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protocols::features::strand_assembly::StrandBundleFeatures Class Reference

#include <StrandBundleFeatures.hh>

Inheritance diagram for protocols::features::strand_assembly::StrandBundleFeatures:
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Public Member Functions

 StrandBundleFeatures ()
 
void init_from_options ()
 
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...
 
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 core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &relevant_residues, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose More...
 
utility::vector1< StrandFragmentget_full_strands (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StrandFragmentget_i_strand_from_full_strand_pairs (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 
utility::vector1< StrandFragmentget_j_strand_from_full_strand_pairs (boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 
bool find_antiparallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
bool find_parallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real check_sheet_dis_antiparallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real check_sheet_dis_parallel (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real sheet_torsion (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real shortest_dis_sidechain (core::pose::Pose const &pose, StrandFragment strand_i, StrandFragment strand_j)
 
core::Real shortest_dis_sidechain (core::Real val_shortest_dis_sidechain_1, core::Real val_shortest_dis_sidechain_2, core::Real val_shortest_dis_sidechain_3, core::Real val_shortest_dis_sidechain_4)
 
core::Real shortest_dis_pairs (core::Real return_of_check_sheet_dis_antiparallel_1, core::Real return_of_check_sheet_dis_antiparallel_2, core::Real return_of_check_sheet_dis_antiparallel_3, core::Real return_of_check_sheet_dis_antiparallel_4)
 
- Public Member Functions inherited from protocols::features::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 &, boost::uuids::uuid, utility::sql_database::sessionOP)
 collect all the feature data for the pose. More...
 
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 
virtual void load_into_pose (utility::sql_database::sessionOP, boost::uuids::uuid, core::pose::Pose &)
 
virtual void delete_record (boost::uuids::uuid, utility::sql_database::sessionOP)
 

Private Attributes

core::Size min_strand_size_
 
core::Size max_strand_size_
 
core::Real min_O_N_dis_
 
core::Real max_O_N_dis_
 
core::Real min_sheet_dis_
 
core::Real max_sheet_dis_
 
core::Real min_sheet_torsion_
 
core::Real max_sheet_torsion_
 

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, boost::uuids::uuid 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...
 

Constructor & Destructor Documentation

protocols::features::strand_assembly::StrandBundleFeatures::StrandBundleFeatures ( )

References init_from_options().

Member Function Documentation

Real protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_antiparallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
Real protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_parallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
utility::vector1< std::string > protocols::features::strand_assembly::StrandBundleFeatures::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.

bool protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
bool protocols::features::strand_assembly::StrandBundleFeatures::find_parallel ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_full_strands ( boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_i_strand_from_full_strand_pairs ( boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

utility::vector1< StrandFragment > protocols::features::strand_assembly::StrandBundleFeatures::get_j_strand_from_full_strand_pairs ( boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)

Referenced by report_features().

void protocols::features::strand_assembly::StrandBundleFeatures::init_from_options ( )
core::Size protocols::features::strand_assembly::StrandBundleFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  relevant_residues,
boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual
Real protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_pairs ( core::Real  return_of_check_sheet_dis_antiparallel_1,
core::Real  return_of_check_sheet_dis_antiparallel_2,
core::Real  return_of_check_sheet_dis_antiparallel_3,
core::Real  return_of_check_sheet_dis_antiparallel_4 
)

Referenced by report_features().

Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain ( core::pose::Pose const &  pose,
StrandFragment  strand_i,
StrandFragment  strand_j 
)
Real protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain ( core::Real  val_shortest_dis_sidechain_1,
core::Real  val_shortest_dis_sidechain_2,
core::Real  val_shortest_dis_sidechain_3,
core::Real  val_shortest_dis_sidechain_4 
)
virtual std::string protocols::features::strand_assembly::StrandBundleFeatures::type_name ( ) const
inlinevirtual
void protocols::features::strand_assembly::StrandBundleFeatures::write_schema_to_db ( utility::sql_database::sessionOP  db_session) const
virtual

generate the table schemas and write them to the database

Implements protocols::features::FeaturesReporter.

Member Data Documentation

core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_O_N_dis_
private
core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_dis_
private
core::Real protocols::features::strand_assembly::StrandBundleFeatures::max_sheet_torsion_
private
core::Size protocols::features::strand_assembly::StrandBundleFeatures::max_strand_size_
private
core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_O_N_dis_
private
core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_dis_
private
core::Real protocols::features::strand_assembly::StrandBundleFeatures::min_sheet_torsion_
private
core::Size protocols::features::strand_assembly::StrandBundleFeatures::min_strand_size_
private

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