ViennaRNA-bindings-0.233.1.1: C/ViennaRNA/part_func_up.c
/*
partiton function for RNA secondary structures
Ivo L Hofacker
Vienna RNA package
*/
/*
$Log: part_func_up.c,v $
Revision 1.4 2008/07/04 14:27:36 ivo
Modify output (again)
Revision 1.3 2008/05/08 14:11:55 ivo
minor output changes
Revision 1.2 2007/12/13 10:19:54 ivo
major RNAup update from Ulli
Revision 1.1 2007/04/30 15:13:13 ivo
merge RNAup into package
Revision 1.11 2006/07/17 11:11:43 ulim
removed all globals from fold_vars.h,c, cleaned code
Revision 1.10 2006/07/12 09:19:29 ulim
global variables w, incr3 and incr5 are now local
Revision 1.9 2006/07/11 12:45:02 ulim
remove redundancy in function pf_interact(...)
Revision 1.8 2006/03/08 15:26:37 ulim
modified -o[1|2], added meaningful default
Revision 1.5 2006/01/23 11:27:04 ulim
include file into new package version. cleaned it
Revision 1.2 2005/07/29 15:13:37 ulim
put the function, calculating the probability of an unpaired region in
an RNA and the function calculating the prob. of interaction between 2 RNAs
in a seperate file (pf_two.c)
Revision 1.1 2005/07/26 13:27:12 ulim
Initial revision
Revision 1.2 2005/07/01 13:14:57 ulim
fixed error in scaling, included new commandline options -incr5, -incr3 to
allow a variable number of unpaired positions 5' and 3' of the site of
interaction between the two RNAs
Revision 1.1 2005/04/19 08:16:38 ulim
Initial revision
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <float.h> /* #defines FLT_MAX ... */
#include <unistd.h>
#include "ViennaRNA/fold.h"
#include "ViennaRNA/utils.h"
#include "ViennaRNA/energy_par.h"
#include "ViennaRNA/fold_vars.h"
#include "ViennaRNA/pair_mat.h"
#include "ViennaRNA/params.h"
#include "ViennaRNA/part_func.h"
#include "ViennaRNA/loop_energies.h"
#include "ViennaRNA/part_func_up.h"
#include "ViennaRNA/duplex.h"
#define CO_TURN 0
#define ZERO(A) (fabs(A) < DBL_EPSILON)
#define EQUAL(A,B) (fabs((A)-(B)) < 1000*DBL_EPSILON)
#define ISOLATED 256.0
/* #define NUMERIC 1 */
/*
#################################
# GLOBAL VARIABLES #
#################################
*/
/*
#################################
# PRIVATE VARIABLES #
#################################
*/
PRIVATE short *S=NULL, *S1=NULL, *SS=NULL, *SS2=NULL;
PRIVATE vrna_exp_param_t *Pf = NULL;/* use this structure for all the exp-arrays*/
PRIVATE FLT_OR_DBL *qb=NULL, *qm=NULL, *prpr=NULL; /* add arrays for pf_unpaired()*/
PRIVATE FLT_OR_DBL *probs=NULL;
PRIVATE FLT_OR_DBL *q1k=NULL, *qln=NULL;
PRIVATE double *qqm2=NULL, *qq_1m2=NULL, *qqm=NULL, *qqm1=NULL;
PRIVATE FLT_OR_DBL *scale=NULL, *expMLbase=NULL;
PRIVATE char *ptype=NULL; /* precomputed array of pair types */
PRIVATE int init_length; /* length in last call to init_pf_fold()*/
PRIVATE double init_temp; /* temperature in last call to scale_pf_params */
PRIVATE int *my_iindx = NULL;
/* make iptypes array for intermolecular constrains (ipidx for indexing)*/
/*
#################################
# PRIVATE FUNCTION DECLARATIONS #
#################################
*/
PRIVATE pu_out *get_u_vals(pu_contrib *p_c,
int **unpaired_values,
char *select_contrib);
PRIVATE int plot_free_pu_out( pu_out* res,
interact *pint,
char *ofile,
char *head);
PRIVATE void scale_stru_pf_params(unsigned int length);
PRIVATE void init_pf_two(int length);
PRIVATE void scale_int(const char *s,
const char *sl,
double *sc_int);
PRIVATE void encode_seq( const char *s1,
const char *s2);
PRIVATE constrain *get_ptypes_up(char *S,
const char *structure);
PRIVATE void get_up_arrays(unsigned int length);
PRIVATE void free_up_arrays(void);
PRIVATE void set_encoded_seq(const char *sequence,
short **S,
short **S1);
PRIVATE void get_interact_arrays(unsigned int n1,
unsigned int n2,
pu_contrib *p_c,
pu_contrib *p_c2,
int w,
int incr5,
int incr3,
double ***p_c_S,
double ***p_c2_S);
/*
#################################
# BEGIN OF FUNCTION DEFINITIONS #
#################################
*/
PUBLIC pu_contrib *get_pu_contrib_struct(unsigned int n, unsigned int w){
unsigned int i;
pu_contrib *pu = (pu_contrib *)vrna_alloc(sizeof(pu_contrib));
pu->length = n;
pu->w = w;
/* contributions to probability of being unpaired witihin a(n)
H hairpin,
I interior loop,
M muliloop,
E exterior loop*/
/* pu_test->X[i][j] where i <= j and i [1...n], j = [1...w[ */
pu->H = (double **)vrna_alloc(sizeof(double *) * (n + 1));
pu->I = (double **)vrna_alloc(sizeof(double *) * (n + 1));
pu->M = (double **)vrna_alloc(sizeof(double *) * (n + 1));
pu->E = (double **)vrna_alloc(sizeof(double *) * (n + 1));
for(i=0;i<=n;i++){
pu->H[i] = (double *)vrna_alloc(sizeof(double) * (w + 1));
pu->I[i] = (double *)vrna_alloc(sizeof(double) * (w + 1));
pu->M[i] = (double *)vrna_alloc(sizeof(double) * (w + 1));
pu->E[i] = (double *)vrna_alloc(sizeof(double) * (w + 1));
}
return pu;
}
PUBLIC void
free_pu_contrib(pu_contrib *pu){
free_pu_contrib_struct(pu);
}
PUBLIC void
free_pu_contrib_struct(pu_contrib *pu){
unsigned int i;
if(pu != NULL){
for(i=0;i<=pu->length;i++){
free(pu->H[i]);
free(pu->I[i]);
free(pu->M[i]);
free(pu->E[i]);
}
free(pu->H);
free(pu->I);
free(pu->M);
free(pu->E);
free(pu);
}
}
/* you have to call pf_fold(sequence, structure); befor pf_unstru */
PUBLIC pu_contrib *pf_unstru(char *sequence, int w){
int n, i, j, v, k, l, o, p, ij, kl, po, u, u1, d, type, type_2, tt;
