64 lines
1.7 KiB
C
64 lines
1.7 KiB
C
|
/*
|
||
|
|
* nnparams.h
|
||
|
|
* PHunterLib
|
||
|
|
*
|
||
|
|
* Nearest Neighbor Model Parameters
|
||
|
|
*
|
||
|
|
* Created by Tiayyba Riaz on 02/07/09.
|
||
|
|
*
|
||
|
|
*/
|
||
|
|
|
||
|
|
#ifndef NNPARAMS_H_
|
||
|
|
#define NNPARAMS_H_
|
||
|
|
|
||
|
|
#include <math.h>
|
||
|
|
#include <string.h>
|
||
|
|
//#include "../libecoprimer/ecoprimer.h"
|
||
|
|
|
||
|
|
// following defines to simplify coding...
|
||
|
|
#define ndH(a,b,c,d) nparm->dH[(int)a][(int)b][(int)c][(int)d]
|
||
|
|
#define ndS(a,b,c,d) nparm->dS[(int)a][(int)b][(int)c][(int)d]
|
||
|
|
#define forbidden_enthalpy 1000000000000000000.0f
|
||
|
|
#define R 1.987f
|
||
|
|
#define SALT_METHOD_SANTALUCIA 1
|
||
|
|
#define SALT_METHOD_OWCZARZY 2
|
||
|
|
|
||
|
|
#define DEF_CONC_PRIMERS 0.0000008
|
||
|
|
#define DEF_CONC_SEQUENCES 0
|
||
|
|
#define DEF_SALT 0.05
|
||
|
|
|
||
|
|
#define GETNUMCODE(a) bpencoder[a - 'A']
|
||
|
|
#define GETREVCODE(a) 5-bpencoder[a - 'A']
|
||
|
|
|
||
|
|
|
||
|
|
extern double forbidden_entropy;
|
||
|
|
|
||
|
|
|
||
|
|
typedef struct CNNParams_st
|
||
|
|
{
|
||
|
|
double Ct1;
|
||
|
|
double Ct2;
|
||
|
|
double rlogc;
|
||
|
|
double kplus;
|
||
|
|
double kfac;
|
||
|
|
int saltMethod;
|
||
|
|
double gcContent;
|
||
|
|
double new_TM;
|
||
|
|
double dH[6][6][6][6]; // A-C-G-T + gap + initiation (dangling end, $ sign)
|
||
|
|
double dS[6][6][6][6];
|
||
|
|
}CNNParams, * PNNParams;
|
||
|
|
|
||
|
|
void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm);
|
||
|
|
int nparam_CountGCContent(char * seq );
|
||
|
|
double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
|
||
|
|
double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
|
||
|
|
double nparam_CalcTM(double entropy,double enthalpy);
|
||
|
|
double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
|
||
|
|
double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len);
|
||
|
|
|
||
|
|
double nparam_GetInitialEntropy(PNNParams nparm) ;
|
||
|
|
double calculateMeltingTemperatureBasic (char * seq);
|
||
|
|
//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
|
||
|
|
|
||
|
|
#endif
|