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protocols::antibody::AntibodyFeatures Class Reference

Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics. More...

#include <AntibodyFeatures.hh>

Inheritance diagram for protocols::antibody::AntibodyFeatures:
Inheritance graph
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Public Member Functions

 AntibodyFeatures ()
 
 AntibodyFeatures (AntibodyInfoOP ab_info)
 
 AntibodyFeatures (AntibodyInfoOP ab_info, core::scoring::ScoreFunctionCOP scorefxn)
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 return string with class name More...
 
void write_ab_metrics_schema_to_db (utility::sql_database::sessionOP db_session) const
 
void write_ab_H3_kink_metrics_schema_to_db (utility::sql_database::sessionOP db_session) const
 Write kink metrics schema. Please add or modify as needed. More...
 
void write_cdr_metrics_schema_to_db (utility::sql_database::sessionOP db_session) const
 
void write_cdr_residue_schema_to_db (utility::sql_database::sessionOP db_session) const
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, features::StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
void report_ab_metrics_features (core::pose::Pose const &pose, features::StructureID struct_id, utility::sql_database::sessionOP db_session)
 
void report_ab_H3_kink_metrics_features (core::pose::Pose const &pose, features::StructureID struct_id, utility::sql_database::sessionOP db_session)
 
void report_cdr_metrics_features (core::pose::Pose const &pose, features::StructureID struct_id, utility::sql_database::sessionOP db_session, CDRNameEnum const &cdr)
 
void report_cdr_residue_features (core::pose::Pose const &pose, features::StructureID struct_id, utility::sql_database::sessionOP db_session, CDRNameEnum const &cdr, utility::vector1< bool > const &relevant_residues)
 
void report_cdr_residue_features_row (core::pose::Pose const &pose, features::StructureID struct_id, utility::sql_database::sessionOP db_session, CDRNameEnum const &cdr, core::Size resnum, core::Size position)
 
void set_ab_info (AntibodyInfoOP ab_info)
 
void set_interface_chains (utility::vector1< std::string > const &intermediate_interfaces) override
 Set intermediate interface chains: Example: L_A, H_A, L_H, LH_A (A stands for antigen) More...
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::InterfaceFeatures
 InterfaceFeatures ()
 
 InterfaceFeatures (core::scoring::ScoreFunctionCOP scorefxn)
 
 ~InterfaceFeatures () override
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 return string with class name More...
 
utility::vector1< std::string > features_reporter_dependencies () const override
 return the set of features reporters that are required to also already be extracted by the time this one is used. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 
core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session) override
 collect all the feature data for the pose More...
 
void set_pack_separated (bool const pack_separated)
 Pack the interface before separation? Default is false. More...
 
void set_pack_together (bool const pack_together)
 Pack the interface after separation? Default is true. More...
 
void set_compute_packstat (bool const compute_packstat)
 Compute the packstat score? Default true. More...
 
void set_defaults ()
 
void set_dSASA_cutoff (core::Real dSASA_cutoff)
 Set the reporter to only include interfaces >dSASA_cutoff. More...
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
virtual void write_interface_schema_to_db (utility::sql_database::sessionOP db_session) const
 
virtual void write_interface_residues_schema_to_db (utility::sql_database::sessionOP db_session) const
 
virtual void write_interface_side_schema_to_db (utility::sql_database::sessionOP db_session) const
 
virtual void report_all_interface_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &interface, std::string const &db_interface)
 Report all features. Called by report_features. Easy interface for subclassing specific interfaces. More...
 
virtual void report_interface_features (core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &chains_side1, std::string const &chains_side2) const
 Add interfaces table data to table. More...
 
virtual void report_interface_side_features (core::pose::Pose const &pose, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &chains_side1, std::string const &chains_side2, protocols::analysis::InterfaceRegion region, std::string const &region_string) const
 Add interface_sides table data to table. More...
 
virtual void report_interface_residue_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &chains_side1, std::string const &chains_side2) const
 Add interface_residues data to table. More...
 
void make_interface_combos (core::pose::Pose const &pose, utility::vector1< std::string > &interfaces)
 Gets all possible interface combinations of a given pose. More...
 
std::string type_name () const override
 
- Public Member Functions inherited from protocols::features::FeaturesReporter
 FeaturesReporter ()
 
 ~FeaturesReporter () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
virtual std::string schema () const
 return sql statements that sets up the appropriate tables to contain the features. This should be removed once everything has been moved to the schema generator More...
 
core::Size report_features (core::pose::Pose const &, StructureID, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void load_into_pose (utility::sql_database::sessionOP, StructureID, core::pose::Pose &)
 
virtual void delete_record (StructureID, utility::sql_database::sessionOP)
 
void set_relevant_residues_mode (RelevantResiduesMode::T setting)
 