unsigned int size;
double temp, tqm2;
double qbt1, *tmp, sum_l, *sum_M;
double *store_H, *store_Io, **store_I2o; /* hairp., interior contribs */
double *store_M_qm_o,*store_M_mlbase; /* multiloop contributions */
pu_contrib *pu_test;
sum_l = 0.0;
temp = 0;
n = (int) strlen(sequence);
sum_M = (double *) vrna_alloc((n+1) * sizeof(double));
pu_test = get_pu_contrib_struct((unsigned)n, (unsigned)w);
size = ((n+1)*(n+2))>>1;
get_up_arrays((unsigned) n);
init_pf_two(n);
/* init everything */
for (d=0; d<=TURN; d++)
for (i=1; i<=n-d; i++){
j=i+d;
ij = my_iindx[i]-j;
if(d < w) {
pu_test->H[i][d]=pu_test->I[i][d]=pu_test->M[i][d]=pu_test->E[i][d]=0.;
}
}
for (i=0; i<size; i++)
prpr[i]= probs[i];
sum_M[0] = 0.;
for (i=1; i<=n; i++){
/* set auxillary arrays to 0, reuse qqm and qqm1, reuse qqm2 and qq_1m2*/
sum_M[i] = qqm[i] = qqm1[i] = qqm2[i] = qq_1m2[i] = 0;
for (j=i+TURN+1; j<=n; j++){
ij = my_iindx[i]-j;
/* i need the part_func of all structures outside bp[ij] */
if(qb[ij] > 0.0) prpr[ij]= (probs[ij]/qb[ij]);
}
}
/* alloc even more memory */
store_I2o = (double **)vrna_alloc(sizeof(double *) * (n + 1)); /* for p,k */
for(i=0;i<=n;i++)
store_I2o[i] = (double *)vrna_alloc(sizeof(double) * (MAXLOOP + 2));
/* expMLbase[i-p]*dangles_po */
store_M_mlbase = (double *)vrna_alloc(sizeof(double) * (size + 1));
/* 2. exterior bp (p,o) encloses unpaired region [i,i+w[*/
for (o=TURN+2;o<=n; o++) {
double sum_h;
/*allocate space for arrays to store different contributions to H, I & M */
store_H = (double *)vrna_alloc(sizeof(double) * (o+2));
/* unpaired between ]l,o[ */
store_Io = (double *)vrna_alloc(sizeof(double) * (o+2));
/* qm[p+1,i-1]*dangles_po */
store_M_qm_o = (double *)vrna_alloc(sizeof(double) * (n+1));
for (p=o-TURN-1; p>=1; p--) {
/* construction of partition function of segment [p,o], given that
an unpaired region [i,i+w[ exists within [p,o] */
u = o-p-1;
po = my_iindx[p]-o;
type = ptype[po];
if(type){
/*hairpin contribution*/
if (((type==3)||(type==4))&&no_closingGU)
temp = 0.;
else
temp = prpr[po] * exp_E_Hairpin(u, type, S1[p+1], S1[o-1], sequence+p-1, Pf) * scale[u+2];
/* all H contribs are collect for the longest unpaired region */
store_H[p+1] = temp;
/* interior loops with interior pair k,l and an unpaired region of
length w between p and k || l and o*/
for (k=p+1; k<=MIN2(p+MAXLOOP+1,o-TURN-2); k++) {
u1 = k-p-1;
sum_l = 0.;
for (l=MAX2(k+TURN+1,o-1-MAXLOOP+u1); l<o; l++) {
kl = my_iindx[k]-l;
type_2 = ptype[kl];
if((l+1) < o) store_Io[l+1] += sum_l;
temp=0.;
if (type_2){
type_2 = rtype[type_2];
temp = prpr[po] * qb[kl] * exp_E_IntLoop(u1, o-l-1, type, type_2, S1[p+1], S1[o-1], S1[k-1], S1[l+1], Pf) *scale[u1+o-l+1];
if((l+1) < o) store_Io[l+1] += temp; /* unpaired region between ]l,o[ */
sum_l += temp;
} /* end of if pair(k,l) */
} /* end of l */
/* unpaired in region ]p,k[ */
for(i=p+1;i <= k-1;i++)
store_I2o[i][MIN2(w-1,k-i-1)] += sum_l;
} /* end of k */
} /*end of if(type) test for bp (p,o) */
/* multiple stem loop contribution
calculate qm2[my_iindx[i]-j] in the course of the calculation
of the multiple stem loop contribution:
advantage: you save memory:
instead of a (n+1)*n array for qqm2 you only need 2*n arrays
disadvantage: you have to use two times the op-loop for the full
multiloop contribution
first op-loop: index o goes from 1...n and
index p from o-TURN-1 ... 1
second op-loop: index o goes from n...1 and
index p from o+TURN+1 ... n !!
HERE index o goes from 1...n and index p o-TURN-1 ... 1 ,
we calculate the contributions to multiple stem loop
where exp(i+w-1-p)*(qqm2 values between i+w and o-1)
AND qm[iindex[p+1]-(i-1)]*exp(beta*w)*qm[iindex[i+w]-(o-1)]
you have to recalculate of qqm matrix containing final stem
contributions to multiple loop partition function
from segment p,o */
/* recalculate qqm[]
qqm[p] := (contribution with exact one loop in region (p,o)*/
qqm[p] = qqm1[p] * expMLbase[1];
if(type){
qbt1 = qb[po] * exp_E_MLstem(type, (p>1) ? S1[p-1] : -1, (o<n) ? S1[o+1] : -1, Pf);
qqm[p] += qbt1;
/* reverse dangles for prpr[po]*... */
temp = 0.;
tt = rtype[type];
temp = prpr[po] * exp_E_MLstem(tt, S1[o-1], S1[p+1], Pf) * scale[2] * Pf->expMLclosing;
for(i=p+1; i < o; i++) {
int p1i = (p+1) < (i-1) ? my_iindx[p+1]-(i-1) : 0;
/*unpaired region expMLbase[i-p] left of structured
region qq_1m2[i+1]*/
/* @expMLbase: note distance of i-p == i-(p+1)+1 */
store_M_mlbase[my_iindx[p+1]-i] += expMLbase[i-p] * temp * qq_1m2[i+1];
/* structured region qm[p1i] left of unpaired region */
/* contribition for unpaired region is added after the p-loop */
store_M_qm_o[i] += qm[p1i] * temp;
} /*end of for i ... */
}
for(tqm2 = 0., i=p+1; i < o; i++)
tqm2 += qm[my_iindx[p]-i] * qqm[i+1];
/* qqm2[p] contrib with at least 2 loops in region (p,o) */
qqm2[p] = tqm2;
} /* end for (p=..) */
for(sum_h = 0., i=1; i < o; i++) {
int max_v, vo;
sum_h += store_H[i];
max_v = MIN2(w-1,o-i-1);
for(v=max_v; v >= 0; v--){
/* Hairpins */
pu_test->H[i][v] += sum_h;/* store_H[i][v] + store_H[i][max_v]; */
/* Interior loops: unpaired region between ]l,o[ calculated here !*/
/* unpaired region between ]p,k[ collected after after o-loop */
if(v <= MIN2(max_v,MAXLOOP)) {
pu_test->I[i][v] += store_Io[i]; /* ]l,o[ */
}
/* Multiloops:*/
/* unpaired region [i,v] between structured regions ]p,i[ and ]v,o[. */
