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protocols::features::BetaTurnDetection Class Reference

#include <BetaTurnDetection.hh>

Inheritance diagram for protocols::features::BetaTurnDetection:
Inheritance graph
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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
core::Real protocols::features::BetaTurnDetection::beta_turn_distance_cutoff ( ) const
inline
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
string const & protocols::features::BetaTurnDetection::beta_turn_type ( core::pose::Pose const &  pose,
core::Size  first_residue 
) const
string protocols::features::BetaTurnDetection::determine_ramachandran_hash ( core::pose::Pose const &  pose,
core::Size  first_residue 
) const
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
vector1< string > const & protocols::features::BetaTurnDetection::get_valid_ramachandran_hashes ( )
static
bool protocols::features::BetaTurnDetection::residue_range_is_protein ( core::pose::Pose const &  pose,
core::Size  range_begin,
core::Size  range_end 
) const
string protocols::features::BetaTurnDetection::type_name ( ) const
virtual

return string with class name

void protocols::features::BetaTurnDetection::validate_ramachandran_hash ( std::string &  rama_hash) const

Member Data Documentation

core::Real const protocols::features::BetaTurnDetection::beta_turn_distance_cutoff_
private
core::Size const protocols::features::BetaTurnDetection::beta_turn_length_
private

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