RelevantResiduesMode::T get_relevant_residues_mode () const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues_range (utility::vector1< bool > const &relevant_residues, core::Size res1, core::Size res2) const
 
bool check_relevant_residues (utility::vector1< bool > const &relevant_residues, utility::vector1< core::Size > const &residues) const
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::features::InterfaceFeatures
static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

core::Real calculate_cdr_totals (CDRNameEnum const cdr, const core::pose::Pose &pose, const utility::vector1< core::Real > &data) const
 
core::Real calculate_cdr_dpSASA (CDRNameEnum const cdr)
 Calculate polar dSASA using IAM results. More...
 
core::Size calculate_cdr_aromatic_nres (const core::pose::Pose &pose, CDRNameEnum const cdr)
 
void calculate_residue_atomic_contacts (const core::pose::Pose &pose, const utility::vector1< bool > &residues_to_match, const utility::vector1< bool > &antigen_residues)
 Calculate residue atomic contacts to antigen according to this metric: More...
 
core::Size calculate_cdr_contacts_total (const core::pose::Pose &pose, CDRNameEnum const cdr)
 Total number of cdr atomic contacts as defined above. More...
 
core::Size calculate_cdr_contacts_nres (const core::pose::Pose &pose, CDRNameEnum const cdr)
 Total number of residues making at least one atomic contact with antigen. More...
 

Private Attributes

AntibodyInfoOP ab_info_
 
bool regenerate_abinfo_ = false
 
CDRDefinitionEnum definition_
 
AntibodyNumberingSchemeEnum scheme_
 
utility::vector1< std::string > intermediate_interfaces_
 
bool skip_antigen_reports_
 
protocols::analysis::PerResidueInterfaceData interface_data_res_
 
protocols::analysis::InterfaceData interface_data_
 
std::pair< ParatopeMetric
< core::Real >, ParatopeMetric
< core::Real > > 
paratope_sasa_
 
ParatopeMetric< core::SSizeparatope_charge_
 
utility::vector1< core::Sizeag_ab_atomic_contacts_
 
bool include_proto_cdr4_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::features::InterfaceFeatures
bool interface_exists (utility::vector1< std::string > &interfaces, std::string &dock_chains) const
 
bool chains_exist_in_pose (core::pose::Pose const &pose, std::string const &interface) const
 
- Protected Member Functions inherited from protocols::features::FeaturesReporter
std::string find_tag (core::pose::Pose const &pose) const
 
void delete_records_from_table (std::string const &table_name, StructureID struct_id, utility::sql_database::sessionOP db_session)
 a helper function for deleting data associated with a given structure from feature database WARNING table_name must be sanitized! More...
 
- Protected Attributes inherited from protocols::features::InterfaceFeatures
protocols::analysis::InterfaceAnalyzerMoverOP interface_analyzer_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
utility::vector1< std::string > interfaces_
 
bool pack_together_
 
bool pack_separated_
 
bool compute_packstat_
 
core::Real dSASA_cutoff_
 
- Protected Attributes inherited from protocols::features::FeaturesReporter
RelevantResiduesMode::T relevant_residues_mode_
 

Detailed Description

Collects data on an antibody including CDRs, interfaces of L_H, L_A, H_A, and LH_A (this can be set), and other metrics.

Adds .... tables to the database. See also protocols/antibody/clusters/CDRClusterFeatures

Constructor & Destructor Documentation

protocols::antibody::AntibodyFeatures::AntibodyFeatures ( )
protocols::antibody::AntibodyFeatures::AntibodyFeatures ( AntibodyInfoOP  ab_info)
protocols::antibody::AntibodyFeatures::AntibodyFeatures ( AntibodyInfoOP  ab_info,
core::scoring::ScoreFunctionCOP  scorefxn 
)

Member Function Documentation

core::Size protocols::antibody::AntibodyFeatures::calculate_cdr_aromatic_nres ( const core::pose::Pose pose,
CDRNameEnum const  cdr 
)
private
core::Size protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_nres ( const core::pose::Pose pose,
CDRNameEnum const  cdr 
)
private

Total number of residues making at least one atomic contact with antigen.

References ab_info_, ag_ab_atomic_contacts_, protocols::antibody::cdr_end, protocols::antibody::cdr_start, and protocols::antibody::TR().

Referenced by report_cdr_metrics_features().

core::Size protocols::antibody::AntibodyFeatures::calculate_cdr_contacts_total ( const core::pose::Pose pose,
CDRNameEnum const  cdr 
)
private

Total number of cdr atomic contacts as defined above.

References ab_info_, ag_ab_atomic_contacts_, protocols::antibody::cdr_end, and protocols::antibody::cdr_start.

