TorsionStatistics Class Reference

sequence dependent torsion statistics More...

#include <torsion_statistics.hh>

Public Types
typedef MultiClassifier < uint32_t, int, Real, Real, Real, Real, Real, Real >	TorsionHistogram
typedef TorsionHistogram::IndexType	IndexType
Public Member Functions
	TorsionStatistics (int prev_torsion_bucket_size, int central_torsion_bucket_size, int next_torsion_bucket_size)
	TorsionStatistics ()
void	Extract (mol::EntityHandle entity)
void	Extract (mol::EntityView view)
void	SaveToFile (const String &file_name) const
uint64_t	GetCount (const AminoAcidSet &central_aa, Real prev_phi_angle, Real prev_psi_angle, Real central_phi_angle, Real central_psi_angle, Real next_phi_angle, Real next_psi_angle) const
uint64_t	GetCount (Real prev_phi_angle, Real prev_psi_angle, Real central_phi_angle, Real central_psi_angle, Real next_phi_angle, Real next_psi_angle) const
uint64_t	GetCount (const AminoAcidSet &central_aa) const
uint64_t	GetCount () const
uint32_t	GetTorsionBucketCountPrev () const
int	GetTorsionBucketSizePrev () const
uint32_t	GetTorsionBucketCountCentral () const
int	GetTorsionBucketSizeCentral () const
uint32_t	GetTorsionBucketCountNext () const
int	GetTorsionBucketSizeNext () const
template<typename DS >
void	Serialize (DS &ds)
Static Public Member Functions
static TorsionStatisticsPtr	LoadFromFile (const String &file_name)

---

Detailed Description

sequence dependent torsion statistics

This implementation of the torsion angle potential combines 3 torsion angle pairs with 1 residues in analogy to the combined potential described by: Pascal Benkert, Silvio C. E. Tosatto, Dietmar Schomburg QMEAN: A comprehensive scoring function for model quality assessment Proteins, 2008

Definition at line 40 of file torsion_statistics.hh.

---

Member Typedef Documentation

typedef TorsionHistogram::IndexType IndexType

Definition at line 108 of file torsion_statistics.hh.

typedef MultiClassifier<uint32_t, int, Real, Real, Real, Real, Real, Real> TorsionHistogram

Definition at line 107 of file torsion_statistics.hh.

---

Constructor & Destructor Documentation

TorsionStatistics	(	int	prev_torsion_bucket_size,
		int	central_torsion_bucket_size,
		int	next_torsion_bucket_size
	)

construct new torsion statistics. In order to get something useful you need to either extract statistics from a set of PDBs or the statistics from file.

Parameters:

	prev_torsion_bucket_size	is torsion bucket size for the first torsion
	central_torsion_bucket_size	is the bucket size for the second torsion
	next_torsion_bucket_size	is the bucket size for the third torsion

TorsionStatistics

(

)

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Member Function Documentation

void Extract

(

mol::EntityView

view

)

extract torsion counts from (filtered) entity

void Extract

(

mol::EntityHandle

entity

)

extract torsion counts from whole entity.

uint64_t GetCount

(

)

const

uint64_t GetCount

(

const AminoAcidSet &

central_aa

)

const

uint64_t GetCount	(	Real	prev_phi_angle,
		Real	prev_psi_angle,
		Real	central_phi_angle,
		Real	central_psi_angle,
		Real	next_phi_angle,
		Real	next_psi_angle
	)			const

uint64_t GetCount	(	const AminoAcidSet &	central_aa,
		Real	prev_phi_angle,
		Real	prev_psi_angle,
		Real	central_phi_angle,
		Real	central_psi_angle,
		Real	next_phi_angle,
		Real	next_psi_angle
	)			const

Get count of phi/psi torsions with the specified torsion bucket size away conditional on the central amino acid.

uint32_t GetTorsionBucketCountCentral

(

)

const

uint32_t GetTorsionBucketCountNext

(

)

const

uint32_t GetTorsionBucketCountPrev

(

)

const

get the number of torsion buckets for every of the torsion angles.

int GetTorsionBucketSizeCentral

(

)

const

int GetTorsionBucketSizeNext

(

)

const

int GetTorsionBucketSizePrev

(

)

const

static TorsionStatisticsPtr LoadFromFile

(

const String &

file_name

)

[static]

load torsion statistics from file

void SaveToFile

(

const String &

file_name

)

const

void Serialize

(

DS &

ds

)

[inline]

Definition at line 97 of file torsion_statistics.hh.

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

• stage/include/ost/qa/torsion_statistics.hh