libfreecontact 1.0.21
|
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 long long __m128i freecontact::__attribute__((__vector_size__(16), __may_alias__)) |
Definition at line 65 of file freecontact.h.
typedef float freecontact::cov_fp_t |
Definition at line 58 of file freecontact.cpp.
typedef float freecontact::fp_t |
Definition at line 59 of file freecontact.cpp.
typedef d2matrix<uint32_t, uint32_t, int> freecontact::simcnt_t |
Definition at line 177 of file freecontact.cpp.
|
static |
Definition at line 1045 of file freecontact.cpp.
|
inlinestatic |
Definition at line 1082 of file freecontact.cpp.
|
inlinestatic |
Definition at line 192 of file freecontact.cpp.
|
inlinestatic |
Definition at line 1064 of file freecontact.cpp.
|
static |
Calculate raw contact scores using given function and collect row/column/overall mean for APC calculation.
[out] | __raw_ctscore | |
[out] | __apc_bg | |
[out] | __apc_mean | |
[in] | __alilen | |
[in] | __key | |
[in] | __fo |
Definition at line 1023 of file freecontact.cpp.
const parset_t freecontact::ps_evfold | ( | 0. | 70, |
0. | 0, | ||
0. | 9, | ||
1 | , | ||
0. | 0, | ||
0. | 5, | ||
false | , | ||
0. | 0, | ||
true | , | ||
true | , | ||
- | 1 | ||
) |
const parset_t freecontact::ps_psicov | ( | 0. | 62, |
0. | 03, | ||
0. | 9, | ||
5 | , | ||
1. | 0, | ||
0. | 0, | ||
true | , | ||
0. | 1, | ||
false | , | ||
false | , | ||
- | 1 | ||
) |
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 | ||
) |
|
static |
Definition at line 39 of file freecontact.h.
|
static |
Definition at line 38 of file freecontact.h.
|
static |
Definition at line 45 of file freecontact.h.