blosum50’, ‘BLOSUM55’, ‘blosum55’, ‘BLOSUM60’, ‘blosum60’,

‘BLOSUM62’, ‘blosum62’, ‘BLOSUM65’, ‘blosum65’, ‘BLOSUM70’, ‘blosum70’, ‘BLOSUM75’, ‘blosum75’,

‘BLOSUM80’, ‘blosum80’, ‘BLOSUM85’, ‘blosum85’, ‘BLOSUM90’, ‘blosum90’, ‘BLOSUM100’, ‘blosum100’

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_cons_design_data_source(std::string) –> void

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

set_design_options(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, seq_design_options: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_antibody_design_CDRSeqDesignOptions_t) → None¶

Set the CDR-level options as opposed to the defaults.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_design_options(class utility::vector1<class std::shared_ptr<class protocols::antibody::design::CDRSeqDesignOptions>, class std::allocator<class std::shared_ptr<class protocols::antibody::design::CDRSeqDesignOptions> > >) –> void

set_fallback_strategy(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, fallback_strategy: pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum) → None¶

Set the fallback strategy for all CDRs. If the primary strategy could not be

completed due to lack of data, will use this fallback strategy. See AntibodyDesignEnum.hh for more

Default is Design using the set of Conservative Mutations for each position (Blosum-62) - seq_design_conservative Set to seq_design_none to disable CDRs as the fallback instead of designing them.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_fallback_strategy(enum protocols::antibody::design::SeqDesignStrategyEnum) –> void

set_force_north_paper_db(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, force_north_db: bool) → None¶

Force the use of the north paper DB. Used for benchmarking and Unit Tests.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_force_north_paper_db(bool) –> void

set_ignore_light_chain(*args, **kwargs)¶

Overloaded function.

set_ignore_light_chain(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation) -> None
set_ignore_light_chain(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, ignore_light_chain: bool) -> None

Ignore the cluster light chain. Only use this for benchmarking.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_ignore_light_chain(bool) –> void

set_include_native_type(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, use_native: bool) → None¶

Include the poses current residue type in the allowed amino acids.: Default True.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_include_native_type(bool) –> void

set_no_probability(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, testing_mode: bool) → None¶

Set to sample all available AAs per position instead of sampling based on weights

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

set_picking_rounds(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, rounds: int) → None¶

Set the number of times a sequence each chosen. Increase this number to increase variability of design.: Default 1 round

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

set_primary_strategy(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, primary_strategy: pyrosetta.rosetta.protocols.antibody.design.SeqDesignStrategyEnum) → None¶

Set the primary strategy for all CDRs. See AntibodyDesignEnum.hh for more: Default is Cluster-based Sequence Probabilities - seq_design_profiles

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_primary_strategy(enum protocols::antibody::design::SeqDesignStrategyEnum) –> void

set_sample_zero_probs_at(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, zero_prob_sample: float) → None¶

For residue types that have a probability of 0, use this setting: to give a probability to them that is not zero. Used to increase variability of designs.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_sample_zero_probs_at(double) –> void

set_stats_cutoff(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, stats_cutoff: int) → None¶

Set the cutoff. Will not add the profile set if the total is less than or equal to this number.: Default is 10.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_stats_cutoff(unsigned long) –> void

set_use_outliers(self: pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation, use_outliers: bool) → None¶

Use cluster outliers as defined using DihedralDistance and RMSD.: Default false.

C++: protocols::antibody::task_operations::AddCDRProfilesOperation::set_use_outliers(bool) –> void

class pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator¶

Bases: TaskOperationCreator

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

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

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

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

Bases: TaskOperation

A TaskOperation that Disables packing +/or design of a particular antibody region. By Default, disables packing and design of the cdr_region. Make sure to set the region you want disabled.

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

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

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

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

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

Configure from a RosettaScripts XML tag.

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

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

set_disable_packing_and_design(self: pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, disable_packing_and_design: bool) → None¶

If disable_packing_and_design is set to False, will only disable design.

C++: protocols::antibody::task_operations::DisableAntibodyRegionOperation::set_disable_packing_and_design(bool) –> void

set_region(self: pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation, region: pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum) → None¶: C++: protocols::antibody::task_operations::DisableAntibodyRegionOperation::set_region(enum protocols::antibody::AntibodyRegionEnum) –> void

class pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator¶

Bases: TaskOperationCreator

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

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

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

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

Bases: TaskOperation

TaskOperation to Disable Packing and/or design of a set of CDRs. By default, disables both Packing and Design of all CDRs.

See options for setting specific CDRs and whether to only disable design.

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

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

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

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

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

Configure from a RosettaScripts XML tag.

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

set_cdr_only(self: pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → None¶

Set only a single CDR to disable.

C++: protocols::antibody::task_operations::DisableCDRsOperation::set_cdr_only(enum protocols::antibody::CDRNameEnum) –> void

set_cdrs(self: pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation, cdrs: pyrosetta.rosetta.utility.vector1_bool) → None¶

Set the CDRs we will be disabling - 6/8 long vector corresponding to Enum.

C++: protocols::antibody::task_operations::DisableCDRsOperation::set_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

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

set_disable_packing_and_design(self: pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation, disable_packing_and_design: bool) → None¶

Set to disable packing and design, or only just design.

C++: protocols::antibody::task_operations::DisableCDRsOperation::set_disable_packing_and_design(bool) –> void

class pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator¶

Bases: TaskOperationCreator

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

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

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

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

Bases: TaskOperation

Task Operation to restrict packing/design to specific CDRs and neighbors. See DisableAntibodyRegionOperation and DisableCDRsOperation further restrict TaskFactory.

See options for control of the design of CDRs, antigen, and framework. By default, restricts to all packing of all CDRs and neighbors.

See options for control of which CDRs, including whether to only restrict design and control of whether we design neighbor antigen and/or framework residues.

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

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

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

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

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

Configure from a RosettaScripts XML tag.

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

set_allow_design_cdr(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_cdr_design: bool) → None¶

Allow design of CDRs?

C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_cdr(bool) –> void

set_allow_design_neighbor_antigen(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_antigen_design: bool) → None¶

Allow design of neighbor antigen residues?

C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_neighbor_antigen(bool) –> void

set_allow_design_neighbor_framework(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, allow_framework_design: bool) → None¶

Allow design of neighbor framework residues?

C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_allow_design_neighbor_framework(bool) –> void

set_cdr_only(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, cdr: pyrosetta.rosetta.protocols.antibody.CDRNameEnum) → None¶: C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_cdr_only(enum protocols::antibody::CDRNameEnum) –> void

set_cdrs(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, cdrs: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_cdrs(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

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

set_neighbor_distance(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, neighbor_dis: float) → None¶

Set the distance for the detection of neighbor residues. 6A default

C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_neighbor_distance(double) –> void

set_stem_size(self: pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors, stem_size: int) → None¶

Set the size of the stem - the number of residues going into the framework. This will be included as part of the loop when determining neighbors.: However, the residues of the stem itself count as part of the framework

C++: protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::set_stem_size(unsigned long) –> void

class pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator¶

Bases: TaskOperationCreator

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

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

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

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