/
hybrid-min.c
2261 lines (2055 loc) · 58.7 KB
/
hybrid-min.c
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#ifdef HAVE_CONFIG_H
# include "config.h"
#endif
#include <math.h>
#include <stdio.h>
#include <sys/stat.h>
#include <time.h>
#include <unistd.h>
#if HAVE_IEEEFP_H
# include <ieeefp.h>
#endif
#include "energy.h"
#include "getopt.h"
#include "util.h"
#include "xmalloc.h"
/* uncomment for debug warnings
#define DEBUG */
/* hybrid-min
* hybridize two NA sequences and output .dG and .ct's
*/
#define Lprime(i, j) lprime[g_len2 * (i) - (j)]
#define Rprime(i, j) rprime[g_len1 * (j) - (i)]
struct stackNode
{
int i;
int j;
struct stackNode* next;
};
struct constraintListNode
{
int i, j, k, l;
struct constraintListNode* next;
} *prohibitList, *forceList;
#if ENABLE_FORCE
char *g_ssok1, *g_ssok2;
#define ssOK1(i, j) g_ssok1[(i) * (g_len1 + 2) + j]
#define ssOK2(i, j) g_ssok2[(i) * (g_len2 + 2) + j]
#endif
struct pairListNode
{
int i, j, length;
ENERGY E;
struct pairListNode* next;
} *pairList;
void initializeMatrices(double);
void limitBasePairs();
void prohibit();
void force();
void prefilter();
void fillMatrixL(double);
void fillMatrixR(double);
void fillMatrixL_noI(double);
void fillMatrixR_noI(double);
void traceback(int, int, double, int*, int*, int*, int*, int*, int*, double*);
void traceback_noI(int, int, double, int*, int*, int*, int*, int*, int*, double*);
void traceback_rev(int, int, double, int*, int*, int*, int*, int*, int*);
void traceback_rev_noI(int, int, double, int*, int*, int*, int*, int*, int*);
void setStackBI(int, int, int, int, int*, int*, int*, int*);
int unique(int*, char**);
void writeStructure(int*, int*, int*, int*, int*, int*, double, ENERGY, double*);
void writePlotExt(int*, int*, double, ENERGY);
void makePairList(ENERGY, int*, int*);
void makePairList_noI(ENERGY, int*, int*);
void writeBoxPlot(double);
void writePnum(int*, int*, double);
ENERGY Es(int, int);
double Hs(int, int);
ENERGY Ebi(int, int, int, int, double);
double Hbi(int, int, int, int);
ENERGY R0(int, int);
ENERGY L0(int, int);
#define auPenalty(a, b) g_aup[a][b]
#define auPenaltyH(a, b) g_aupH[a][b]
void push(struct stackNode**, int, int);
int equal(ENERGY, ENERGY);
ENERGY* recalloc2(ENERGY*, int, int);
#define min2(a, b) ((a) < (b) ? (a) : (b))
ENERGY min4(ENERGY, ENERGY, ENERGY, ENERGY);
void pushPairList(int, int, int, ENERGY);
void sortPairList();
ENERGY *lprime, *rprime;
int g_allPairs, g_maxLoop, g_nodangle, g_prefilter1, g_prefilter2, g_mfoldMax, g_mfoldP, g_mfoldW, g_quiet, g_zip, g_stream;
int g_numSeqs;
char *g_name1, *g_name2, *g_string1, *g_string2;
unsigned char *g_seq1, *g_seq2; /* [0-4] for [A,C,G,TU,N] */
char *g_file1, *g_file2, *g_prefix, *g_bpFile;
int g_len1, g_len2;
int g_oneTemp, g_firstSeq;
ENERGY g_homodimer;
double dangleEnergies3[4][4][4];
double dangleEnthalpies3[5][5][6];
double dangleEnergies5[4][4][4];
double dangleEnthalpies5[5][5][6];
double stackEnergies[4][4][4][4];
double stackEnthalpies[5][5][5][5];
double interiorLoopEnergies[30];
double bulgeLoopEnergies[30];
double hairpinLoopEnergies[30];
double interiorLoopEnthalpies[30];
double bulgeLoopEnthalpies[30];
double hairpinLoopEnthalpies[30];
double sint2Energies[6][6][4][4];
double sint2Enthalpies[7][7][5][5];
double asint1x2Energies[6][6][4][4][4];
double asint1x2Enthalpies[7][7][5][5][5];
double sint4Energies[6][6][4][4][4][4];
double sint4Enthalpies[7][7][5][5][5][5];
double tstackiEnergies[4][4][4][4];
double tstackiEnthalpies[5][5][5][5];
double tstacki23Energies[4][4][4][4];
double tstacki23Enthalpies[5][5][5][5];
double tstackeEnergies[4][4][4][4];
double tstackeEnthalpies[5][5][6][6];
