protocols::features::InterfaceFeatures Class Reference

Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS. More...

#include <InterfaceFeatures.hh>

Inheritance diagram for protocols::features::InterfaceFeatures:

Public Member Functions
	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...
virtual void	set_interface_chains (utility::vector1< std::string > const &interfaces)
	Set the fixed chain combinations that will be analyzed. Default is all of them. 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)

Protected Member Functions
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
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_

Private Member Functions
void	write_interface_residue_data_row_to_db (StructureID struct_id, utility::sql_database::sessionOP db_session, std::string const &chains_side1, std::string const &chains_side2, std::string const &side, core::Size const resnum, protocols::analysis::PerResidueInterfaceData const &interface_data) const
void	get_all_string_combos (std::string &interface, std::string current, utility::vector1< std::string > &chains) const
	Recursive function. Get all orders of ex ABCD. More...
void	get_length_combos (std::string current, utility::vector1< std::string > &sizes) const
std::string	get_all_pose_chains (core::pose::Pose const &pose)

Detailed Description

Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover. By default, will analyze every interface with and report any that have dSASA > cutoff. Interfaces to report can be set via code or RS.

Should work (but untested) with most ligands if loaded, rna chains, and dna chains. Note that interfacial waters and ions are currently ignored, but separate features reporters may soon be in the works to accomplish this.

Most main functions are virtual so you can derive from this and have more-specific interface analysis, such as an AntibodyInterfaceFeature class.

Constructor & Destructor Documentation

InterfaceFeatures() [1/2]

protocols::features::InterfaceFeatures::InterfaceFeatures

(

)

References core::scoring::get_score_function(), interface_analyzer_, scorefxn_, and set_defaults().

InterfaceFeatures() [2/2]

protocols::features::InterfaceFeatures::InterfaceFeatures

(

core::scoring::ScoreFunctionCOP

scorefxn

)

References interface_analyzer_, scorefxn_, and set_defaults().

~InterfaceFeatures()

protocols::features::InterfaceFeatures::~InterfaceFeatures ( )

overridedefault

Member Function Documentation

chains_exist_in_pose()

bool protocols::features::InterfaceFeatures::chains_exist_in_pose ( core::pose::Pose const &  pose, std::string const &  interface  ) const

protected

References core::pose::has_chain().

Referenced by report_all_interface_features().

class_name()

std::string protocols::features::InterfaceFeatures::class_name ( )

static

Referenced by provide_xml_schema(), type_name(), and protocols::features::InterfaceFeaturesCreator::type_name().

features_reporter_dependencies()

utility::vector1< std::string > protocols::features::InterfaceFeatures::features_reporter_dependencies ( ) const

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.

get_all_pose_chains()

std::string protocols::features::InterfaceFeatures::get_all_pose_chains ( core::pose::Pose const &  pose )

private

References core::pose::Pose::conformation(), core::pose::get_chain_from_chain_id(), core::id::to_string(), and protocols::features::TR().

Referenced by make_interface_combos().

get_all_string_combos()

void protocols::features::InterfaceFeatures::get_all_string_combos ( std::string &  interface, std::string  current, utility::vector1< std::string > &  chains  ) const

private

Recursive function. Get all orders of ex ABCD.

Referenced by make_interface_combos().

get_length_combos()

void protocols::features::InterfaceFeatures::get_length_combos ( std::string  current, utility::vector1< std::string > &  sizes  ) const

private

Referenced by make_interface_combos().

interface_exists()

bool protocols::features::InterfaceFeatures::interface_exists ( utility::vector1< std::string > &  interfaces, std::string &  dock_chains  ) const

protected

References core::sequence::end.

Referenced by make_interface_combos().

make_interface_combos()

void protocols::features::InterfaceFeatures::make_interface_combos	(	core::pose::Pose const &	pose,
		utility::vector1< std::string > &	interfaces
	)

Gets all possible interface combinations of a given pose.

References get_all_pose_chains(), get_all_string_combos(), get_length_combos(), interface_exists(), and protocols::features::TR().

Referenced by report_features().

parse_my_tag()

void protocols::features::InterfaceFeatures::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References compute_packstat_, dSASA_cutoff_, interfaces_, pack_separated_, pack_together_, and scorefxn_.

provide_xml_schema()

void protocols::features::InterfaceFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

Referenced by protocols::features::InterfaceFeaturesCreator::provide_xml_schema().

report_all_interface_features()

void protocols::features::InterfaceFeatures::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  )

virtual

Report all features. Called by report_features. Easy interface for subclassing specific interfaces.

interface is the interface analyzed, db_interface is the name that is actually inserted into the database Usually this is the same, but useful when dealing with different chain ids but same interface type. db_interface should have sides as well (L_H))

References chains_exist_in_pose(), compute_packstat_, dSASA_cutoff_, interface_analyzer_, pack_separated_, pack_together_, report_interface_features(), report_interface_residue_features(), report_interface_side_features(), scorefxn_, protocols::analysis::side1, protocols::analysis::side2, protocols::analysis::total, and protocols::features::TR().

