libfreecontact 1.0.21
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Protein residue contact predictor. More...
#include <freecontact.h>
Public Types | |
typedef std::map< std::string, std::vector< contact_t > > | cont_res_t |
typedef double | freq_t |
typedef float | pairfreq_t |
typedef std::vector< freq_t > | freq_vec_t |
typedef std::map< std::string, double > | time_res_t |
Public Member Functions | |
predictor (bool __dbg=false) | |
virtual | ~predictor () |
void | get_seq_weights (freq_vec_t &__aliw, double &__wtot, const ali_t &__ali, double __clustpc, bool __veczw=true, int __num_threads=0) |
Calculate alignment sequence weights. | |
cont_res_t | run (const ali_t &__ali, const freq_vec_t &__aliw, const double __wtot, double __density, double __gapth, uint16_t __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __apply_gapth, double __rho, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL) |
Predict residue contacts. | |
cont_res_t | run (const ali_t &__ali, double __clustpc, double __density, double __gapth, uint16_t __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __apply_gapth, double __rho, bool __veczw=true, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL) |
Predict residue contacts. | |
cont_res_t | run (const ali_t &__ali, const parset_t &__parset, bool __veczw=true, int __num_threads=0, time_t __icme_timeout=1800, time_res_t *__timing=NULL) |
Predict residue contacts. | |
Public Attributes | |
bool | dbg |
Protein residue contact predictor.
A sufficiently large multiple alignment is required for meaningful results.
Definition at line 160 of file freecontact.h.
typedef std::map<std::string, std::vector<contact_t> > freecontact::predictor::cont_res_t |
Definition at line 162 of file freecontact.h.
typedef double freecontact::predictor::freq_t |
Definition at line 163 of file freecontact.h.
typedef std::vector<freq_t> freecontact::predictor::freq_vec_t |
Definition at line 165 of file freecontact.h.
typedef float freecontact::predictor::pairfreq_t |
Definition at line 164 of file freecontact.h.
typedef std::map<std::string, double> freecontact::predictor::time_res_t |
Definition at line 166 of file freecontact.h.
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inline |
Definition at line 169 of file freecontact.h.
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inlinevirtual |
Definition at line 170 of file freecontact.h.
void freecontact::predictor::get_seq_weights | ( | freq_vec_t & | __aliw, |
double & | __wtot, | ||
const ali_t & | __ali, | ||
double | __clustpc, | ||
bool | __veczw = true , |
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int | __num_threads = 0 |
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) |
Calculate alignment sequence weights.
[out] | __aliw | Vector of alignment sequence weights. |
[out] | __wtot | Total alignment weight. |
[in] | __ali | Input alignment. |
[in] | __clustpc | BLOSUM-style clustering similarity threshold [0-1]. |
[in] | __veczw | Use vectorized sequence weighting when available. |
[in] | __num_threads | Number of OpenMP threads, effective if non-zero. The default is as many threads as cores in host. Ineffective if library is not compiled with OMP support. |
Definition at line 236 of file freecontact.cpp.
predictor::cont_res_t freecontact::predictor::run | ( | const ali_t & | __ali, |
const freq_vec_t & | __aliw, | ||
const double | __wtot, | ||
double | __density, | ||
double | __gapth, | ||
uint16_t | __mincontsep, | ||
double | __pseudocnt, | ||
double | __pscnt_weight, | ||
bool | __estimate_ivcov, | ||
double | __shrink_lambda, | ||
bool | __cov20, | ||
bool | __apply_gapth, | ||
double | __rho, | ||
int | __num_threads = 0 , |
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time_t | __icme_timeout = 1800 , |
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time_res_t * | __timing = NULL |
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) |
Predict residue contacts.
[in] | __ali | Input alignment. |
[in] | __aliw | Vector of alignment sequence weights. Obtain this with get_seq_weights(). |
[in] | __wtot | Total weight of alignment. Obtain this with get_seq_weights(). |
[in] | __density | Target precision matrix density [0-1]. Set to 0 to not control density. |
[in] | __gapth | Threshold of weighted gap frequency for ignoring alignment columns with too many gaps [0-1]. Set to 1.00 to keep all columns. This is implemented by using a very high regularization value for gap columns, and by excluding gap columns from the covariance matrix, see __apply_gapth. |
[in] | __mincontsep | Minimum sequence-wise contacting residue pair separation given in amino acids as (j-i). 1 for adjacent residues. [1-). |
[in] | __pseudocnt | Number to initialize single and pair amino acid counts with [0-). |
[in] | __pscnt_weight | Pseudocount weight to apply to single and pair amino acid frequencies [0-1]. |
[in] | __estimate_ivcov | Estimate inverse covariance matrix instead of fully inverting matrix. This is currently done by GLASSOFAST. |
[in] | __shrink_lambda | Covariance matrix shrinkage parameter, controlling rate of shrinkage [0-1]. |
[in] | __cov20 | Leave one amino acid off the covariance matrix, making it non-overdetermined. |
[in] | __apply_gapth | When true, exclude residue columns and rows with a weighted gap frequency > __gapth from the covariance matrix. |
[in] | __rho | Initial value of Glasso regularization parameter. Negative values trigger an automatic choice for rho. |
[in] | __num_threads | Number of OpenMP threads, effective if non-zero. The default is as many threads as cores in host. Ineffective if library is not compiled with OMP support. |
[in] | __icme_timeout | Inverse covariance matrix estimation timeout in seconds. Default: 1800. Applied to each inversion call independently. |
[out] | __timing | Pointer to map of timing results for certain components of this method. Useful for debugging. Keys are: [num_threads|seqw|pairfreq|shrink|inv|all]. |
Definition at line 434 of file freecontact.cpp.
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inline |
Predict residue contacts.
Definition at line 231 of file freecontact.h.
predictor::cont_res_t freecontact::predictor::run | ( | const ali_t & | __ali, |
double | __clustpc, | ||
double | __density, | ||
double | __gapth, | ||
uint16_t | __mincontsep, | ||
double | __pseudocnt, | ||
double | __pscnt_weight, | ||
bool | __estimate_ivcov, | ||
double | __shrink_lambda, | ||
bool | __cov20, | ||
bool | __apply_gapth, | ||
double | __rho, | ||
bool | __veczw = true , |
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int | __num_threads = 0 , |
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time_t | __icme_timeout = 1800 , |
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time_res_t * | __timing = NULL |
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) |
Predict residue contacts.
Definition at line 971 of file freecontact.cpp.
bool freecontact::predictor::dbg |
Definition at line 168 of file freecontact.h.