/* Last changed Time-stamp: <2008-06-27 17:21:42 ivo> */
/**
*** \file fold_vars.c
*** global variables to change behaviour of folding routines
*** Also there are some functions that make the live easier when
*** using functions of the Vienna RNA package
**/
#include
#include
#include "fold_vars.h"
int circ = 0;
int noGU = 0; /* GU not allowed at all */
int no_closingGU = 0; /* GU allowed only inside stacks */
int tetra_loop = 1; /* Fold with specially stable 4-loops */
int energy_set = 0; /* 0 = BP; 1=any with GC; 2=any with AU parameters */
int dangles = 2; /* use dangling end energies */
char *nonstandards = (char *)0; /* contains allowed non standard bases */
double temperature = 37.0;
int james_rule = 1; /* interior loops of size 2 get energy 0.8Kcal and
no mismatches (no longer used) */
int oldAliEn = 0; /* use old alifold-energies (without removing gaps) */
int ribo = 0; /* use ribosum instead of classic covariance term */
char *RibosumFile = NULL; /* TODO: compile ribosums into program
Warning: this variable will vanish */
int csv = 0; /*generate comma seperated output*/
bondT *base_pair = NULL;
FLT_OR_DBL *pr = NULL; /* base pairing prob. matrix */
int *iindx = NULL; /* pr[i,j] -> pr[iindx[i]-j] */
double pf_scale = -1; /* scaling factor to avoid floating point overflows */
int fold_constrained = 0; /* fold with constraints */
int do_backtrack = 1; /* calculate pair prob matrix in part_func() */
int noLonelyPairs = 0; /* avoid helices of length 1 */
char backtrack_type = 'F'; /* 'C' require (1,N) to be bonded;
'M' seq is part of s multi loop */
int *cut_points;
int *strand;
int gquad = 0; /* consider g-qudruplexes in the calculations */
PUBLIC char * option_string(void){
static char options[100];
*options = '\0';
if (noGU) strcat(options, "-noGU ");
if (no_closingGU) strcat(options, "-noCloseGU ");
if (!tetra_loop) strcat(options, "-4 ");
if (noLonelyPairs) strcat(options, "-noLP ");
if (fold_constrained) strcat(options, "-C ");
if (dangles!=1) sprintf(options+strlen(options), "-d%d ", dangles);
if (temperature!=37.0)
sprintf(options+strlen(options), "-T %f ", temperature);
return options;
}
PUBLIC void set_model_details(model_detailsT *md){
if(md){
md->dangles = dangles;
md->special_hp = tetra_loop;
md->noLP = noLonelyPairs;
md->noGU = noGU;
md->noGUclosure = no_closingGU;
md->logML = logML;
md->gquad = gquad;
}
}