Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::features::helixAssembly::HelixBundleFeatures Class Reference

#include <HelixBundleFeatures.hh>

Public Member Functions

 HelixBundleFeatures ()
 
virtual std::string type_name () const
 
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 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 &pose)
 
utility::vector1< std::stringfeatures_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...
 
bool overlapping (HelicalFragmentOP const &fragment_1, HelicalFragmentOP const &fragment_2)
 
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...
 
utility::vector1
< HelicalFragmentOP
get_helix_fragments (StructureID struct_id, utility::sql_database::sessionOP db_session)
 
void calc_pc_and_com (core::pose::Pose const &pose, HelicalFragmentOP fragment)
 
void record_helix_sasas (core::pose::Pose const &pose, std::set< HelicalFragmentOP > const &frag_set)
 create a bundle-pose from the combination of fragments and record the "interface" SASA for each helix against the rest of the bundle More...
 
PairMap get_helix_pairs (core::pose::Pose const &pose, utility::vector1< HelicalFragmentOP > helix_fragments)
 
void calc_fa_energy (core::pose::Pose const &pose, FragmentPair &fragment_pair)
 calculate the shared fa_attr for each pair of helices in the bundle More...
 
void calc_crossing_angles (core::pose::Pose const &pose, FragmentPair &fragment_pair)
 calculate the crossing angles of the helix fragment in the bundle set 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 Attributes

core::Real helix_cap_dist_cutoff_
 
core::Size bundle_size_
 
core::Size helix_size_
 
core::Real min_per_residue_fa_attr_
 
core::Real min_interacting_set_fraction_
 
core::Real max_degrees_off_parallel_
 
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

void protocols::features::helixAssembly::HelixBundleFeatures::calc_crossing_angles ( core::pose::Pose const &  pose,
FragmentPair fragment_pair 
)
void protocols::features::helixAssembly::HelixBundleFeatures::calc_fa_energy ( core::pose::Pose const &  pose,
FragmentPair fragment_pair 
)
void protocols::features::helixAssembly::HelixBundleFeatures::calc_pc_and_com ( core::pose::Pose const &  pose,
HelicalFragmentOP  fragment 
)
utility::vector1< std::string > protocols::features::helixAssembly::HelixBundleFeatures::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.

utility::vector1< HelicalFragmentOP > protocols::features::helixAssembly::HelixBundleFeatures::get_helix_fragments ( StructureID  struct_id,
utility::sql_database::sessionOP  db_session 
)
PairMap protocols::features::helixAssembly::HelixBundleFeatures::get_helix_pairs ( core::pose::Pose const &  pose,
utility::vector1< HelicalFragmentOP helix_fragments 
)
bool protocols::features::helixAssembly::HelixBundleFeatures::overlapping ( HelicalFragmentOP const &  fragment_1,
HelicalFragmentOP const &  fragment_2 
)

Referenced by report_features().

void protocols::features::helixAssembly::HelixBundleFeatures::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 &  pose 
)
virtual
void protocols::features::helixAssembly::HelixBundleFeatures::record_helix_sasas ( core::pose::Pose const &  pose,
std::set< HelicalFragmentOP > const &  frag_set 
)

create a bundle-pose from the combination of fragments and record the "interface" SASA for each helix against the rest of the bundle

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 
)
virtual
virtual std::string protocols::features::helixAssembly::HelixBundleFeatures::type_name ( ) const
inlinevirtual

Reimplemented from protocols::features::FeaturesReporter.

Referenced by parse_my_tag().

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

Member Data Documentation

core::Size protocols::features::helixAssembly::HelixBundleFeatures::bundle_size_
private

Referenced by parse_my_tag(), and report_features().

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

Referenced by get_helix_pairs(), and parse_my_tag().

core::Size protocols::features::helixAssembly::HelixBundleFeatures::helix_size_
private
core::Real protocols::features::helixAssembly::HelixBundleFeatures::max_degrees_off_parallel_
private

Referenced by parse_my_tag().

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

Referenced by get_helix_pairs(), and parse_my_tag().

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

Referenced by get_helix_pairs(), and parse_my_tag().

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

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