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>

Public Member Functions
	InterfaceFeatures ()

	InterfaceFeatures (core::scoring::ScoreFunctionCOP scorefxn)

virtual	~InterfaceFeatures ()

virtual std::string	type_name () const
	return string with class name More...

virtual void	write_schema_to_db (utility::sql_database::sessionOP db_session) const
	generate the table schemas and write them to the database More...

virtual utility::vector1 < std::string >	features_reporter_dependencies () const
	return the set of features reporters that are required to also already be extracted by the time this one is used. More...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

virtual core::Size	report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, StructureID struct_id, utility::sql_database::sessionOP db_session)
	collect all the feature data for the pose More...

void	set_interface_chains (vector1< std::string > 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...

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_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 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 const region, std::string const region_string) const

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

void	make_interface_combos (core::pose::Pose const &pose, vector1< std::string > &interfaces)
	Gets all possible interface combinations of a given pose. More...

Public Member Functions inherited from protocols::features::FeaturesReporter
	FeaturesReporter ()

virtual	~FeaturesReporter ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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

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
	Writes interface data to the database from analyzer. InterfaceAnalyzer's apply should be called already. More...

void	get_all_string_combos (std::string &interface, std::string current, vector1< std::string > &chains) const
	Recursive function. Get all orders of ex ABCD. More...

void	get_length_combos (std::string current, vector1< std::string > &sizes) const

bool	interface_exists (vector1< std::string > &interfaces, std::string &dock_chains) const

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

std::string	get_all_pose_chains (core::pose::Pose const &pose)

Private Attributes
protocols::analysis::InterfaceAnalyzerMoverOP	interface_analyzer_

core::scoring::ScoreFunctionCOP	scorefxn_

vector1< std::string >	interfaces_

bool	pack_together_

bool	pack_separated_

bool	compute_packstat_

core::Real	dSASA_cutoff_

Additional Inherited Members
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::FeaturesReporter
RelevantResiduesMode::T	relevant_residues_mode_

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

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

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

protocols::features::InterfaceFeatures::InterfaceFeatures ( core::scoring::ScoreFunctionCOP scorefxn )

References interface_analyzer_, scorefxn_, and set_defaults().

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

virtual

Member Function Documentation

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

private

References chain, core::pose::has_chain(), and utility::string_split().

Referenced by report_features().

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

virtual

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.

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

private

References chain, core::pose::Pose::conformation(), core::pose::get_chain_from_chain_id(), core::conformation::Conformation::num_chains(), utility::to_string(), and protocols::features::TR.

Referenced by make_interface_combos().

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

private

Recursive function. Get all orders of ex ABCD.

Referenced by make_interface_combos().

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

private

Referenced by make_interface_combos().

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

private

References begin, end, and utility::string_split().

Referenced by make_interface_combos().

void protocols::features::InterfaceFeatures::make_interface_combos	(	core::pose::Pose const &	pose,
		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(), s, and protocols::features::TR.

Referenced by report_features().

void protocols::features::InterfaceFeatures::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Reimplemented from protocols::features::FeaturesReporter.

References compute_packstat_, dSASA_cutoff_, basic::datacache::DataMap::get(), interfaces_, pack_separated_, pack_together_, scorefxn_, utility::string_split_multi_delim(), and utility_exit_with_message.

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
	)

virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

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

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

References protocols::analysis::InterfaceAnalyzerMover::get_all_data(), protocols::analysis::InterfaceAnalyzerMover::get_all_per_residue_data(), protocols::features::get_question_mark_string(), interface_analyzer_, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), protocols::analysis::total, and core::pose::Pose::total_residue().

Referenced by report_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

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

Referenced by report_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 const	region,
		std::string const	region_string
	)		const

virtual

Referenced by report_features().

void protocols::features::InterfaceFeatures::set_compute_packstat ( bool const compute_packstat )

Compute the packstat score? Default true.

References compute_packstat_.

void protocols::features::InterfaceFeatures::set_defaults ( )

References compute_packstat_, dSASA_cutoff_, pack_separated_, and pack_together_.

Referenced by InterfaceFeatures().

void protocols::features::InterfaceFeatures::set_dSASA_cutoff ( core::Real dSASA_cutoff )

Set the reporter to only include interfaces >dSASA_cutoff.

References dSASA_cutoff_.

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

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.

References interfaces_.

void protocols::features::InterfaceFeatures::set_pack_separated ( bool const pack_separated )

Pack the interface before separation? Default is false.

References pack_separated_.

void protocols::features::InterfaceFeatures::set_pack_together ( bool const pack_together )

Pack the interface after separation? Default is true.

References pack_together_.

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

virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

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