libfreecontact 1.0.21
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Classes | Typedefs | Functions | Variables
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.
 
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,
,
0.  0,
0.  5,
false  ,
0.  0,
true  ,
true  ,
1 
)

◆ ps_psicov()

const parset_t freecontact::ps_psicov ( 0.  62,
0.  03,
0.  9,
,
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,
,
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.