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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:
Inheritance graph
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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

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

Member Function Documentation

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

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

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

Referenced by make_interface_combos().

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().

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().

void protocols::features::InterfaceFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::features::InterfaceFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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 report_features(), and protocols::antibody::AntibodyFeatures::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().

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
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
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
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 ( )
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 ( 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_.

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_.

void protocols::features::InterfaceFeatures::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn_.

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

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

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

bool protocols::features::InterfaceFeatures::compute_packstat_
protected
core::Real protocols::features::InterfaceFeatures::dSASA_cutoff_
protected
protocols::analysis::InterfaceAnalyzerMoverOP protocols::features::InterfaceFeatures::interface_analyzer_
protected
utility::vector1< std::string > protocols::features::InterfaceFeatures::interfaces_
protected
bool protocols::features::InterfaceFeatures::pack_separated_
protected
bool protocols::features::InterfaceFeatures::pack_together_
protected
core::scoring::ScoreFunctionCOP protocols::features::InterfaceFeatures::scorefxn_
protected

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