libfreecontact 1.0.21
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Public Types | Public Member Functions | Public Attributes | List of all members
freecontact::predictor Class Reference

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_tfreq_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
 

Detailed Description

Protein residue contact predictor.

A sufficiently large multiple alignment is required for meaningful results.

Definition at line 160 of file freecontact.h.

Member Typedef Documentation

◆ cont_res_t

typedef std::map<std::string, std::vector<contact_t> > freecontact::predictor::cont_res_t

Definition at line 162 of file freecontact.h.

◆ freq_t

Definition at line 163 of file freecontact.h.

◆ freq_vec_t

Definition at line 165 of file freecontact.h.

◆ pairfreq_t

Definition at line 164 of file freecontact.h.

◆ time_res_t

typedef std::map<std::string, double> freecontact::predictor::time_res_t

Definition at line 166 of file freecontact.h.

Constructor & Destructor Documentation

◆ predictor()

freecontact::predictor::predictor ( bool  __dbg = false)
inline

Definition at line 169 of file freecontact.h.

◆ ~predictor()

virtual freecontact::predictor::~predictor ( )
inlinevirtual

Definition at line 170 of file freecontact.h.

Member Function Documentation

◆ get_seq_weights()

void freecontact::predictor::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.

Parameters
[out]__aliwVector of alignment sequence weights.
[out]__wtotTotal alignment weight.
[in]__aliInput alignment.
[in]__clustpcBLOSUM-style clustering similarity threshold [0-1].
[in]__veczwUse vectorized sequence weighting when available.
[in]__num_threadsNumber 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.

◆ run() [1/3]

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,
time_t  __icme_timeout = 1800,
time_res_t __timing = NULL 
)

Predict residue contacts.

Parameters
[in]__aliInput alignment.
[in]__aliwVector of alignment sequence weights. Obtain this with get_seq_weights().
[in]__wtotTotal weight of alignment. Obtain this with get_seq_weights().
[in]__densityTarget precision matrix density [0-1]. Set to 0 to not control density.
[in]__gapthThreshold 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]__mincontsepMinimum sequence-wise contacting residue pair separation given in amino acids as (j-i). 1 for adjacent residues. [1-).
[in]__pseudocntNumber to initialize single and pair amino acid counts with [0-).
[in]__pscnt_weightPseudocount weight to apply to single and pair amino acid frequencies [0-1].
[in]__estimate_ivcovEstimate inverse covariance matrix instead of fully inverting matrix. This is currently done by GLASSOFAST.
[in]__shrink_lambdaCovariance matrix shrinkage parameter, controlling rate of shrinkage [0-1].
[in]__cov20Leave one amino acid off the covariance matrix, making it non-overdetermined.
[in]__apply_gapthWhen true, exclude residue columns and rows with a weighted gap frequency > __gapth from the covariance matrix.
[in]__rhoInitial value of Glasso regularization parameter. Negative values trigger an automatic choice for rho.
[in]__num_threadsNumber 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_timeoutInverse covariance matrix estimation timeout in seconds. Default: 1800. Applied to each inversion call independently.
[out]__timingPointer to map of timing results for certain components of this method. Useful for debugging. Keys are: [num_threads|seqw|pairfreq|shrink|inv|all].
Returns
Map of vectors of predicted contacts. Key is contact score calculation method name: 'l1norm', 'MI' (mutual information), 'fro' (Frobenius norm after zero-sum gauge). Vectors may not contain all contact pairs. Contacts are ordered by residue index (i,j).

Definition at line 434 of file freecontact.cpp.

◆ run() [2/3]

cont_res_t freecontact::predictor::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 
)
inline

Predict residue contacts.

Definition at line 231 of file freecontact.h.

◆ run() [3/3]

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,
int  __num_threads = 0,
time_t  __icme_timeout = 1800,
time_res_t __timing = NULL 
)

Predict residue contacts.

Definition at line 971 of file freecontact.cpp.

Member Data Documentation

◆ dbg

bool freecontact::predictor::dbg

Definition at line 168 of file freecontact.h.


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