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protocols::antibody::task_operations::AddCDRProfilesOperation Class Reference

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

#include <AddCDRProfilesOperation.hh>

Inheritance diagram for protocols::antibody::task_operations::AddCDRProfilesOperation:
Inheritance graph
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Public Member Functions

 AddCDRProfilesOperation ()
 
 AddCDRProfilesOperation (AntibodyInfoCOP ab_info)
 
 AddCDRProfilesOperation (AntibodyInfoCOP ab_info, utility::vector1< bool > const &cdrs)
 
 AddCDRProfilesOperation (AddCDRProfilesOperation const &src)
 
 ~AddCDRProfilesOperation () override
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Configure from a RosettaScripts XML tag. More...
 
void pre_load_data (core::pose::Pose const &pose)
 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. More...
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
 
void set_design_options (design::AntibodyCDRSeqDesignOptions seq_design_options)
 Set the CDR-level options as opposed to the defaults. More...
 
void set_cdr_only (CDRNameEnum cdr)
 
void set_cdrs (utility::vector1< bool > const &cdrs)
 
void set_primary_strategy (design::SeqDesignStrategyEnum primary_strategy)
 Set the primary strategy for all CDRs. See AntibodyDesignEnum.hh for more Default is Cluster-based Sequence Probabilities - seq_design_profiles. More...
 
void set_fallback_strategy (design::SeqDesignStrategyEnum fallback_strategy)
 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. More...
 
void set_picking_rounds (core::Size rounds)
 Set the number of times a sequence each chosen. Increase this number to increase variability of design. Default 1 round. More...
 
void set_include_native_type (bool use_native)
 Include the poses current residue type in the allowed amino acids. Default True. More...
 
void set_use_outliers (bool use_outliers)
 Use cluster outliers as defined using DihedralDistance and RMSD. Default false. More...
 
void set_defaults ()
 
void set_force_north_paper_db (bool force_north_db)
 Force the use of the north paper DB. Used for benchmarking and Unit Tests. More...
 
void set_stats_cutoff (core::Size stats_cutoff)
 Set the cutoff. Will not add the profile set if the total is less than or equal to this number. Default is 10. More...
 
void set_sample_zero_probs_at (core::Real zero_prob_sample)
 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. More...
 
void set_cons_design_data_source (std::string data_source)
 Set the data source for conservative design. Default is blosum62. Increased blosum are more stringent, more conservative design. More...
 
void set_ignore_light_chain (bool ignore_light_chain=false)
 Ignore the cluster light chain. Only use this for benchmarking. More...
 
void set_no_probability (bool testing_mode)
 Set to sample all available AAs per position instead of sampling based on weights. More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Static Public Member Functions

static std::string keyname ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

utility::vector1< bool > get_profile_and_design_cdrs () const
 
utility::vector1< bool > get_profile_set_and_design_cdrs () const
 
utility::vector1< bool > get_design_cdrs () const
 

Private Attributes

AntibodyInfoCOP ab_info_
 
design::AntibodyCDRSeqDesignOptions seq_design_options_
 
protocols::task_operations::ConservativeDesignOperationOP cons_task_
 
AddCDRProfileSetsOperationOP profile_sets_task_
 
core::Size picking_rounds_
 
bool include_native_restype_
 
bool force_north_paper_db_
 
bool use_outliers_
 
core::Size stats_cutoff_
 
core::Real zero_prob_sample_
 
std::string cons_design_data_source_
 
bool pre_loaded_data_
 
std::map< core::Size, std::map
< core::chemical::AA,
core::Real > > 		prob_set_
 
utility::vector1< bool > no_profile_data_cdrs_
 
utility::vector1< bool > no_profile_sets_data_cdrs_
 
AntibodyNumberingSchemeEnum numbering_scheme_
 Needed for default and RS constructor. More...
 
bool ignore_light_chain_ = false
 
bool no_probability_ = false
 

Additional Inherited Members

- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Detailed Description

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)

Constructor & Destructor Documentation

protocols::antibody::task_operations::AddCDRProfilesOperation::AddCDRProfilesOperation ( )

References set_defaults().

protocols::antibody::task_operations::AddCDRProfilesOperation::AddCDRProfilesOperation ( AntibodyInfoCOP  ab_info)

References set_defaults().

protocols::antibody::task_operations::AddCDRProfilesOperation::AddCDRProfilesOperation ( AntibodyInfoCOP  ab_info,
utility::vector1< bool > const &  cdrs 
)

References set_cdrs(), and set_defaults().

protocols::antibody::task_operations::AddCDRProfilesOperation::AddCDRProfilesOperation ( AddCDRProfilesOperation const &  src)

References ab_info_, cons_task_, and profile_sets_task_.

protocols::antibody::task_operations::AddCDRProfilesOperation::~AddCDRProfilesOperation ( )
overridedefault