double miscEnergies[13];
double miscEnthalpies[13];
ENERGY g_dangle3[5][5][6];
ENERGY g_dangle5[5][5][6];
ENERGY g_stack[5][5][5][5];
ENERGY g_interiorLoop[30];
ENERGY g_bulgeLoop[30];
ENERGY g_hairpinLoop[30];
ENERGY g_sint2[7][7][5][5];
ENERGY g_asint1x2[7][7][5][5][5];
ENERGY g_sint4[7][7][5][5][5][5];
ENERGY g_tstacki[5][5][5][5];
ENERGY g_tstacki23[5][5][5][5];
ENERGY g_tstacke[5][5][6][6];
ENERGY g_misc[13];
ENERGY g_aup[5][5];
double g_aupH[5][5];
#include "options.h"
int main(int argc, char** argv)
{
int NA, polymer, skipTraceback, noIsolate, constraints;
char* constraintsFile;
double tMin, tInc, tMax;
double naConc, mgConc;
double saltCorrection;
ENERGY Eleft;/*, Eright; */
char gotSeqs;
int count, i, j;
int bestI, bestJ;
double t, tRatio, RT;
char *buffer, *suffix;
FILE *in1, *in2, *file, *dGFile;
time_t now;
struct constraintListNode* newTop;
lprime = rprime = NULL;
#if ENABLE_FORCE
g_ssok1 = g_ssok2 = NULL;
#endif
NA = 0;
gotSeqs = 0;
g_allPairs = 0;
g_nodangle = 0;
g_maxLoop = 30;
tMin = 37;
tInc = 1;
tMax = 37;
suffix = NULL;
g_prefix = NULL;
naConc = 1;
mgConc = 0;
polymer = 0;
g_prefilter1 = g_prefilter2 = 2;
noIsolate = 0;
prohibitList = forceList = NULL;
skipTraceback = 0;
g_mfoldMax = 0;
g_mfoldP = 0;
g_mfoldW = 0;
g_quiet = 0;
g_zip = 0;
constraints = 0;
constraintsFile = g_bpFile = NULL;
/* initializations below are unnecessary but prevent compiler warnings */
bestI = bestJ = 0;
dGFile = NULL;
in1 = in2 = NULL;
while ((count = getopt_long(argc, argv, "Vhn:t:i:T:s:o:dN:M:pr:f:EIF::qzm:c::b:", OPTIONS, NULL)) != -1)
{
if (count == 0)
{
if (option_code == 1)
g_maxLoop = atoi(optarg);
else if (option_code == 2)
++g_nodangle;
else if (option_code == 8)
{
if ((optarg = strtok(optarg, ",")))
{
g_prefilter1 = g_prefilter2 = atoi(optarg);
if ((optarg = strtok(NULL, ",")))
g_prefilter2 = atoi(optarg);
}
}
else if (option_code == 11)
++g_allPairs;
else if (option_code == 12)
{
in1 = in2 = stdin;
++g_quiet;
}
else
fputs("Unsupported long option specified\nRun 'hybrid-min -h' for help\n", stderr);
}
else if (count == 'V')
version("hybrid-min");
else if (count == 'h')
usage("hybrid-min", OPTION_TAKES_TWO | OPTION_NOISOLATE | OPTION_MIN | OPTION_QUIET | OPTION_ZIP | OPTION_NODANGLE);
else if (count == 'n')
{
if (!strcmp(optarg, "RNA"))
NA = 0;
else if (!strcmp(optarg, "DNA"))
NA = 1;
}
else if (count == 't')
tMin = atof(optarg);
else if (count == 'i')
tInc = atof(optarg);
else if (count == 'T')
tMax = atof(optarg);
else if (count == 's')
suffix = optarg;
else if (count == 'a')
++g_allPairs;
else if (count == 'o')
g_prefix = optarg;
else if (count == 'd')
fputs("Warning: --debug option ignored\n", stderr);
else if (count == 'N')
naConc = atof(optarg);
else if (count == 'M')
mgConc = atof(optarg);
else if (count == 'p')
++polymer;
else if (count == 'h')
{
newTop = xmalloc(sizeof(struct constraintListNode));
newTop->i = newTop->j = newTop->l = 0;
newTop->k = 1;
if ((optarg = strtok(optarg, ",")))
{
newTop->i = atoi(optarg);
if ((optarg = strtok(NULL, ",")))
{
newTop->j = atoi(optarg);
if ((optarg = strtok(NULL, ",")))
newTop->k = atoi(optarg);
}
}
newTop->next = prohibitList;
prohibitList = newTop;
}
else if (count == 'f')
{
newTop = xmalloc(sizeof(struct constraintListNode));
newTop->i = newTop->j = 0;
newTop->k = 1;
if ((optarg = strtok(optarg, ",")))
{
newTop->i = atoi(optarg);
if ((optarg = strtok(NULL, ",")))
{
newTop->j = atoi(optarg);
if ((optarg = strtok(NULL, ",")))
newTop->k = atoi(optarg);
}
}
newTop->next = forceList;
forceList = newTop;
}
else if (count == 'E')
++skipTraceback;
else if (count == 'I')
++noIsolate;
else if (count == 'F')
{
g_mfoldMax = 100;
