Eric Coissac
f7e25b2082
Take care file format have change. You must use corresponding version of ecogrep You can use -t option to go back to the old format without tm computation git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@238 60f365c0-8329-0410-b2a4-ec073aeeaa1d
64 lines
1.7 KiB
C
64 lines
1.7 KiB
C
/*
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* nnparams.h
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* PHunterLib
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*
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* Nearest Neighbor Model Parameters
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*
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* Created by Tiayyba Riaz on 02/07/09.
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*
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*/
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#ifndef NNPARAMS_H_
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#define NNPARAMS_H_
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#include <math.h>
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#include <string.h>
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//#include "../libecoprimer/ecoprimer.h"
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// following defines to simplify coding...
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#define ndH(a,b,c,d) nparm->dH[(int)a][(int)b][(int)c][(int)d]
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#define ndS(a,b,c,d) nparm->dS[(int)a][(int)b][(int)c][(int)d]
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#define forbidden_enthalpy 1000000000000000000.0f
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#define R 1.987f
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#define SALT_METHOD_SANTALUCIA 1
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#define SALT_METHOD_OWCZARZY 2
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#define DEF_CONC_PRIMERS 0.0000008
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#define DEF_CONC_SEQUENCES 0
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#define DEF_SALT 0.05
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#define GETNUMCODE(a) bpencoder[a - 'A']
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#define GETREVCODE(a) 5-bpencoder[a - 'A']
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extern double forbidden_entropy;
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typedef struct CNNParams_st
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{
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double Ct1;
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double Ct2;
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double rlogc;
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double kplus;
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double kfac;
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int saltMethod;
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double gcContent;
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double new_TM;
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double dH[6][6][6][6]; // A-C-G-T + gap + initiation (dangling end, $ sign)
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double dS[6][6][6][6];
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}CNNParams, * PNNParams;
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void nparam_InitParams(PNNParams nparm, double c1, double c2, double kp, int sm);
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int nparam_CountGCContent(char * seq );
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double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
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double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
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double nparam_CalcTM(double entropy,double enthalpy);
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double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
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double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len);
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double nparam_GetInitialEntropy(PNNParams nparm) ;
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double calculateMeltingTemperatureBasic (char * seq);
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//void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options);
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#endif
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