Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::features::helixAssembly::HelixBundleFeatures Class Reference

#include <HelixBundleFeatures.hh>

Inheritance diagram for protocols::features::helixAssembly::HelixBundleFeatures:
Inheritance graph
[legend]

Public Member Functions

 HelixBundleFeatures ()
 
void write_schema_to_db (utility::sql_database::sessionOP db_session) const override
 generate the table schemas and write them to the database More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 calculate the shared fa_attr for each pair of helices in the bundle 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...
 
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...
 
utility::vector1
< HelicalFragmentOP
get_helices (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
bool validate_bundle (core::pose::Pose const &pose, utility::vector1< HelicalFragment > const &helices)
 
void write_bundle_to_db (protocols::features::StructureID const &struct_id, utility::sql_database::sessionOP db_session, utility::vector1< HelicalFragment > const &bundle)
 
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)
 

Private Attributes

core::Real helix_cap_dist_cutoff_
 
core::Size num_helices_per_bundle_
 
core::Size min_helix_size_
 
core::Real min_per_residue_fa_attr_
 
core::Real min_interacting_set_fraction_
 
protocols::simple_filters::InterfaceSasaFilter sasa_filter_
 
core::scoring::ScoreFunctionOP scorefxn_
 

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_
 

Constructor & Destructor Documentation

protocols::features::helixAssembly::HelixBundleFeatures::HelixBundleFeatures ( )

Member Function Documentation

std::string protocols::features::helixAssembly::HelixBundleFeatures::class_name ( )
static
utility::vector1< std::string > protocols::features::helixAssembly::HelixBundleFeatures::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.

utility::vector1< HelicalFragmentOP > protocols::features::helixAssembly::HelixBundleFeatures::get_helices ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
void protocols::features::helixAssembly::HelixBundleFeatures::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

calculate the shared fa_attr for each pair of helices in the bundle

Reimplemented from protocols::features::FeaturesReporter.

References helix_cap_dist_cutoff_, min_helix_size_, min_interacting_set_fraction_, min_per_residue_fa_attr_, num_helices_per_bundle_, and type_name().

void protocols::features::helixAssembly::HelixBundleFeatures::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::features::helixAssembly::HelixBundleFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
overridevirtual
std::string protocols::features::helixAssembly::HelixBundleFeatures::type_name ( ) const
overridevirtual

Reimplemented from protocols::features::FeaturesReporter.

References class_name().

Referenced by parse_my_tag().

bool protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle ( core::pose::Pose const &  pose,
utility::vector1< HelicalFragment > const &  helices 
)

validate that the bundle fits all the requirements. Currently, the only requirement is that each helix in the bundle has a c-alpha, c-alpha distance less than the specified cutoff with at least 2 other helices in the same bundle

References core::conformation::Residue::atom(), core::sequence::end, helix_cap_dist_cutoff_, num_helices_per_bundle_, core::pose::Pose::residue(), protocols::loops::start, protocols::features::TR(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::write_bundle_to_db ( protocols::features::StructureID const &  struct_id,
utility::sql_database::sessionOP  db_session,
utility::vector1< HelicalFragment > const &  bundle 
)

Write the given bundle to the database. This involves writing to three tables: helix_bundles - the top-level table. Has a unique bundle_id. FK to the structure bundle_helices - the individual helical segments that make up the bundle. FK to the bundle table bundle_pairs - the pairs of helices that make up the bundle. FKs to the bundle table and the bundle_helices table

References num_helices_per_bundle_.

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
overridevirtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Member Data Documentation

core::Real protocols::features::helixAssembly::HelixBundleFeatures::helix_cap_dist_cutoff_
private

Referenced by parse_my_tag(), and validate_bundle().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::min_helix_size_
private
core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_interacting_set_fraction_
private

Referenced by parse_my_tag().

core::Real protocols::features::helixAssembly::HelixBundleFeatures::min_per_residue_fa_attr_
private

Referenced by parse_my_tag().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::num_helices_per_bundle_
private
protocols::simple_filters::InterfaceSasaFilter protocols::features::helixAssembly::HelixBundleFeatures::sasa_filter_
private
core::scoring::ScoreFunctionOP protocols::features::helixAssembly::HelixBundleFeatures::scorefxn_
private

Referenced by HelixBundleFeatures().


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