Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
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>

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...
 
virtual 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...
 
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 const 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, 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
 

Protected Member Functions

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
 
- 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_
 
vector1< std::stringinterfaces_
 
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, 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
 
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 ( )
virtual

Member Function Documentation

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

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
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 protocols::analysis::InterfaceAnalyzerMover::apply_const(), chains_exist_in_pose(), compute_packstat_, dSASA_cutoff_, protocols::analysis::InterfaceAnalyzerMover::get_interface_delta_sasa(), interface_analyzer_, pack_separated_, pack_together_, report_interface_features(), report_interface_residue_features(), report_interface_side_features(), scorefxn_, protocols::analysis::InterfaceAnalyzerMover::set_use_centroid_dG(), protocols::analysis::side1, protocols::analysis::side2, utility::string_split(), protocols::analysis::total, protocols::features::TR, and utility_exit_with_message.

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 
)
virtual

collect all the feature data for the pose

Implements protocols::features::FeaturesReporter.

Reimplemented in protocols::antibody::AntibodyFeatures.

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 const  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::analysis::InterfaceAnalyzerMover::get_all_data(), protocols::analysis::InterfaceAnalyzerMover::get_all_per_residue_data(), 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, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), 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().

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 ( vector1< std::string 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.

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
virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

Reimplemented in protocols::antibody::AntibodyFeatures.

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
virtual

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
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: