protocols::features::BetaTurnDetectionFeatures Class Reference

#include <BetaTurnDetectionFeatures.hh>

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 &, StructureID 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
	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	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
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 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_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, 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::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

References beta_turn_length, chain, core::conformation::Residue::chain(), and core::pose::Pose::residue().

Referenced by report_features().

bool protocols::features::BetaTurnDetectionFeatures::beta_turn_present ( core::pose::Pose const &  pose, Size  first_residue  ) const

private

References beta_turn_distance_cutoff, beta_turn_length, norm(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by report_features().

string const & protocols::features::BetaTurnDetectionFeatures::beta_turn_type ( core::pose::Pose const &  pose, Size  first_residue  ) const

private

References determine_ramachandran_hash(), get_conformation_to_turn_type_map(), and validate_ramachandran_hash().

Referenced by report_features().

string protocols::features::BetaTurnDetectionFeatures::determine_ramachandran_hash ( core::pose::Pose const &  pose, core::Size  first_residue  ) const

private

References beta_turn_length, determine_ramachandran_hash_for_residue_with_dihedrals(), core::pose::Pose::omega(), core::pose::Pose::phi(), and core::pose::Pose::psi().

Referenced by beta_turn_type().

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::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

Referenced by beta_turn_type(), and validate_ramachandran_hash().

vector1< string > const & protocols::features::BetaTurnDetectionFeatures::get_valid_ramachandran_hashes ( )

staticprivate

References protocols::features::B, protocols::features::E, protocols::features::L, and protocols::features::number_of_ramachandran_hashes.

Referenced by determine_ramachandran_hash_for_residue_with_dihedrals(), and validate_ramachandran_hash().

Size protocols::features::BetaTurnDetectionFeatures::report_features ( core::pose::Pose const &  pose, utility::vector1< bool > const &  , StructureID  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(), begin, beta_turn_length, beta_turn_present(), beta_turn_type(), protocols::features::FeaturesReporter::check_relevant_residues_range(), end, residue_range_is_protein(), safely_prepare_statement(), basic::database::safely_write_to_database(), 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

References core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

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

References protocols::sparta::contains(), get_conformation_to_turn_type_map(), and get_valid_ramachandran_hashes().

Referenced by beta_turn_type().

void protocols::features::BetaTurnDetectionFeatures::write_beta_turns_table_schema ( utility::sql_database::sessionOP  db_session ) const

private

generate the beta_turns table schema

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

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

Referenced by all_turn_residues_are_on_the_same_chain(), beta_turn_present(), determine_ramachandran_hash(), and report_features().

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

• symlinks/rosetta/src/protocols/features/BetaTurnDetectionFeatures.hh
• symlinks/rosetta/src/protocols/features/BetaTurnDetectionFeatures.cc