freecontact Namespace Reference

Classes
class	_glasso_timer
class	_rawscore_calc_t
	Calculates raw score for an i,j contact. More...
class	af_vector
class	ali_t
	Protein sequence alignment. More...
class	alilen_error
	Alignment length exception. More...
struct	contact_t
	Contact prediction. More...
class	cov_vector
class	ct_vector
class	d2matrix
	2-dimensional matrix. More...
class	icme_timeout_error
	Inverse covariance matrix estimation timeout exception. More...
struct	parset_t
	Parameter set structure for predictor::run(). More...
class	pf_vector
class	predictor
	Protein residue contact predictor. More...

Typedefs
typedef float	cov_fp_t
typedef float	fp_t
typedef d2matrix< uint32_t, uint32_t, int >	simcnt_t
typedef long long __m128i	__attribute__((__vector_size__(16), __may_alias__))

Functions
static void	_raw_score_matrix (map< string, ct_vector< fp_t > > &__raw_ctscore, map< string, vector< double > > &__apc_bg, map< string, double > &__apc_mean, const uint16_t __alilen, const string &__key, const _rawscore_calc_t &__fo)
	Calculate raw contact scores using given function and collect row/column/overall mean for APC calculation. More...
static vector< contact_t >	_apc (const ct_vector< fp_t > &__raw_ctscore, const vector< double > &__apc_bg, const double __apc_mean, const uint16_t __mincontsep, bool __filt)
static vector< contact_t >	_raw_as_is (const ct_vector< fp_t > &__raw_ctscore, const uint16_t __mincontsep)
static uint32_t	_cache_holds_nseq (uint16_t __seqsize)
static __m128i	_mm_setzero_si128 ()
const parset_t	ps_evfold (0.70, 0.0, 0.9, 1, 0.0, 0.5, false, 0.0, true, true, -1)
const parset_t	ps_psicov (0.62, 0.03, 0.9, 5, 1.0, 0.0, true, 0.1, false, false, -1)
const parset_t	ps_psicov_sd (0.62, 0.0, 0.9, 5, 1.0, 0.0, true, 0.1, false, false, 0.001)

Variables
static const uint8_t	aamap_gapidx = 20
static const uint8_t	aamap []
static const uint8_t	mapaa []

Typedef Documentation

__attribute__

typedef long long __m128i freecontact::__attribute__((__vector_size__(16), __may_alias__))

Definition at line 65 of file freecontact.h.

cov_fp_t

typedef float freecontact::cov_fp_t

Definition at line 58 of file freecontact.cpp.

fp_t

typedef float freecontact::fp_t

Definition at line 59 of file freecontact.cpp.

simcnt_t

typedef d2matrix<uint32_t, uint32_t, int> freecontact::simcnt_t

Definition at line 177 of file freecontact.cpp.

Function Documentation

_apc()

vector< contact_t > freecontact::_apc ( const ct_vector< fp_t > &  __raw_ctscore, const vector< double > &  __apc_bg, const double  __apc_mean, const uint16_t  __mincontsep, bool  __filt  )

static

Definition at line 1045 of file freecontact.cpp.

_cache_holds_nseq()

static uint32_t freecontact::_cache_holds_nseq ( uint16_t  __seqsize )

inlinestatic

Definition at line 1082 of file freecontact.cpp.

_mm_setzero_si128()

static __m128i freecontact::_mm_setzero_si128 ( )

inlinestatic

Definition at line 192 of file freecontact.cpp.

_raw_as_is()

vector< contact_t > freecontact::_raw_as_is ( const ct_vector< fp_t > &  __raw_ctscore, const uint16_t  __mincontsep  )

inlinestatic

Definition at line 1064 of file freecontact.cpp.

_raw_score_matrix()

void freecontact::_raw_score_matrix ( map< string, ct_vector< fp_t > > &  __raw_ctscore, map< string, vector< double > > &  __apc_bg, map< string, double > &  __apc_mean, const uint16_t  __alilen, const string &  __key, const _rawscore_calc_t &  __fo  )

static

Calculate raw contact scores using given function and collect row/column/overall mean for APC calculation.

Parameters

[out]	__raw_ctscore
[out]	__apc_bg
[out]	__apc_mean
[in]	__alilen
[in]	__key
[in]	__fo

Definition at line 1023 of file freecontact.cpp.

ps_evfold()

const parset_t freecontact::ps_evfold	(	0.	70,
		0.	0,
		0.	9,
		1	,
		0.	0,
		0.	5,
		false	,
		0.	0,
		true	,
		true	,
		-	1
	)

ps_psicov()

const parset_t freecontact::ps_psicov	(	0.	62,
		0.	03,
		0.	9,
		5	,
		1.	0,
		0.	0,
		true	,
		0.	1,
		false	,
		false	,
		-	1
	)

ps_psicov_sd()

const parset_t freecontact::ps_psicov_sd	(	0.	62,
		0.	0,
		0.	9,
		5	,
		1.	0,
		0.	0,
		true	,
		0.	1,
		false	,
		false	,
		0.	001
	)

Variable Documentation

aamap

const uint8_t freecontact::aamap[]

static

Initial value:

= {
    
    21, 0, 3, 4, 3, 6, 13, 7, 8, 9, 21, 11, 10, 12, 2,
    
        21, 14, 5, 1, 15, 16, 21, 19, 17, 21, 18, 6
}

Definition at line 39 of file freecontact.h.

aamap_gapidx

const uint8_t freecontact::aamap_gapidx = 20

static

Definition at line 38 of file freecontact.h.

mapaa

const uint8_t freecontact::mapaa[]

static

Initial value:

= {
   
    'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I',
    'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V',
    '-', 'X'
}

Definition at line 45 of file freecontact.h.