TorsionStatisticsSolis Class Reference

sequence dependent torsion statistics More...

#include <solis_torsion_statistics.hh>

Public Types
typedef MultiClassifier< int, int, int, int, Real, Real >	TorsionHistogram
typedef TorsionHistogram::IndexType	IndexType
Public Member Functions
	TorsionStatisticsSolis (int torsion_bucket_size)
	TorsionStatisticsSolis ()
void	Extract (mol::EntityHandle entity)
void	Extract (mol::EntityView view)
void	SaveToFile (const String &file_name) const
uint32_t	GetCount (const AminoAcidSet &prev_aa, const AminoAcidSet &central_aa, const AminoAcidSet &next_aa, Real phi_angle, Real psi_angle) const
uint32_t	GetCount (const AminoAcidSet &prev_aa, const AminoAcidSet &central_aa, const AminoAcidSet &next_aa) const
uint32_t	GetCount (Real phi_angle, Real psi_angle) const
uint32_t	GetCount (AminoAcid central_aa, Real phi_angle, Real psi_angle) const
Real	GetFrequency (AminoAcid aa, Real phi_angle, Real psi_angle) const
Real	GetFrequency (Real phi_angle, Real psi_angle) const
uint32_t	GetTorsionBucketCount () const
int	GetTorsionBucketSize () const
int	GetCount () const
template<typename DS >
void	Serialize (DS &ds)
Static Public Member Functions
static TorsionStatisticsSolisPtr	LoadFromFile (const String &file_name)

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Detailed Description

sequence dependent torsion statistics

Definition at line 45 of file solis_torsion_statistics.hh.

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Member Typedef Documentation

typedef TorsionHistogram::IndexType IndexType

Definition at line 111 of file solis_torsion_statistics.hh.

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

Definition at line 110 of file solis_torsion_statistics.hh.

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Constructor & Destructor Documentation

TorsionStatisticsSolis

(

int

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:

torsion_bucket_size

is the histogram bucket size for torsion angles.

TorsionStatisticsSolis

(

)

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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.

int GetCount

(

)

const

uint32_t GetCount	(	AminoAcid	central_aa,
		Real	phi_angle,
		Real	psi_angle
	)			const

Get count of amino acids with the given phi/psi angle conditional on the central residue.

uint32_t GetCount	(	Real	phi_angle,
		Real	psi_angle
	)			const

Get count of amino acids with the given phi/psi angle.

uint32_t GetCount	(	const AminoAcidSet &	prev_aa,
		const AminoAcidSet &	central_aa,
		const AminoAcidSet &	next_aa
	)			const

uint32_t GetCount	(	const AminoAcidSet &	prev_aa,
		const AminoAcidSet &	central_aa,
		const AminoAcidSet &	next_aa,
		Real	phi_angle,
		Real	psi_angle
	)			const

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

Real GetFrequency	(	Real	phi_angle,
		Real	psi_angle
	)			const

Get frequency of phi/psi angle in bucket phi_angle/psi_angle regardless of the amino acid type.

Returns:

frequency in the range of [0, 1]

Real GetFrequency	(	AminoAcid	aa,
		Real	phi_angle,
		Real	psi_angle
	)			const

Get frequency of phi/psi angle in bucket phi_angle/psi_angle when the amino acid is aa.

Returns:

frequency in the range of [0, 1]

uint32_t GetTorsionBucketCount

(

)

const

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

int GetTorsionBucketSize

(

)

const

static TorsionStatisticsSolisPtr 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 104 of file solis_torsion_statistics.hh.

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

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