Referenced by protocols::antibody::AntibodyFeatures::report_features(), and report_features().

report_features()

core::Size protocols::features::InterfaceFeatures::report_features ( core::pose::Pose const &  pose, utility::vector1< bool > const &  relevant_residues, StructureID  struct_id, utility::sql_database::sessionOP  db_session  )

overridevirtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

References interfaces_, make_interface_combos(), and report_all_interface_features().

report_interface_features()

void protocols::features::InterfaceFeatures::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

virtual

Add interfaces table data to table.

References protocols::analysis::InterfaceData::complex_total_energy, protocols::analysis::InterfaceData::crossterm_interface_energy, protocols::analysis::InterfaceData::crossterm_interface_energy_dSASA_ratio, protocols::analysis::InterfaceData::delta_unsat_hbonds, protocols::analysis::InterfaceData::dG, protocols::analysis::InterfaceData::dG_dSASA_ratio, protocols::analysis::InterfaceData::dhSASA, protocols::analysis::InterfaceData::dSASA, protocols::features::get_question_mark_string(), protocols::analysis::InterfaceData::hbond_E_fraction, interface_analyzer_, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::InterfaceData::packstat, protocols::analysis::InterfaceData::sc_value, core::pose::Pose::size(), and protocols::analysis::total.

Referenced by report_all_interface_features().

report_interface_residue_features()

void protocols::features::InterfaceFeatures::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

virtual

Add interface_residues data to table.

References protocols::features::FeaturesReporter::check_relevant_residues(), interface_analyzer_, protocols::analysis::PerResidueInterfaceData::interface_residues, protocols::analysis::InterfaceData::interface_residues, protocols::analysis::side1, protocols::analysis::side2, core::pose::Pose::size(), protocols::analysis::total, and write_interface_residue_data_row_to_db().

Referenced by report_all_interface_features().

report_interface_side_features()

void protocols::features::InterfaceFeatures::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

virtual

Add interface_sides table data to table.

References protocols::analysis::InterfaceData::aromatic_dG_fraction, protocols::analysis::InterfaceData::aromatic_dSASA_fraction, protocols::analysis::InterfaceData::aromatic_nres, protocols::analysis::InterfaceData::complexed_interface_score, protocols::analysis::InterfaceData::dG, protocols::analysis::InterfaceData::dhSASA, protocols::analysis::InterfaceData::dhSASA_rel_by_charge, protocols::analysis::InterfaceData::dhSASA_sc, protocols::analysis::InterfaceData::dSASA, protocols::analysis::InterfaceData::dSASA_sc, protocols::features::get_question_mark_string(), interface_analyzer_, protocols::analysis::InterfaceData::interface_nres, protocols::analysis::InterfaceData::interface_to_surface_fraction, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_dG, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_dSASA, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_int, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_energy_sep, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_SASA_int, protocols::analysis::PerResidueInterfaceData::regional_avg_per_residue_SASA_sep, protocols::analysis::InterfaceData::separated_interface_score, protocols::analysis::InterfaceData::ss_helix_nres, protocols::analysis::InterfaceData::ss_loop_nres, and protocols::analysis::InterfaceData::ss_sheet_nres.

Referenced by report_all_interface_features().

set_compute_packstat()

void protocols::features::InterfaceFeatures::set_compute_packstat

(

bool const

compute_packstat

)

Compute the packstat score? Default true.

References compute_packstat_.

set_defaults()

void protocols::features::InterfaceFeatures::set_defaults

(

)

References compute_packstat_, dSASA_cutoff_, pack_separated_, and pack_together_.

Referenced by InterfaceFeatures().

set_dSASA_cutoff()

void protocols::features::InterfaceFeatures::set_dSASA_cutoff

(

core::Real

dSASA_cutoff

)

Set the reporter to only include interfaces >dSASA_cutoff.

References dSASA_cutoff_.

set_interface_chains()

void protocols::features::InterfaceFeatures::set_interface_chains ( utility::vector1< std::string > const &  interfaces )

virtual

Set the fixed chain combinations that will be analyzed. Default is all of them.

Example: AB_C would analyze the interface between AB and C, keeping AB fixed while separating C. Note that here, you can also give A_C and a new pose would be created with only A and C so that this interface can be tested. Note also that multiple pose interfaces can be set.

Reimplemented in protocols::antibody::AntibodyFeatures.

