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:

[legend]

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::SSize >	paratope_charge_

utility::vector1< core::Size >	ag_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 ( )

References ab_info_, include_proto_cdr4_, and skip_antigen_reports_.

protocols::antibody::AntibodyFeatures::AntibodyFeatures ( AntibodyInfoOP ab_info )

References ab_info_, include_proto_cdr4_, and skip_antigen_reports_.

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

References ab_info_, include_proto_cdr4_, and skip_antigen_reports_.

Member Function Documentation

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

private

References ab_info_, protocols::antibody::cdr_end, protocols::antibody::cdr_start, core::chemical::ResidueType::is_aromatic(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by report_cdr_metrics_features().

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

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

Referenced by report_cdr_metrics_features().

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

Referenced by provide_xml_schema(), protocols::antibody::AntibodyFeaturesCreator::type_name(), and type_name().

void protocols::antibody::AntibodyFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

return the set of features reporters that are required to also already be extracted by the time this one is used.

Reimplemented from protocols::features::FeaturesReporter.

References protocols::antibody::AntibodyEnumManager::cdr_definition_string_to_enum(), protocols::features::InterfaceFeatures::compute_packstat_, definition_, protocols::features::InterfaceFeatures::dSASA_cutoff_, include_proto_cdr4_, intermediate_interfaces_, protocols::antibody::AntibodyEnumManager::numbering_scheme_string_to_enum(), protocols::features::InterfaceFeatures::pack_separated_, protocols::features::InterfaceFeatures::pack_together_, regenerate_abinfo_, scheme_, protocols::features::InterfaceFeatures::scorefxn_, skip_antigen_reports_, and protocols::antibody::TR().

void protocols::antibody::AntibodyFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::features::xsd_type_definition_w_attributes().

Referenced by protocols::antibody::AntibodyFeaturesCreator::provide_xml_schema().

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
	)

References ab_info_, protocols::features::get_question_mark_string(), protocols::antibody::kink_bb_Hbond(), protocols::antibody::kink_dihedral(), protocols::antibody::kink_RD_Hbond(), and protocols::antibody::kink_Trp_Hbond().

Referenced by report_features().

void protocols::antibody::AntibodyFeatures::report_ab_metrics_features	(	core::pose::Pose const &	pose,
		features::StructureID	struct_id,
		utility::sql_database::sessionOP	db_session
	)

References ab_info_, protocols::features::get_question_mark_string(), include_proto_cdr4_, protocols::antibody::ParatopeMetric< T >::paratope, paratope_charge_, paratope_sasa_, protocols::antibody::pose_charge(), and protocols::antibody::vl_vh_orientation_coords().

Referenced by report_features().

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
	)

References ab_info_, calculate_cdr_aromatic_nres(), calculate_cdr_contacts_nres(), calculate_cdr_contacts_total(), calculate_cdr_totals(), protocols::antibody::ParatopeMetric< T >::cdr, protocols::antibody::cdr_CN_anchor_distance(), protocols::antibody::cdr_energy(), protocols::analysis::PerResidueInterfaceData::dG, protocols::analysis::PerResidueInterfaceData::dhSASA, protocols::analysis::PerResidueInterfaceData::dhSASA_rel_by_charge, protocols::analysis::PerResidueInterfaceData::dhSASA_sc, protocols::analysis::PerResidueInterfaceData::dSASA, protocols::analysis::PerResidueInterfaceData::dSASA_sc, protocols::features::get_question_mark_string(), interface_data_res_, paratope_charge_, paratope_sasa_, and protocols::features::InterfaceFeatures::scorefxn_.

Referenced by report_features().

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
	)

References ab_info_, and report_cdr_residue_features_row().

Referenced by report_features().

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
	)

References ab_info_, ag_ab_atomic_contacts_, and protocols::features::get_question_mark_string().

Referenced by report_cdr_residue_features().