/* store_M_qm_o[i] = part. funct over all structured regions ]p,i[ */
vo = (i+v+1) <= (o-1) ? my_iindx[i+v+1]-(o-1): 0;
pu_test->M[i][v] += store_M_qm_o[i]*expMLbase[v+1]*qm[vo];
}
}
tmp = qqm1; qqm1=qqm; qqm=tmp;
tmp = qqm2; qqm2=qq_1m2; qq_1m2=tmp;
free(store_Io);
free(store_H);
free(store_M_qm_o);
}/* end for (o=..) */
for(i=1; i < n; i++) {
int max_v;
double sum_iv;
sum_iv = 0.;
max_v = MIN2(w-1,n-i);
for(v=n; v >=0; v--) {
if(v <= MIN2(max_v,MAXLOOP)) {
/* all unpaired regions [i,v] between p and k in interior loops */
/* notice v runs from max_v -> 0, sum_iv sums all int. l. contribs */
/* for each x, v < x =< max_v, since they contribute to [i,v] */
sum_iv += store_I2o[i][v];
pu_test->I[i][v] += sum_iv;
}
/* all unpaired region [i,v] for a fixed v, given that */
/* region ]v,o[ contains at least 2 structures qq_1m2[v+1]; */
if(v >= i) {
sum_M[v] += store_M_mlbase[my_iindx[i]-v];
if(v-i<=max_v) {
pu_test->M[i][v-i] += sum_M[v];
}
}
}
}
for(i=0;i<=n;i++) {
free(store_I2o[i]);
}
free(store_I2o);
for (i=1; i<=n; i++) {
/* set auxillary arrays to 0 */
qqm[i] = qqm1[i] = qqm2[i] = qq_1m2[i] = 0;
}
/* 2. exterior bp (p,o) encloses unpaired region [i,j]
HERE index o goes from n...1 and index p from o+TURN+1 ... n,
that is, we add the one multiloop contribution that we
could not calculate before */
/* is free'ing plus allocating faster than looping over all entries an setting them to 0? */
#if 0
free(store_M_mlbase);
store_M_mlbase = (double *) vrna_alloc(sizeof(double) * (size + 1));
#else
/* this should be the fastest way to set everything to 0 */
memset(store_M_mlbase, 0, sizeof(double) * (size + 1));
#endif
for (o=n-TURN-1;o>=1; o--) {
for (p=o+TURN+1; p<=n; p++) {
po = my_iindx[o]-p;
type = ptype[po];
/* recalculate of qqm matrix containing final stem
contributions to multiple loop partition function
from segment [o,p] */
qqm[p] = qqm1[p] * expMLbase[1];
if (type) {
qbt1 = qb[po];
qbt1 *= exp_E_MLstem(type, (o>1) ? S1[o-1] : -1, (p<n) ? S1[p+1] : -1, Pf);
qqm[p] += qbt1;
/* revers dangles for prpr[po]... */
temp=0.;
tt=rtype[type];
temp = prpr[po]*exp_E_MLstem(tt, S1[p-1], S1[o+1], Pf) * Pf->expMLclosing * scale[2];
}
tqm2=0.;
for(i=o+1; i < p; i++) {
tqm2+=qqm[i]*qm[my_iindx[i+1]-p];
if(type !=0) {
/* structured region qq_1m2[i-1] left of unpaired r. expMLbase[p-i]*/
/* @expMLbase: note distance of p-i == p+1-i+1 */
store_M_mlbase[my_iindx[i]-p+1] += qq_1m2[i-1]*expMLbase[p-i]*temp;
}
}/*end of for i ....*/
qqm2[p] = tqm2;
}/* end for (p=..) */
tmp = qqm1; qqm1=qqm; qqm=tmp;
tmp = qqm2; qqm2=qq_1m2; qq_1m2=tmp;
}/* end for (o=..) */
/* now collect the missing multiloop contributions */
for(i=0;i<=n;i++) { sum_M[i]=0.; }
for(i=1; i<=n;i++) {
int v_max = MIN2(w-1,n-i);
for(v=n; v>=i; v--){
sum_M[i] += store_M_mlbase[my_iindx[i]-v];
if ((v-i <= v_max) ) {
pu_test->M[i][v-i] += sum_M[i];
}
}
}
/* 1. region [i,j] exterior to all loops */
for (i=1; i<=n; i++) {
for(j=i; j<MIN2(i+w,n+1);j++){
ij=my_iindx[i]-j;
temp=q1k[i-1]*1*scale[j-i+1]*qln[j+1]/q1k[n];
pu_test->E[i][j-i]+=temp;
}
}
free(sum_M);
free(store_M_mlbase);
free_up_arrays();
return pu_test;
}
PRIVATE void get_interact_arrays(unsigned int n1,
unsigned int n2,
pu_contrib *p_c,
pu_contrib *p_c2,
int w,
int incr5,
int incr3,
double ***p_c_S,
double ***p_c2_S){
unsigned int i;
int pc_size, j;
*p_c_S = (double **)vrna_alloc(sizeof(double *)*(n1+1));
for (i=1; i<=n1; i++){
pc_size = MIN2((w + incr5 + incr3), (int)n1);
(*p_c_S)[i] = (double *)vrna_alloc(sizeof(double) * (pc_size + 1));
for (j=0; j < pc_size; j++)
(*p_c_S)[i][j] = p_c->H[i][j] + p_c->I[i][j] + p_c->M[i][j] + p_c->E[i][j];
}
if(p_c2 != NULL){
(*p_c2_S) = (double **)vrna_alloc(sizeof(double *) * (n2 + 1));
for (i=1; i<=n2; i++){
pc_size = MIN2(w, (int)n2);
(*p_c2_S)[i] = (double *)vrna_alloc(sizeof(double) * (pc_size + 2));
for (j=0; j < pc_size; j++)
(*p_c2_S)[i][j] = p_c2->H[i][j] + p_c2->I[i][j] + p_c2->M[i][j] + p_c2->E[i][j];
}
}
}
/*------------------------------------------------------------------------*/
/* s1 is the longer seq */
PUBLIC interact *pf_interact( const char *s1,
const char *s2,
pu_contrib *p_c,
pu_contrib *p_c2,
int w,
char *cstruc,
int incr3,
int incr5){
int i, j, k,l,n1,n2,add_i5,add_i3, pc_size;
double temp, Z, rev_d, E, Z2,**p_c_S, **p_c2_S, int_scale;
FLT_OR_DBL ****qint_4, **qint_ik;
/* PRIVATE double **pint; array for pf_up() output */
interact *Int;
double G_min, G_is,Gi_min;
int gi,gj,gk,gl,ci,cj,ck,cl,prev_k,prev_l;
FLT_OR_DBL **int_ik;
double Z_int, temp_int, temppfs;
double const_scale, const_T;
constrain *cc = NULL; /* constrains for cofolding */
char *Seq, *i_long,*i_short,*pos=NULL; /* short seq appended to long one */
/* int ***pu_jl; */ /* positions of interaction in the short RNA */
G_min = G_is = Gi_min = 100.0;
gi = gj = gk = gl = ci = cj = ck = cl = 0;
n1 = (int) strlen(s1);
n2 = (int) strlen(s2);
prev_k = 1;
prev_l = n2;
i_long = (char *) vrna_alloc(sizeof(char)*(n1+1));
i_short = (char *) vrna_alloc(sizeof(char)*(n2+1));
Seq = (char *) vrna_alloc(sizeof(char)*(n1+n2+2));
strcpy(Seq,s1);
strcat(Seq,s2);
set_encoded_seq(s1, &S, &S1);
set_encoded_seq(s2, &SS, &SS2);
cc = get_ptypes_up(Seq,cstruc);
get_interact_arrays(n1, n2, p_c, p_c2, w, incr5, incr3, &p_c_S, &p_c2_S);
/*array for pf_up() output */
Int = (interact *) vrna_alloc(sizeof(interact)*1);
Int->Pi = (double *) vrna_alloc(sizeof(double)*(n1+2));
Int->Gi = (double *) vrna_alloc(sizeof(double)*(n1+2));
/* use a different scaling for pf_interact*/
scale_int(s2, s1, &int_scale);
/* set the global scale array and the global variable pf_scale to the
values used to scale the interaction, keep their former values !! */
temppfs = pf_scale;
pf_scale = int_scale;
/* in order to scale expLoopEnergy correctly call*/
/* we also pass twice the seq-length to avoid bogus access to scale[] array */
scale_stru_pf_params((unsigned) 2*n1);
qint_ik = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *) * (n1+1));
for (i=1; i<=n1; i++) {
qint_ik[i] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n1+1));
}
/* int_ik */
int_ik = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *) * (n1+1));
for (i=1; i<=n1; i++) {
int_ik[i] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n1+1));
}
Z_int=0.;
/* Gint = ( -log(int_ik[gk][gi])-( ((int) w/2)*log(pf_scale)) )*((Pf->temperature+K0)*GASCONST/1000.0); */
const_scale = ((int) w/2)*log(pf_scale);
const_T = (Pf->kT/1000.0);
encode_seq(s1, s2);
/* static short *S~S1, *S1~SS1, *SS~S2, *SS2; */
for (i=0; i<=n1; i++) {
Int->Pi[i]=Int->Gi[i]=0.;
}
E=0.;
Z=0.;
if ( fold_constrained && cstruc != NULL) {
pos = strchr(cstruc,'|');
if(pos) {
ci=ck=cl=cj=0;
/* long seq & short seq
.........||..|||||....&....||||... w = maximal interaction length
ck ci cj cl */
strncpy(i_long,cstruc,n1);
i_long[n1] = '\0';
strncpy(i_short,&cstruc[n1],n2);
i_short[n2] ='\0';
pos = strchr(i_long,'|');
if(pos) ck = (int) (pos-i_long)+1; /* k */
pos = strrchr(i_long,'|');
if(pos) ci = (int) (pos-i_long)+1; /* i */
pos = strrchr(i_short,'|');
if(pos) cl = (int) (pos-i_short)+1; /* l */
pos = strchr(i_short,'|');
if(pos) cj = (int) (pos-i_short)+1; /* j */
if(ck > 0 && ci > 0 && ci-ck+1 > w) {
vrna_message_warning("distance between constrains in longer seq, %d, larger than -w = %d",ci-ck+1,w);
vrna_message_error("pf_interact: could not satisfy all constraints");
}
if(cj > 0 && cl > 0 && cl-cj+1 > w) {
vrna_message_warning("distance between constrains in shorter seq, %d, larger than -w = %d",cl-cj+1,w);
vrna_message_error("pf_interact: could not satisfy all constraints");
}
}
} else if ( fold_constrained && cstruc == NULL) {
vrna_message_error("option -C selected, but no constrained structure given\n");
}
if(fold_constrained) pos = strchr(cstruc,'|');
/* qint_4[i][j][k][l] contribution that region (k-i) in seq1 (l=n1)
is paired to region (l-j) in seq 2(l=n2) that is
a region closed by bp k-l and bp i-j */
qint_4 = (FLT_OR_DBL ****) vrna_alloc(sizeof(FLT_OR_DBL ***) * (n1+1));
/* qint_4[i][j][k][l] */
for (i=1; i<=n1; i++) {
int end_k;
end_k = i-w;
if(fold_constrained && pos && ci) end_k= MAX2(i-w, ci-w);
/* '|' constrains for long sequence: index i from 1 to n1 (5' to 3')*/
/* interaction has to include 3' most '|' constrain, ci */
if(fold_constrained && pos && ci && i==1 && i<ci)
i= ci-w+1 > 1 ? ci-w+1 : 1;
/* interaction has to include 5' most '|' constrain, ck*/
if(fold_constrained && pos && ck && i > ck+w-1) break;
/* note: qint_4[i] will be freed before we allocate qint_4[i+1] */
qint_4[i] = (FLT_OR_DBL ***) vrna_alloc(sizeof(FLT_OR_DBL **) * (n2+1));
for (j=n2; j>0; j--) {
qint_4[i][j] = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL*) * (w+1));
for (k=0; k<=w; k++) {
qint_4[i][j][k] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (w+1));
}
}
prev_k=1;
for (j=n2; j>0; j--) {
int type, type2,end_l;
end_l = j+w;
if(fold_constrained && pos && ci) end_l= MIN2(cj+w,j+w);
/* '|' constrains for short sequence: index j from n2 to 1 (3' to 5')*/
/* interaction has to include 5' most '|' constrain, cj */
if(fold_constrained && pos && cj && j==n2 && j>cj)
j = cj+w-1 > n2 ? n2 : cj+w-1;
/* interaction has to include 3' most '|' constrain, cl*/
if(fold_constrained && pos && cl && j < cl-w+1) break;
type = cc->ptype[cc->indx[i]-(n1+j)];
qint_4[i][j][0][0] = type ? Pf->expDuplexInit : 0;
if (!type) continue;
qint_4[i][j][0][0] *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, Pf);
rev_d = exp_E_ExtLoop(rtype[type], (j>1) ? SS2[j-1] : -1, (i<n1) ? S1[i+1] : -1, Pf);
/* add inc5 and incr3 */
if((i-incr5) > 0 ) add_i5=i-incr5;
else add_i5=1;
add_i3=incr3;
pc_size = MIN2((w+incr3+incr5),n1);
if(incr3 < pc_size) add_i3=incr3;
else add_i3=pc_size-1;
/* only one bp (no interior loop) */
if(p_c2 == NULL) {/* consider only structure of longer seq. */
qint_ik[i][i]+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*scale[((int) w/2)];
Z+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*scale[((int) w/2)];
} else {/* consider structures of both seqs. */
qint_ik[i][i]+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*p_c2_S[j][0]*scale[((int) w/2)];
Z+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*p_c2_S[j][0]*scale[((int) w/2)];
}
/* int_ik */
/* check deltaG_ges = deltaG_int + deltaG_unstr; */
int_ik[i][i]+=qint_4[i][j][0][0]*rev_d*scale[((int) w/2)];
Z_int+=qint_4[i][j][0][0]*rev_d*scale[((int) w/2)];
temp_int=0.;
temp=0.;
prev_l = n2;
for (k=i-1; k>end_k && k>0; k--) {
if (fold_constrained && pos && cstruc[k-1] == '|' && k > prev_k)
prev_k=k;
for (l=j+1; l< end_l && l<=n2; l++) {
int a,b,ia,ib,isw;
double scalew, tt, intt;
type2 = cc->ptype[cc->indx[k]-(n1+l)];
/* '|' : l HAS TO be paired: not pair (k,x) where x>l allowed */
if(fold_constrained && pos && cstruc[n1+l-1] == '|' && l < prev_l)
prev_l=l; /*break*/
if(fold_constrained && pos && (k<=ck || i>=ci) && !type2) continue;
if(fold_constrained && pos && ((cstruc[k-1] == '|') || (cstruc[n1+l-1] == '|')) && !type2) break;
if (!type2) continue;
/* to save memory keep only qint_4[i-w...i][][][] in memory
use indices qint_4[i][j][a={0,1,...,w-1}][b={0,1,...,w-1}] */
a=i-k;/* k -> a from 1...w-1*/
b=l-j;/* l -> b from 1...w-1 */
/* scale everything to w/2 */
isw = ((int) w/2);
if ((a+b) < isw ){
scalew = ( scale[isw - (a+b)] );
} else if ( (a+b) > isw ) {
scalew = 1/( scale[(a+b) - isw] );
} else {
scalew = 1;
}
if (i-k+l-j-2<=MAXLOOP) {
if(k >= prev_k && l <= prev_l) { /* don't violate constrains */
E = exp_E_IntLoop(i-k-1,l-j-1, type2, rtype[type],
S1[k+1], SS2[l-1], S1[i-1], SS2[j+1], Pf) *
scale[i-k+l-j]; /* add *scale[u1+u2+2] */
qint_4[i][j][a][b] += ( qint_4[k][l][0][0]*E);
/* use ia and ib to go from a....w-1 and from b....w-1 */
ia=ib=1;
while((a+ia)<w && i-(a+ia)>=1 && (b+ib)<w && (j+b+ib)<=n2) {
int iaa,ibb;
qint_4[i][j][a+ia][b+ib] += qint_4[k][l][ia][ib]*E;
iaa=ia+1;
while(a+iaa<w && i-(a+iaa)>=1) {
qint_4[i][j][a+iaa][b+ib] += qint_4[k][l][iaa][ib]*E;
++iaa;
}
ibb=ib+1;
while( (b+ibb)<w && (j+b+ibb)<=n2 ) {
qint_4[i][j][a+ia][b+ibb] += qint_4[k][l][ia][ibb]*E;
++ibb;
}
++ia;
++ib;
}
}
}
/* '|' constrain in long sequence */
/* collect interactions starting before 5' most '|' constrain */
if ( fold_constrained && pos && ci && i < ci) continue;
/* collect interactions ending after 3' most '|' constrain*/
if ( fold_constrained && pos && ck && k > ck) continue;
/* '|' constrain in short sequence */
/* collect interactions starting before 5' most '|' constrain */
if ( fold_constrained && pos && cj && j > cj) continue;
/* collect interactions ending after 3' most '|' constrain*/
if ( fold_constrained && pos && cl && l < cl) continue;
/* scale everything to w/2*/
/* qint_ik[k][i] all interactions where k and i both are paired */
/* substract incr5 from k */
if(k-incr5 > 0) add_i5=k-incr5;
else add_i5=1;
/* add incr3 to i */
pc_size = MIN2((w+incr3+incr5),n1);
if(i-k+incr3 < pc_size) add_i3=i-k+incr3;
else add_i3=pc_size-1;
if(p_c2 == NULL) {/* consider only structure of longer seq. */
tt = qint_4[i][j][a][b]*p_c_S[add_i5][add_i3]*scalew*rev_d;
} else { /* consider structures of both seqs. */
tt = qint_4[i][j][a][b]*p_c_S[add_i5][add_i3]*p_c2_S[j][b]*scalew*rev_d;
}
temp+= tt;
qint_ik[k][i]+= tt;
/* int_ik */
/* check deltaG_ges = deltaG_int + deltaG_unstr; */
intt = qint_4[i][j][a][b]*scalew*rev_d;
temp_int += intt;
int_ik[k][i]+= intt;
G_is = (-log(tt)-const_scale)*(const_T);
if (G_is < G_min || EQUAL(G_is,G_min)) {
G_min = G_is;
Gi_min =(-log(intt)-const_scale)*(const_T);
gi=i;
gj=j;
gk=k;
gl=l;
}
}
}
Z+=temp;
/* int_ik */
Z_int+=temp_int;
}
/* free qint_4 values not needed any more */
if(i > w) {
int bla;
bla=i-w;
if (fold_constrained && pos && ci && i-w < ci-w+1) continue;
if (fold_constrained && pos && ci) bla = MAX2(ci-w+1,i-w);
for (j=n2; j>0; j--) {
for (k=0; k<=w; k++){
free(qint_4[bla][j][k]);
}
free(qint_4[bla][j]);
}
free(qint_4[bla]);
qint_4[bla] = NULL;
}
}
Z2=0.0;
for (i=1; i<=n1; i++) {
for (k=i; k<=n1 && k<i+w; k++) {
Z2+=qint_ik[i][k];
for(l=i;l<=k;l++) {
/* Int->Pi[l]: prob that position l is within a paired region */
/* qint_ik[i][k] as well as Z are scaled to scale[((int) w/2) */
Int->Pi[l]+=qint_ik[i][k]/Z;
/* Int->Gi[l]: minimal delta G at position [l] */
Int->Gi[l]=MIN2(Int->Gi[l],
( -log(qint_ik[i][k])-( ((int) w/2)*log(pf_scale)) )*
(Pf->kT/1000.0) );
}
}
}
if(n1 > w){
int start_i,end_i;
start_i = n1-w+1;
end_i=n1;
if (fold_constrained && pos && ci) {
/* a break in the k loop might result in unfreed values */
start_i = ci-w+1 < n1-w+1 ? ci-w+1 : n1-w+1;
start_i = start_i > 0 ? start_i : 1;
/* start_i = ck; */
end_i = ck+w-1 > n1 ? n1 : ck+w-1;
}
for (i=start_i; i<=end_i; i++) {
if(qint_4[i] == NULL ) continue;
for (j=n2; j>0; j--) {
for (k=0; k<=w; k++) {
free(qint_4[i][j][k]);
}
free(qint_4[i][j]);
}
free(qint_4[i]);
}
free(qint_4);
} else {
int start_i,end_i;
start_i = 1;
end_i=n1;
if (fold_constrained && pos) {
start_i = ci-w+1 > 0 ? ci-w+1 : 1;
end_i = ck+w-1 > n1 ? n1 : ck+w-1;
}
for (i=start_i; i<=end_i; i++) {
for (j=n2; j>0; j--) {
for (k=0; k<=w; k++) {
free(qint_4[i][j][k]);
}
free(qint_4[i][j]);
}
free(qint_4[i]);
}
free(qint_4);
}
if(fold_constrained && (gi==0 || gk==0 || gl==0 || gj==0)) {
vrna_message_error("pf_interact: could not satisfy all constraints");
}
/* fill structure interact */
Int->length = n1;
Int->i = gi;
Int->j = gj;
Int->k = gk;
Int->l = gl;
Int->Gikjl = G_min;
Int->Gikjl_wo = Gi_min;
free(i_long);
free(i_short);
for (i=1; i<=n1; i++) {
free(int_ik[i]);
}
free(int_ik);
for (i=1; i<=n1; i++) {
free(qint_ik[i]);
}
free(qint_ik);
/* reset the global variables pf_scale and scale to their original values */
pf_scale = temppfs;/* reset pf_scale */
scale_stru_pf_params((unsigned) n1);/* reset the scale array */
free_pf_arrays(); /* for arrays for pf_fold(...) */
if(expMLbase != NULL) {
free(expMLbase);
expMLbase = NULL;
}
if(scale != NULL) {
free(scale);
scale = NULL;
}
for (i=1; i<=n1; i++) {
free(p_c_S[i]);
}
free(p_c_S);
if(p_c2 != NULL) {
for (i=1; i<=n2; i++) {
free(p_c2_S[i]);
}
free(p_c2_S);
}
free(Seq);
free(cc->indx);
free(cc->ptype);
free(cc);
return(Int);
}
/*------------------------------------------------------------------------*/
/* use an extra scale for pf_interact, here sl is the longer sequence */
PRIVATE void scale_int(const char *s, const char *sl, double *sc_int){
int n,nl;
duplexT mfe;
double kT;
n = strlen(s);
nl = strlen(sl);
free(expMLbase);
free(scale);
expMLbase = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*((nl+1)*2));
scale = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*((nl+1)*2));
/* use RNA duplex to get a realistic estimate for the best possible
interaction energy between the short RNA s and its target sl */
mfe = duplexfold(s,sl);
kT = Pf->kT/1000.0; /* in Kcal */
/* sc_int is similar to pf_scale: i.e. one time the scale */
*sc_int = exp(-(mfe.energy)/kT/n);
/* free the structure returned by duplexfold */
free(mfe.structure);
}
/*----------------------------------------------------------------------*/
/* init_pf_two(n) :gets the arrays, that you need, from part_func.c */
/* get_pf_arrays(&S, &S1, &ptype, &qb, &qm, &q1k, &qln);*/
/* init_pf_fold(), update_pf_params, encode_char(), make_ptypes() are called by pf_fold() */
PRIVATE void init_pf_two(int length){
#ifdef SUN4
nonstandard_arithmetic();
#else
#ifdef HP9
fpsetfastmode(1);
#endif
#endif
make_pair_matrix();
/* gets the arrays, that we need, from part_func.c */
if(!get_pf_arrays(&S, &S1, &ptype, &qb, &qm, &q1k, &qln))
vrna_message_error("init_pf_two: pf_fold() has to be called before calling pf_unstru()\n");
/* get a pointer to the base pair probs */
probs = export_bppm();
scale_stru_pf_params((unsigned) length);
init_length=length;
if(init_temp != Pf->temperature)
vrna_message_error("init_pf_two: inconsistency with temperature");
}
PRIVATE void get_up_arrays(unsigned int length){
unsigned int l1 = length + 1;
unsigned int l2 = length + 2;
prpr = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * ((l1*l2)>>1));
expMLbase = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * l2);
scale = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * l2);
qqm2 = (double *) vrna_alloc(sizeof(double) * l2);
qq_1m2 = (double *) vrna_alloc(sizeof(double) * l2);
qqm = (double *) vrna_alloc(sizeof(double) * l2);
qqm1 = (double *) vrna_alloc(sizeof(double) * l2);
my_iindx = vrna_idx_row_wise(length);
}
PRIVATE void free_up_arrays(void){
if(prpr != NULL){ free(prpr); prpr = NULL;}
if(expMLbase != NULL){ free(expMLbase); expMLbase = NULL;}
if(scale != NULL){ free(scale); scale = NULL;}
if(qqm != NULL){ free(qqm); qqm = NULL;}
if(qqm1 != NULL){ free(qqm1); qqm1 = NULL;}
if(qqm2 != NULL){ free(qqm2); qqm2 = NULL;}
if(qq_1m2 != NULL){ free(qq_1m2); qq_1m2 = NULL;}
if(my_iindx != NULL){ free(my_iindx); my_iindx = NULL;}
}
PUBLIC void free_interact(interact *pin) {
if(S != NULL && pin != NULL){
free(S);
S=NULL;
}
if(S1 != NULL && pin != NULL){
free(S1);
S1=NULL;
}
if(pin != NULL){
free(pin->Pi);
free(pin->Gi);
free(pin);
pin=NULL;
}
}
/*---------------------------------------------------------------------------*/
PRIVATE void encode_seq(const char *s1, const char *s2) {
unsigned int i,l;
l = strlen(s1);
/* S and S1 are freed by free_pf_arrays(); ! */
S = (short *) vrna_alloc(sizeof(short)*(l+1));
S1= (short *) vrna_alloc(sizeof(short)*(l+1));
/* S1 exists only for the special X K and I bases and energy_set!=0 */
S[0] = l;
for (i=1; i<=l; i++) { /* make numerical encoding of sequence */
S[i]= (short) encode_char(toupper(s1[i-1]));
S1[i] = alias[S[i]]; /* for mismatches of nostandard bases */
}
if(s2 != NULL) {
l = strlen(s2);
/* SS2 exists only for the special X K and I bases and energy_set!=0 */
SS[0] = l;
for (i=1; i<=l; i++) { /* make numerical encoding of sequence */
SS[i]= (short) encode_char(toupper(s2[i-1]));
SS2[i] = alias[SS[i]]; /* for mismatches of nostandard bases */
}
}
}
/*-------------------------------------------------------------------------*/
/* scale energy parameters and pre-calculate Boltzmann weights:
most of this is done in structure Pf see params.c,h (function:
get_scaled_pf_parameters(), only arrays scale and expMLbase are handled here*/
PRIVATE void scale_stru_pf_params(unsigned int length)
{
unsigned int i;
double kT;
/* Do this only at the first call for get_scaled_pf_parameters()
and/or if temperature has changed*/
if(init_temp != temperature) {
if(Pf) free(Pf);
vrna_md_t md;
set_model_details(&md);
Pf=vrna_exp_params(&md);
}
init_temp = Pf->temperature;
kT = Pf->kT; /* kT in cal/mol */
/* scaling factors (to avoid overflows) */
if (pf_scale == -1) { /* mean energy for random sequences: 184.3*length cal */
pf_scale = exp(-(-185+(Pf->temperature-37.)*7.27)/kT);
if (pf_scale<1) pf_scale=1;
}
Pf->pf_scale = pf_scale;
scale[0] = 1.;
scale[1] = 1./pf_scale;
expMLbase[0] = 1;
expMLbase[1] = Pf->expMLbase/pf_scale;
for (i=2; i<=length+1; i++) {
scale[i] = scale[i/2]*scale[i-(i/2)];
expMLbase[i] = pow(Pf->expMLbase, (double)i) * scale[i];
}
}
/*-------------------------------------------------------------------------*/
/* make a results structure containing all u-values & the header */
PUBLIC pu_out *get_u_vals(pu_contrib *p_c, int **unpaired_values, char *select_contrib) {
int i, j, k, l, num_u_vals,count,contribs,size,w,len;
int S,E,H,I,M;
int off_S, off_E, off_H, off_I, off_M;
/* double **p_cont,**p_cont_sh, dG_u; p_u AND its contributions */
pu_out* u_results;
len = p_c->length;
/* number of different -u values */
for (num_u_vals = 0, i = 1; i <= unpaired_values[0][0]; i++) {
j = unpaired_values[i][0];
do num_u_vals++; while(++j <= unpaired_values[i][1]);
}
/* check which contributions ([-c "SHIME"] ) are desired by the user,
set the offset for each contribution */
contribs = 0;
S = E = H = I = M = 0;
off_S = off_E = off_H = off_I = off_M = 0;
if(strchr(select_contrib, 'S')) {
S=1;
off_S = contribs;
++contribs;
}
if(strchr(select_contrib, 'E')) {
E=1;
off_E = contribs;
++contribs;
}
if(strchr(select_contrib, 'H')) {
H=1;
off_H = contribs;
++contribs;
}
if(strchr(select_contrib, 'I')) {
I=1;
off_I = contribs;
++contribs;
}
if(strchr(select_contrib, 'M')) {
M=1;
off_M = contribs;
++contribs;
}
if(contribs > 5) {
vrna_message_error("get_u_vals: error with contribs!");
}
/* allocate the results structure */
u_results = (pu_out *) vrna_alloc(1*sizeof(pu_out));
u_results->len = len; /* sequence length */
/*num_u_vals differnet -u values, contribs [-c "SHIME"] */
u_results->u_vals = num_u_vals;
u_results->contribs = contribs;
/* add 1 column for position within the sequence and
add 1 column for the free energy of interaction values */
/* header e.g. u3I (contribution for u3 interior loops */
size = 1 + (num_u_vals*contribs) + 1;
u_results->header = (char **) vrna_alloc((size+1)*sizeof(char*));
for(i=0;i<(size+1);i++){
u_results->header[i] = (char *) vrna_alloc(10*sizeof(char));
}
/* different free energies for all -u and -c combinations */
u_results->u_values = (double**) vrna_alloc((size+1) *sizeof(double*));
for(i=0;i<(size+1);i++){
/* position within the sequence */
u_results->u_values[i] = (double*) vrna_alloc((len+3)*sizeof(double));
}
/* write the position within the sequence in the u_results array
at column zerro */
sprintf(u_results->header[0],"pos");
for(i=0;i<=len;i++){
/* add the position*/
u_results->u_values[0][i] = i;
}
/* go over the different -u values, u_vals[] listy of different -u values*/
for (count = k = 1; k <= unpaired_values[0][0]; k++) {
l = unpaired_values[k][0];
do{
int offset; /* offset for the respective -u value (depents on the number
of the -u value and on the numbers of contribs */
offset = ((count - 1) * contribs) + 1; /* first colum is the position */
/* set the current value of -u : here we call it w */
w = l; /* set w to the actual -u value */
if(w > len) break; /* corr caro */
/* make the header - look which contribitions are wanted */
if(S) sprintf(u_results->header[offset+off_S],"u%dS",w);
if(E) sprintf(u_results->header[offset+off_E],"u%dE",w);
if(H) sprintf(u_results->header[offset+off_H],"u%dH",w);
if(I) sprintf(u_results->header[offset+off_I],"u%dI",w);
if(M) sprintf(u_results->header[offset+off_M],"u%dM",w);
if(p_c != NULL) {
for (i=1; i<=len; i++) { /* for each position */
/* w goes form j to i (intervall end at i) */
for (j=i; j < MIN2((i+w),len+1); j++) { /* for each -u value < w
this is not necessay ->
calculate j from i and w
: (j-i+1) == w */
double blubb;
/* if (j-i+1) == w we have the -u = w value wanted */
if( (j-i+1) == w && i+w-1 <= len) {
blubb = p_c->H[i][j-i]+p_c->I[i][j-i]+p_c->M[i][j-i]+p_c->E[i][j-i];
/* printf("len %d blubb %.3f \n",len, blubb); */
if(S) u_results->u_values[offset+off_S][i+w-1]+=blubb;
if(E) u_results->u_values[offset+off_E][i+w-1]+=p_c->E[i][j-i];
if(H) u_results->u_values[offset+off_H][i+w-1]+=p_c->H[i][j-i];
if(I) u_results->u_values[offset+off_I][i+w-1]+=p_c->I[i][j-i];
if(M) u_results->u_values[offset+off_M][i+w-1]+=p_c->M[i][j-i];
}
if(i<w && (j-i+1) != w && i+w-1 > len && i+w-1 < len+3) {
if(S) u_results->u_values[offset+off_S][i+w-1]=-1;
if(E) u_results->u_values[offset+off_E][i+w-1]=-1;
if(H) u_results->u_values[offset+off_H][i+w-1]=-1;
if(I) u_results->u_values[offset+off_I][i+w-1]=-1;
if(M) u_results->u_values[offset+off_M][i+w-1]=-1;
}
}
}
} else return(NULL); /* error */
count++;
} while(++l <= unpaired_values[k][1]);
}
return(u_results); /*success*/
}
/* plot the results structure */
/* when plotting the results for the target seq we add a header */
/* when plotting the results for the interaction partner u want no header,
set s1 to NULL to avoid plotting the header */
/* currently we plot the free energies to a file: the probability of
being unpaired for region [i,j], p_u[i,j], is related to the free
energy to open region [i,j], dG_u[i,j] by:
dG_u[i,j] = -log(p_u[i,j])*(temperature+K0)*GASCONST/1000.0; */
PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) {
int size,s,i,len;
double dG_u;
char nan[4], *time, dg[11];
FILE *wastl;
double kT = Pf->kT;
wastl = fopen(ofile,"a");
if (wastl==NULL) {
vrna_message_warning("p_cont: can't open %s for Up_plot", ofile);
return(0);
}
sprintf(dg,"dG");
/* printf("T=%.16f \n(temperature+K0)*GASCONST/1000.0 = %.16f\n",temperature,(temperature+K0)*GASCONST/1000.0); */
/* write the header of the output file: */
/* # timestamp commandlineaufruf */
/* # length and name of first sequence (target) */
/* # first seq */
/* # length and name of second sequence (interaction partner) */