References interfaces_.

set_pack_separated()

void protocols::features::InterfaceFeatures::set_pack_separated

(

bool const

pack_separated

)

Pack the interface before separation? Default is false.

References pack_separated_.

set_pack_together()

void protocols::features::InterfaceFeatures::set_pack_together

(

bool const

pack_together

)

Pack the interface after separation? Default is true.

References pack_together_.

set_scorefxn()

void protocols::features::InterfaceFeatures::set_scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn_.

type_name()

std::string protocols::features::InterfaceFeatures::type_name ( ) const

overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

write_interface_residue_data_row_to_db()

void protocols::features::InterfaceFeatures::write_interface_residue_data_row_to_db ( StructureID  struct_id, utility::sql_database::sessionOP  db_session, std::string const &  chains_side1, std::string const &  chains_side2, std::string const &  side, core::Size const  resnum, protocols::analysis::PerResidueInterfaceData const &  interface_data  ) const

private

References protocols::analysis::PerResidueInterfaceData::complexed_energy, protocols::analysis::PerResidueInterfaceData::complexed_sasa, 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(), protocols::analysis::PerResidueInterfaceData::separated_energy, and protocols::analysis::PerResidueInterfaceData::separated_sasa.

Referenced by report_interface_residue_features().

write_interface_residues_schema_to_db()

void protocols::features::InterfaceFeatures::write_interface_residues_schema_to_db ( utility::sql_database::sessionOP  db_session ) const

virtual

Referenced by protocols::antibody::AntibodyFeatures::write_schema_to_db(), and write_schema_to_db().

write_interface_schema_to_db()

void protocols::features::InterfaceFeatures::write_interface_schema_to_db ( utility::sql_database::sessionOP  db_session ) const

virtual

Referenced by protocols::antibody::AntibodyFeatures::write_schema_to_db(), and write_schema_to_db().

write_interface_side_schema_to_db()

void protocols::features::InterfaceFeatures::write_interface_side_schema_to_db ( utility::sql_database::sessionOP  db_session ) const

virtual

Referenced by protocols::antibody::AntibodyFeatures::write_schema_to_db(), and write_schema_to_db().

write_schema_to_db()

void protocols::features::InterfaceFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session ) const

overridevirtual

return string with class name

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

References write_interface_residues_schema_to_db(), write_interface_schema_to_db(), and write_interface_side_schema_to_db().

Member Data Documentation

compute_packstat_

bool protocols::features::InterfaceFeatures::compute_packstat_

protected

Referenced by protocols::antibody::AntibodyFeatures::parse_my_tag(), parse_my_tag(), report_all_interface_features(), protocols::antibody::AntibodyFeatures::report_features(), set_compute_packstat(), and set_defaults().

dSASA_cutoff_

core::Real protocols::features::InterfaceFeatures::dSASA_cutoff_

protected

Referenced by protocols::antibody::AntibodyFeatures::parse_my_tag(), parse_my_tag(), report_all_interface_features(), set_defaults(), and set_dSASA_cutoff().

interface_analyzer_

protocols::analysis::InterfaceAnalyzerMoverOP protocols::features::InterfaceFeatures::interface_analyzer_

protected

Referenced by InterfaceFeatures(), report_all_interface_features(), protocols::antibody::AntibodyFeatures::report_features(), report_interface_features(), report_interface_residue_features(), and report_interface_side_features().

interfaces_

utility::vector1< std::string > protocols::features::InterfaceFeatures::interfaces_

protected

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

pack_separated_

bool protocols::features::InterfaceFeatures::pack_separated_

protected

Referenced by protocols::antibody::AntibodyFeatures::parse_my_tag(), parse_my_tag(), report_all_interface_features(), protocols::antibody::AntibodyFeatures::report_features(), set_defaults(), and set_pack_separated().

pack_together_

bool protocols::features::InterfaceFeatures::pack_together_

protected

Referenced by protocols::antibody::AntibodyFeatures::parse_my_tag(), parse_my_tag(), report_all_interface_features(), protocols::antibody::AntibodyFeatures::report_features(), set_defaults(), and set_pack_together().

scorefxn_

core::scoring::ScoreFunctionCOP protocols::features::InterfaceFeatures::scorefxn_

protected

Referenced by InterfaceFeatures(), protocols::antibody::AntibodyFeatures::parse_my_tag(), parse_my_tag(), report_all_interface_features(), protocols::antibody::AntibodyFeatures::report_cdr_metrics_features(), protocols::antibody::AntibodyFeatures::report_features(), and set_scorefxn().

---

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

• src/protocols/features/InterfaceFeatures.hh
• src/protocols/features/InterfaceFeatures.cc