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

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References ab_info_, calculate_residue_atomic_contacts(), core::conformation::Residue::chain(), protocols::features::InterfaceFeatures::compute_packstat_, definition_, include_proto_cdr4_, protocols::features::InterfaceFeatures::interface_analyzer_, interface_data_, interface_data_res_, intermediate_interfaces_, protocols::features::InterfaceFeatures::pack_separated_, protocols::features::InterfaceFeatures::pack_together_, protocols::antibody::paratope_charge(), paratope_charge_, protocols::antibody::paratope_sasa(), paratope_sasa_, regenerate_abinfo_, report_ab_H3_kink_metrics_features(), report_ab_metrics_features(), protocols::features::InterfaceFeatures::report_all_interface_features(), report_cdr_metrics_features(), report_cdr_residue_features(), core::pose::Pose::residue(), scheme_, protocols::features::InterfaceFeatures::scorefxn_, core::pose::Pose::size(), skip_antigen_reports_, and protocols::antibody::TR().

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

References protocols::antibody::paratope_charge().

Referenced by write_schema_to_db().

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

References core::sequence::end, protocols::buns::energy, and protocols::loops::start.

Referenced by write_schema_to_db().

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

return string with class name

Implements protocols::features::FeaturesReporter.

References write_ab_H3_kink_metrics_schema_to_db(), write_ab_metrics_schema_to_db(), write_cdr_metrics_schema_to_db(), write_cdr_residue_schema_to_db(), protocols::features::InterfaceFeatures::write_interface_residues_schema_to_db(), protocols::features::InterfaceFeatures::write_interface_schema_to_db(), and protocols::features::InterfaceFeatures::write_interface_side_schema_to_db().

Member Data Documentation

AntibodyInfoOP protocols::antibody::AntibodyFeatures::ab_info_

private

Referenced by AntibodyFeatures(), calculate_cdr_aromatic_nres(), calculate_cdr_contacts_nres(), calculate_cdr_contacts_total(), calculate_cdr_totals(), report_ab_H3_kink_metrics_features(), report_ab_metrics_features(), report_cdr_metrics_features(), report_cdr_residue_features(), report_cdr_residue_features_row(), report_features(), and set_ab_info().

utility::vector1<core::Size> protocols::antibody::AntibodyFeatures::ag_ab_atomic_contacts_

private

Referenced by calculate_cdr_contacts_nres(), calculate_cdr_contacts_total(), calculate_residue_atomic_contacts(), and report_cdr_residue_features_row().

CDRDefinitionEnum protocols::antibody::AntibodyFeatures::definition_

private

Referenced by parse_my_tag(), and report_features().

bool protocols::antibody::AntibodyFeatures::include_proto_cdr4_

private

Referenced by AntibodyFeatures(), parse_my_tag(), report_ab_metrics_features(), and report_features().

protocols::analysis::InterfaceData protocols::antibody::AntibodyFeatures::interface_data_

private

Referenced by report_features().

protocols::analysis::PerResidueInterfaceData protocols::antibody::AntibodyFeatures::interface_data_res_

private

Referenced by report_cdr_metrics_features(), and report_features().

utility::vector1<std::string> protocols::antibody::AntibodyFeatures::intermediate_interfaces_

private

Referenced by parse_my_tag(), report_features(), and set_interface_chains().

ParatopeMetric< core::SSize> protocols::antibody::AntibodyFeatures::paratope_charge_

private

Referenced by report_ab_metrics_features(), report_cdr_metrics_features(), and report_features().

std::pair<ParatopeMetric< core::Real >, ParatopeMetric<core::Real> > protocols::antibody::AntibodyFeatures::paratope_sasa_

private

Referenced by report_ab_metrics_features(), report_cdr_metrics_features(), and report_features().

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

Referenced by AntibodyFeatures(), parse_my_tag(), and report_features().

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

src/protocols/antibody/AntibodyFeatures.hh
src/protocols/antibody/AntibodyFeatures.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation