#include <BetaTurnDetection.hh>

Inheritance diagram for protocols::features::BetaTurnDetection:

Public Member Functions
	BetaTurnDetection ()

	BetaTurnDetection (BetaTurnDetection const &)

	~BetaTurnDetection () override

virtual std::string	type_name () const
	return string with class name More...

core::Size	beta_turn_length () const

core::Real	beta_turn_distance_cutoff () const

bool	all_turn_residues_are_on_the_same_chain (core::pose::Pose const &pose, core::Size first_residue) const

bool	residue_range_is_protein (core::pose::Pose const &pose, core::Size range_begin, core::Size range_end) const

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

std::string const &	beta_turn_type (core::pose::Pose const &pose, core::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 Public 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
core::Size const	beta_turn_length_

core::Real const	beta_turn_distance_cutoff_

Constructor & Destructor Documentation

protocols::features::BetaTurnDetection::BetaTurnDetection ( )

protocols::features::BetaTurnDetection::BetaTurnDetection ( BetaTurnDetection const & )

protocols::features::BetaTurnDetection::~BetaTurnDetection ( )

overridedefault

Member Function Documentation

bool protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain	(	core::pose::Pose const &	pose,
		core::Size	first_residue
	)		const

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

core::Real protocols::features::BetaTurnDetection::beta_turn_distance_cutoff ( ) const

inline

References beta_turn_distance_cutoff_.

core::Size protocols::features::BetaTurnDetection::beta_turn_length ( ) const

inline

References beta_turn_length_.

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

References beta_turn_distance_cutoff_, beta_turn_length_, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

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

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

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

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::BetaTurnDetection::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.

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().

map< string, string > const & protocols::features::BetaTurnDetection::get_conformation_to_turn_type_map ( )

static

Referenced by beta_turn_type(), and validate_ramachandran_hash().

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

static

References protocols::features::A, 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().

bool protocols::features::BetaTurnDetection::residue_range_is_protein	(	core::pose::Pose const &	pose,
		core::Size	range_begin,
		core::Size	range_end
	)		const