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protocols::features::BetaTurnDetectionFeatures Class Reference

#include <BetaTurnDetectionFeatures.hh>

Inheritance diagram for protocols::features::BetaTurnDetectionFeatures:
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Collaboration diagram for protocols::features::BetaTurnDetectionFeatures:
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Public Member Functions

 BetaTurnDetectionFeatures ()
 
 BetaTurnDetectionFeatures (BetaTurnDetectionFeatures const &)
 
virtual ~BetaTurnDetectionFeatures ()
 
virtual std::string type_name () const
 return string with class name More...
 
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 core::Size report_features (core::pose::Pose const &pose, utility::vector1< bool > const &, boost::uuids::uuid struct_id, utility::sql_database::sessionOP db_session)
 collect all the feature data for the pose More...
 
- 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 Member Functions

void write_beta_turns_table_schema (utility::sql_database::sessionOP db_session) const
 generate the beta_turns table schema More...
 
bool all_turn_residues_are_on_the_same_chain (core::pose::Pose const &pose, Size first_residue) const
 
bool residue_range_is_relevant (utility::vector1< bool > const &relevant_residues, Size range_begin, Size range_end) const
 
bool residue_range_is_protein (core::pose::Pose const &pose, Size range_begin, Size range_end) const
 
bool beta_turn_present (core::pose::Pose const &pose, Size first_residue) const
 
std::string const & beta_turn_type (core::pose::Pose const &pose, Size first_residue) const
 
std::string determine_ramachandran_hash (core::pose::Pose const &pose, core::Size first_residue) const
 
std::string determine_ramachandran_hash_for_residue_with_dihedrals (core::Real phi, core::Real psi, core::Real omega) const
 For the purposes of classifying beta-turns, Ramachandran space has been hashed into four large areas. In most turns the dihedral angles are not close to the boundaries as defined, so this provides a simple way of accurately classifying beta-turns. More...
 
void validate_ramachandran_hash (std::string &rama_hash) const
 

Static Private Member Functions

static std::map< std::string,
std::string > const & 
get_conformation_to_turn_type_map ()
 
static utility::vector1
< std::string > const & 
get_valid_ramachandran_hashes ()
 

Private Attributes

Size const beta_turn_length
 
core::Real const beta_turn_distance_cutoff
 

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::BetaTurnDetectionFeatures::BetaTurnDetectionFeatures ( )
protocols::features::BetaTurnDetectionFeatures::BetaTurnDetectionFeatures ( BetaTurnDetectionFeatures const &  )
protocols::features::BetaTurnDetectionFeatures::~BetaTurnDetectionFeatures ( )
virtual

Member Function Documentation

bool protocols::features::BetaTurnDetectionFeatures::all_turn_residues_are_on_the_same_chain ( core::pose::Pose const &  pose,
Size  first_residue 
) const
private
bool protocols::features::BetaTurnDetectionFeatures::beta_turn_present ( core::pose::Pose const &  pose,
Size  first_residue 
) const
private
string const & protocols::features::BetaTurnDetectionFeatures::beta_turn_type ( core::pose::Pose const &  pose,
Size  first_residue 
) const
private
string protocols::features::BetaTurnDetectionFeatures::determine_ramachandran_hash ( core::pose::Pose const &  pose,
core::Size  first_residue 
) const
private
string protocols::features::BetaTurnDetectionFeatures::determine_ramachandran_hash_for_residue_with_dihedrals ( core::Real  phi,
core::Real  psi,
core::Real  omega 
) const
private

For the purposes of classifying beta-turns, Ramachandran space has been hashed into four large areas. In most turns the dihedral angles are not close to the boundaries as defined, so this provides a simple way of accurately classifying beta-turns.

The four regions of space are defined as: A: phi <= 0, -100 < psi <= 50 B: phi <= 0, psi > 50 OR psi <= -100 L: phi > 0, -50 < psi <= 100 E: phi > 0, psi > 100 OR psi <= -50

Note: In the case of a Cis peptide plane, the lowercase letter for the hash will be returned.

Pictoral representation of Ramachandran hashing used for beta-turn classification:

  |----------------------|
  |          |           |
  |    B     |     E     |
  |          |===========| 100

50 |==========| | p | | L | s 0 |— A -------------—| i | | | | |===========| -50 -100 |==========| | | | E | | B | | |-------------------—| -180 0 180 phi

References protocols::features::A, protocols::features::B, protocols::features::E, get_valid_ramachandran_hashes(), and protocols::features::L.

Referenced by determine_ramachandran_hash().

utility::vector1< std::string > protocols::features::BetaTurnDetectionFeatures::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.

map< string, string > const & protocols::features::BetaTurnDetectionFeatures::get_conformation_to_turn_type_map ( )
staticprivate
vector1< string > const & protocols::features::BetaTurnDetectionFeatures::get_valid_ramachandran_hashes ( )
staticprivate
Size protocols::features::BetaTurnDetectionFeatures::report_features ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  ,
boost::uuids::uuid  struct_id,
utility::sql_database::sessionOP  db_session 
)
virtual

collect all the feature data for the pose

An anchor is a take off and landing for a loop. Every residue in the loop must be relevant in order for the loop to be stored.

Implements protocols::features::FeaturesReporter.

References all_turn_residues_are_on_the_same_chain(), beta_turn_length, beta_turn_present(), beta_turn_type(), core::sequence::end, residue_range_is_protein(), residue_range_is_relevant(), and core::pose::Pose::total_residue().

bool protocols::features::BetaTurnDetectionFeatures::residue_range_is_protein ( core::pose::Pose const &  pose,
Size  range_begin,
Size  range_end 
) const
private
bool protocols::features::BetaTurnDetectionFeatures::residue_range_is_relevant ( utility::vector1< bool > const &  relevant_residues,
Size  range_begin,
Size  range_end 
) const
private

Referenced by report_features().

string protocols::features::BetaTurnDetectionFeatures::type_name ( ) const
virtual

return string with class name

Reimplemented from protocols::features::FeaturesReporter.

void protocols::features::BetaTurnDetectionFeatures::validate_ramachandran_hash ( std::string &  rama_hash) const
private
void protocols::features::BetaTurnDetectionFeatures::write_beta_turns_table_schema ( utility::sql_database::sessionOP  db_session) const
private

generate the beta_turns table schema

Referenced by write_schema_to_db().

void protocols::features::BetaTurnDetectionFeatures::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.

References write_beta_turns_table_schema().

Member Data Documentation

core::Real const protocols::features::BetaTurnDetectionFeatures::beta_turn_distance_cutoff
private

Referenced by beta_turn_present().

Size const protocols::features::BetaTurnDetectionFeatures::beta_turn_length
private

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