Member Function Documentation

void protocols::antibody::task_operations::AddCDRProfilesOperation::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask &   
) const
overridevirtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

References ab_info_, protocols::task_operations::ResidueProbDesignOperation::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), cons_task_, force_north_paper_db_, protocols::antibody::design::get_cluster_profile_probability_data(), protocols::antibody::design::get_native_sequence(), get_profile_and_design_cdrs(), get_profile_set_and_design_cdrs(), protocols::antibody::design::has_native_sequence(), include_native_restype_, core::pack::task::operation::RestrictResidueToRepacking::include_residue(), no_probability_, no_profile_data_cdrs_, no_profile_sets_data_cdrs_, protocols::antibody::North, numbering_scheme_, picking_rounds_, pre_loaded_data_, prob_set_, protocols::antibody::design::seq_design_conservative, protocols::antibody::design::seq_design_none, seq_design_options_, protocols::task_operations::ResidueProbDesignOperation::set_aa_probability_set(), protocols::task_operations::ResidueProbDesignOperation::set_include_native_restype(), protocols::task_operations::ResidueProbDesignOperation::set_no_probability(), protocols::task_operations::ResidueProbDesignOperation::set_picking_rounds(), protocols::task_operations::ResidueProbDesignOperation::set_sample_zero_probs_at(), stats_cutoff_, protocols::antibody::TR(), use_outliers_, and zero_prob_sample_.

TaskOperationOP protocols::antibody::task_operations::AddCDRProfilesOperation::clone ( ) const
overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

utility::vector1< bool > protocols::antibody::task_operations::AddCDRProfilesOperation::get_design_cdrs ( ) const
private

References protocols::antibody::CDRNameEnum_proto_total, and seq_design_options_.

utility::vector1< bool > protocols::antibody::task_operations::AddCDRProfilesOperation::get_profile_and_design_cdrs ( ) const
private

References protocols::antibody::CDRNameEnum_proto_total, seq_design_options_, protocols::antibody::design::seq_design_profile_sets_combined, and protocols::antibody::design::seq_design_profiles.

Referenced by apply(), and pre_load_data().

utility::vector1< bool > protocols::antibody::task_operations::AddCDRProfilesOperation::get_profile_set_and_design_cdrs ( ) const
private

References protocols::antibody::CDRNameEnum_proto_total, seq_design_options_, protocols::antibody::design::seq_design_profile_sets, and protocols::antibody::design::seq_design_profile_sets_combined.

Referenced by apply(), and pre_load_data().

std::string protocols::antibody::task_operations::AddCDRProfilesOperation::keyname ( )
static

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperationCreator::keyname(), and provide_xml_schema().

void protocols::antibody::task_operations::AddCDRProfilesOperation::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Configure from a RosettaScripts XML tag.

Reimplemented from core::pack::task::operation::TaskOperation.

References cons_design_data_source_, force_north_paper_db_, protocols::antibody::get_cdr_bool_from_tag(), include_native_restype_, no_probability_, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), picking_rounds_, protocols::antibody::design::AntibodyDesignEnumManager::seq_design_strategy_string_to_enum(), set_cdrs(), set_cons_design_data_source(), set_fallback_strategy(), set_no_probability(), stats_cutoff_, protocols::antibody::TR(), use_outliers_, and zero_prob_sample_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::pre_load_data ( core::pose::Pose const &  pose)

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.

References ab_info_, force_north_paper_db_, protocols::antibody::design::get_cluster_profile_probability_data(), get_profile_and_design_cdrs(), get_profile_set_and_design_cdrs(), ignore_light_chain_, no_profile_data_cdrs_, no_profile_sets_data_cdrs_, protocols::antibody::North, numbering_scheme_, pre_loaded_data_, prob_set_, profile_sets_task_, stats_cutoff_, protocols::antibody::TR(), and use_outliers_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::antibody::task_operations::AddCDRProfilesOperationCreator::provide_xml_schema().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_cdr_only ( CDRNameEnum  cdr)

References protocols::antibody::CDRNameEnum_proto_total, and seq_design_options_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_cdrs ( utility::vector1< bool > const &  cdrs)

References core::pack::dunbrack::c, protocols::antibody::CDRNameEnum_proto_total, and seq_design_options_.

Referenced by AddCDRProfilesOperation(), and parse_tag().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_cons_design_data_source ( std::string  data_source)

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'

References cons_design_data_source_, and cons_task_.

Referenced by parse_tag().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_defaults ( )

References protocols::antibody::CDRNameEnum_proto_total, cons_design_data_source_, cons_task_, force_north_paper_db_, protocols::antibody::h4, include_native_restype_, protocols::antibody::l4, numbering_scheme_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), picking_rounds_, pre_loaded_data_, prob_set_, seq_design_options_, stats_cutoff_, use_outliers_, and zero_prob_sample_.