/* # second seq */
/* the next line is the output for the target: colums
position in target | dG_unpaired values for target | interaction energy */
/* # pos u1S u1H dg */
/* values for target */
/* if -b was choosen: the next lines are the dG_unpaired values for
the interaction partner */
/* # pos u1S u1H */
/* values for the interaction partner */
/* print header, if nh is zerro */
if(head){
time = vrna_time_stamp();
fprintf(wastl,"# %s\n", time);
fprintf(wastl,"%s\n",head);
}
fprintf(wastl,"# ");
/* } else { fprintf(wastl," "); } close if before */
len = res->len;
size = res->u_vals * res->contribs;
sprintf(nan,"NA");
nan[2] = '\0';
for(i=0;i<=len; i++) {
for(s=0;s<=size+1;s++) { /* that is for different contribution */
if ( i== 0 && s > size && pint != NULL)
fprintf(wastl,"%8s ",dg);
if(i != 0) {
if(s>0 && s<=size) {
if(res->u_values[s][i] > 0.0) {
dG_u = -log(res->u_values[s][i])*kT/1000.0;
fprintf(wastl,"%8.3f ",dG_u);
} else { /* no p_u value was defined print nan*/
fprintf(wastl,"%8s ",nan);
}
} else if (s > size && pint != NULL) {
fprintf(wastl,"%8.3f ",pint->Gi[i]);
} else if (s == 0) {
fprintf(wastl,"%8.0f ",res->u_values[s][i]);
}
} else {
if(s>1) {
fprintf(wastl,"%8s ",res->header[s]);
} else {
fprintf(wastl,"%7s ",res->header[s]);
}
}
}
fprintf(wastl,"\n");
}
fclose(wastl);
/*free pu_out* res */
if(res != NULL) {
for(i=0;i<=(size+2);i++) {
free(res->u_values[i]);
free(res->header[i]);
}
free(res->u_values);
free(res->header);
free(res);
res = NULL;
}
return(1); /* success */
}
PUBLIC int Up_plot(pu_contrib *p_c, pu_contrib *p_c_sh, interact *pint, char *ofile, int **unpaired_values, char *select_contrib, char *head, unsigned int mode) {
pu_out *dada;
int ret;
/* check what case we have */
/* upmode = 1 only one seq */
/* if(p_c != NULL && pint == NULL) { */
if(mode & RNA_UP_MODE_1){
dada = get_u_vals(p_c,unpaired_values,select_contrib);
ret = plot_free_pu_out(dada,NULL,ofile,head);
/* upmode > 1 cofolding */
/* } else if (p_c != NULL && pint != NULL) { */
} else if(mode & RNA_UP_MODE_2) {
dada = get_u_vals(p_c,unpaired_values,select_contrib);
ret = plot_free_pu_out(dada,pint,ofile,head);
/* upmode = 3 cofolding*/
/* } else if (p_c == NULL && p_c_sh != NULL) { */
}
if(mode & RNA_UP_MODE_3) {
dada = get_u_vals(p_c,unpaired_values, select_contrib);
ret = plot_free_pu_out(dada, pint, ofile, head);
dada = get_u_vals(p_c_sh, unpaired_values, select_contrib);
ret = plot_free_pu_out(dada,NULL,ofile, NULL);
}
return(ret);
}
/*-------------------------------------------------------------------------*/
/* copy from part_func_co.c */
PRIVATE constrain *get_ptypes_up(char *Seq, const char *structure) {
int n,i,j,k,l, length;
constrain *con;
short *s, *s1;
length = strlen(Seq);
make_pair_matrix();
con = (constrain *) vrna_alloc(sizeof(constrain));
con->indx = (int *) vrna_alloc(sizeof(int)*(length+1));
for (i=1; i<=length; i++) {
con->indx[i] = ((length+1-i)*(length-i))/2 +length+1;
}
con->ptype = (char *) vrna_alloc(sizeof(char)*((length+1)*(length+2)/2));
set_encoded_seq((const char *)Seq, &s, &s1);
n=s[0];
for (k=1; k<=n-CO_TURN-1; k++)
for (l=1; l<=2; l++) {
int type,ntype=0,otype=0;
i=k; j = i+CO_TURN+l; if (j>n) continue;
type = pair[s[i]][s[j]];
while ((i>=1)&&(j<=n)) {
if ((i>1)&&(j<n)) ntype = pair[s[i-1]][s[j+1]];
if (noLonelyPairs && (!otype) && (!ntype))
type = 0; /* i.j can only form isolated pairs */
con->ptype[con->indx[i]-j] = (char) type;
otype = type;
type = ntype;
i--; j++;
}
}
if (fold_constrained&&(structure!=NULL)) {
int hx, *stack;
char type;
stack = (int *) vrna_alloc(sizeof(int)*(n+1));
for(hx=0, j=1; j<=n; j++) {
switch (structure[j-1]) {
case 'x': /* can't pair */
for (l=1; l<j-CO_TURN; l++) con->ptype[con->indx[l]-j] = 0;
for (l=j+CO_TURN+1; l<=n; l++) con->ptype[con->indx[j]-l] = 0;
break;
case '(':
stack[hx++]=j;
/* fallthrough */
case '<': /* pairs upstream */
break;
case ')':
if (hx<=0) {
vrna_message_error("1. unbalanced brackets in constraints\n%s", structure);
}
i = stack[--hx];
type = con->ptype[con->indx[i]-j];
/* don't allow pairs i<k<j<l */
for (k=i; k<=j; k++)
for (l=j; l<=n; l++) con->ptype[con->indx[k]-l] = 0;
/* don't allow pairs k<i<l<j */
for (k=1; k<=i; k++)
for (l=i; l<=j; l++) con->ptype[con->indx[k]-l] = 0;
con->ptype[con->indx[i]-j] = (type==0)?7:type;
case '>': /* pairs downstream */
break;
}
}
if (hx!=0) {
vrna_message_error("2. unbalanced brackets in constraint string\n%s", structure);
}
free(stack);
}
free(s);
free(s1);
return con;
}
PRIVATE void set_encoded_seq(const char *sequence, short **S, short **S1){
unsigned int i,l;
l = strlen(sequence);
if(S!= NULL){
*S = (short *)vrna_alloc(sizeof(short) * (l + 2));
for(i=1; i<=l; i++) /* make numerical encoding of sequence */
(*S)[i]= (short) encode_char(toupper(sequence[i-1]));
(*S)[l+1] = (*S)[1];
(*S)[0] = (short) l;
}
/* S1 exists only for the special X K and I bases and energy_set!=0 */
if(S1 != NULL){
*S1 = (short *)vrna_alloc(sizeof(short) * (l + 2));
for(i=1; i<=l; i++) /* make numerical encoding of sequence */
(*S1)[i] = alias[(short) encode_char(toupper(sequence[i-1]))]; /* for mismatches of nostandard bases */
/* for circular folding add first base at position n+1 and last base at position 0 in S1 */
(*S1)[l+1] = (*S1)[1];
(*S1)[0] = (*S1)[l];
}
}