Referenced by report_cdr_metrics_features().

core::Real protocols::antibody::AntibodyFeatures::calculate_cdr_dpSASA ( CDRNameEnum const  cdr)
private

Calculate polar dSASA using IAM results.

core::Real protocols::antibody::AntibodyFeatures::calculate_cdr_totals ( CDRNameEnum const  cdr,
const core::pose::Pose pose,
const utility::vector1< core::Real > &  data 
) const
private
void protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts ( const core::pose::Pose pose,
const utility::vector1< bool > &  residues_to_match,
const utility::vector1< bool > &  antigen_residues 
)
private

Calculate residue atomic contacts to antigen according to this metric:

An atomic contact is defined as at least 5 atoms of the antigen that are within 5 angstroms of an atom

References ag_ab_atomic_contacts_, core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::antibody::TR(), and core::conformation::Residue::xyz().

Referenced by report_features().

std::string protocols::antibody::AntibodyFeatures::class_name ( )
static
void protocols::antibody::AntibodyFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::antibody::AntibodyFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::antibody::AntibodyFeatures::report_ab_H3_kink_metrics_features ( core::pose::Pose const &  pose,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::antibody::AntibodyFeatures::report_ab_metrics_features ( core::pose::Pose const &  pose,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::antibody::AntibodyFeatures::report_cdr_metrics_features ( core::pose::Pose const &  pose,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
CDRNameEnum const &  cdr 
)
void protocols::antibody::AntibodyFeatures::report_cdr_residue_features ( core::pose::Pose const &  pose,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
CDRNameEnum const &  cdr,
utility::vector1< bool > const &  relevant_residues 
)
void protocols::antibody::AntibodyFeatures::report_cdr_residue_features_row ( core::pose::Pose const &  pose,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session,
CDRNameEnum const &  cdr,
core::Size  resnum,
core::Size  position 
)
core::Size protocols::antibody::AntibodyFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
features::StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
void protocols::antibody::AntibodyFeatures::set_ab_info ( AntibodyInfoOP  ab_info)

References ab_info_.

void protocols::antibody::AntibodyFeatures::set_interface_chains ( utility::vector1< std::string > const &  intermediate_interfaces)
overridevirtual

Set intermediate interface chains: Example: L_A, H_A, L_H, LH_A (A stands for antigen)

Any other chains, use InterfaceFeatures.

Reimplemented from protocols::features::InterfaceFeatures.

References intermediate_interfaces_.

std::string protocols::antibody::AntibodyFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

void protocols::antibody::AntibodyFeatures::write_ab_H3_kink_metrics_schema_to_db ( utility::sql_database::sessionOP  db_session) const

Write kink metrics schema. Please add or modify as needed.

Referenced by write_schema_to_db().

void protocols::antibody::AntibodyFeatures::write_ab_metrics_schema_to_db ( utility::sql_database::sessionOP  db_session) const
void protocols::antibody::AntibodyFeatures::write_cdr_metrics_schema_to_db ( utility::sql_database::sessionOP  db_session) const
void protocols::antibody::AntibodyFeatures::write_cdr_residue_schema_to_db ( utility::sql_database::sessionOP  db_session) const

Referenced by write_schema_to_db().

void protocols::antibody::AntibodyFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
overridevirtual

Member Data Documentation

AntibodyInfoOP protocols::antibody::AntibodyFeatures::ab_info_
private
utility::vector1<core::Size> protocols::antibody::AntibodyFeatures::ag_ab_atomic_contacts_
private
CDRDefinitionEnum protocols::antibody::AntibodyFeatures::definition_
private

Referenced by parse_my_tag(), and report_features().

bool protocols::antibody::AntibodyFeatures::include_proto_cdr4_
private
protocols::analysis::InterfaceData protocols::antibody::AntibodyFeatures::interface_data_
private

Referenced by report_features().

protocols::analysis::PerResidueInterfaceData protocols::antibody::AntibodyFeatures::interface_data_res_
private
utility::vector1<std::string> protocols::antibody::AntibodyFeatures::intermediate_interfaces_
private
ParatopeMetric< core::SSize> protocols::antibody::AntibodyFeatures::paratope_charge_
private
std::pair<ParatopeMetric< core::Real >, ParatopeMetric<core::Real> > protocols::antibody::AntibodyFeatures::paratope_sasa_
private
bool protocols::antibody::AntibodyFeatures::regenerate_abinfo_ = false
private

Referenced by parse_my_tag(), and report_features().

AntibodyNumberingSchemeEnum protocols::antibody::AntibodyFeatures::scheme_
private

Referenced by parse_my_tag(), and report_features().

bool protocols::antibody::AntibodyFeatures::skip_antigen_reports_
private

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