Referenced by AddCDRProfilesOperation().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_design_options ( design::AntibodyCDRSeqDesignOptions  seq_design_options)

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

References seq_design_options_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_fallback_strategy ( design::SeqDesignStrategyEnum  fallback_strategy)

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.

References protocols::antibody::CDRNameEnum_proto_total, and seq_design_options_.

Referenced by parse_tag().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_force_north_paper_db ( bool  force_north_db)

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

References force_north_paper_db_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_ignore_light_chain ( bool  ignore_light_chain = false)
inline

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

References ignore_light_chain_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_include_native_type ( bool  use_native)

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

References include_native_restype_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_no_probability ( bool  testing_mode)

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

Set to sample all available AAs per position at a weight of 1.0 instead of sampling based on weights.

References no_probability_.

Referenced by parse_tag().

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_picking_rounds ( core::Size  rounds)

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

References picking_rounds_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_primary_strategy ( design::SeqDesignStrategyEnum  primary_strategy)

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

References protocols::antibody::CDRNameEnum_proto_total, and seq_design_options_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_sample_zero_probs_at ( core::Real  zero_prob_sample)

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.

References zero_prob_sample_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_stats_cutoff ( core::Size  stats_cutoff)

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

References stats_cutoff_.

void protocols::antibody::task_operations::AddCDRProfilesOperation::set_use_outliers ( bool  use_outliers)

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

References use_outliers_.

Member Data Documentation

AntibodyInfoCOP protocols::antibody::task_operations::AddCDRProfilesOperation::ab_info_
private

Referenced by AddCDRProfilesOperation(), apply(), and pre_load_data().

std::string protocols::antibody::task_operations::AddCDRProfilesOperation::cons_design_data_source_
private

Referenced by parse_tag(), set_cons_design_data_source(), and set_defaults().

protocols::task_operations::ConservativeDesignOperationOP protocols::antibody::task_operations::AddCDRProfilesOperation::cons_task_
private

Referenced by AddCDRProfilesOperation(), apply(), set_cons_design_data_source(), and set_defaults().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::force_north_paper_db_
private

Referenced by apply(), parse_tag(), pre_load_data(), set_defaults(), and set_force_north_paper_db().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::ignore_light_chain_ = false
private

Referenced by pre_load_data(), and set_ignore_light_chain().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::include_native_restype_
private

Referenced by apply(), parse_tag(), set_defaults(), and set_include_native_type().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::no_probability_ = false
private

Referenced by apply(), parse_tag(), and set_no_probability().

utility::vector1<bool> protocols::antibody::task_operations::AddCDRProfilesOperation::no_profile_data_cdrs_
private

Referenced by apply(), and pre_load_data().

utility::vector1<bool> protocols::antibody::task_operations::AddCDRProfilesOperation::no_profile_sets_data_cdrs_
private

Referenced by apply(), and pre_load_data().

AntibodyNumberingSchemeEnum protocols::antibody::task_operations::AddCDRProfilesOperation::numbering_scheme_
private

Needed for default and RS constructor.

Referenced by apply(), parse_tag(), pre_load_data(), and set_defaults().

core::Size protocols::antibody::task_operations::AddCDRProfilesOperation::picking_rounds_
private

Referenced by apply(), parse_tag(), set_defaults(), and set_picking_rounds().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::pre_loaded_data_
private

Referenced by apply(), pre_load_data(), and set_defaults().

std::map< core::Size, std::map< core::chemical::AA, core::Real > > protocols::antibody::task_operations::AddCDRProfilesOperation::prob_set_
private

Referenced by apply(), pre_load_data(), and set_defaults().

AddCDRProfileSetsOperationOP protocols::antibody::task_operations::AddCDRProfilesOperation::profile_sets_task_
private

Referenced by AddCDRProfilesOperation(), and pre_load_data().

design::AntibodyCDRSeqDesignOptions protocols::antibody::task_operations::AddCDRProfilesOperation::seq_design_options_
private

Referenced by apply(), get_design_cdrs(), get_profile_and_design_cdrs(), get_profile_set_and_design_cdrs(), set_cdr_only(), set_cdrs(), set_defaults(), set_design_options(), set_fallback_strategy(), and set_primary_strategy().

core::Size protocols::antibody::task_operations::AddCDRProfilesOperation::stats_cutoff_
private

Referenced by apply(), parse_tag(), pre_load_data(), set_defaults(), and set_stats_cutoff().

bool protocols::antibody::task_operations::AddCDRProfilesOperation::use_outliers_
private

Referenced by apply(), parse_tag(), pre_load_data(), set_defaults(), and set_use_outliers().

core::Real protocols::antibody::task_operations::AddCDRProfilesOperation::zero_prob_sample_
private

Referenced by apply(), parse_tag(), set_defaults(), and set_sample_zero_probs_at().

The documentation for this class was generated from the following files:
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