g_mfoldP = 5;
g_mfoldW = -1;
if (optarg && strtok(optarg, ","))
{
g_mfoldP = atoi(optarg);
optarg += strlen(optarg) + 1;
if (strtok(NULL, ","))
{
if (optarg[0])
g_mfoldW = atoi(optarg);
optarg += strlen(optarg) + 1;
if (strtok(NULL, ","))
g_mfoldMax = atoi(optarg);
}
}
}
else if (count == 'q')
++g_quiet;
else if (count == 'z')
++g_zip;
else if (count == 'm')
; /* ignore for compatibility with hybrid-ss */
else if (count == 'c')
{
++constraints;
if (optarg)
constraintsFile = optarg;
}
else if (count == 'b')
g_bpFile = optarg;
}
if (optind + 1 >= argc && !in1)
{
fputs("Error: data not specified\nRun 'hybrid-min -h' for help\n", stderr);
return EXIT_FAILURE;
}
if (NA == 0 && (naConc != 1 || mgConc != 0 || polymer))
fputs("Warning: salt concentrations ignored for RNA\n", stderr);
if (suffix && (naConc != 1 || mgConc != 0 || polymer))
fputs("Warning: salt concentrations ignored with suffix\n", stderr);
/* tMin..tInc..tMax better make sense */
if (!suffix && tMin > tMax)
{
fputs("Error: tMax must be greater than or equal to tMin.\n", stderr);
return EXIT_FAILURE;
}
if (tMin + tInc == tMin)
{
fputs("Error: tInc is too small compared to tMin.\n", stderr);
return EXIT_FAILURE;
}
g_oneTemp = (tMin + tInc > tMax) ? 1 : 0;
if (g_maxLoop < 0)
g_maxLoop = 999999999;
if (!g_quiet)
{
g_file1 = xmalloc(strlen(argv[optind]) + 1);
strcpy(g_file1, argv[optind]);
if (strlen(g_file1) > 4 && !strcmp(g_file1 + strlen(g_file1) - 4, ".seq"))
g_file1[strlen(g_file1) - 4] = 0;
g_file2 = xmalloc(strlen(argv[optind + 1]) + 1);
strcpy(g_file2, argv[optind + 1]);
if (strlen(g_file2) > 4 && !strcmp(g_file2 + strlen(g_file2) - 4, ".seq"))
g_file2[strlen(g_file2) - 4] = 0;
/* figure out prefix */
if (!g_prefix)
{
g_prefix = xmalloc(strlen(g_file1) + strlen(g_file2) + 2);
strcpy(g_prefix, filename(g_file1));
strcatc(g_prefix, '-');
strcat(g_prefix, filename(g_file2));
}
}
#include "constraints.h"
saltCorrection = ion(NA, polymer, naConc, mgConc);
/* read free energies and entropies */
if (suffix)
{
loadRTSuffix(&RT, suffix);
t = RT / R - 273.15;
tMin = tMax = t;
tInc = fabs(t);
loadStackSuffix(g_stack, suffix);
if (!g_nodangle)
loadDangleSuffix(g_dangle3, g_dangle5, suffix);
loadLoopSuffix(g_hairpinLoop, g_interiorLoop, g_bulgeLoop, suffix);
loadSint2Suffix(g_sint2, suffix);
loadAsint1x2Suffix(g_asint1x2, suffix);
loadSint4Suffix(g_sint4, suffix);
loadTstackiSuffix(g_tstacki, suffix);
loadTstacki23Suffix(g_tstacki23, suffix);
if (!g_nodangle)
loadTstackeSuffix(g_tstacke, suffix);
loadMiscSuffix(g_misc, suffix);
}
else
{
loadStack(stackEnergies, stackEnthalpies, NA, saltCorrection);
symmetryCheckStack(stackEnergies, "energy");
/* symmetryCheckStack(stackEnthalpies, "enthalpy"); */
if (!g_nodangle)
loadDangle(dangleEnergies3, dangleEnthalpies3, dangleEnergies5, dangleEnthalpies5, NA, saltCorrection);
loadLoop(hairpinLoopEnergies, interiorLoopEnergies, bulgeLoopEnergies, hairpinLoopEnthalpies, interiorLoopEnthalpies, bulgeLoopEnthalpies, NA, saltCorrection);
loadSint2(sint2Energies, sint2Enthalpies, NA, saltCorrection);
symmetryCheckSint2(sint2Energies, "energy");
/* symmetryCheckSint2(sint2Enthalpies, "enthalpy"); */
loadAsint1x2(asint1x2Energies, asint1x2Enthalpies, NA, saltCorrection);
loadSint4(sint4Energies, sint4Enthalpies, NA, saltCorrection);
symmetryCheckSint4(sint4Energies, "energy");
/* symmetryCheckSint4(sint4Enthalpies, "enthalpy"); */
loadTstacki(tstackiEnergies, tstackiEnthalpies, NA);
loadTstacki23(tstacki23Energies, tstacki23Enthalpies, NA);
if (!g_nodangle)
loadTstacke(tstackeEnergies, tstackeEnthalpies, NA, saltCorrection);
loadMisc(miscEnergies, miscEnthalpies, NA);
}
if (!g_quiet)
{
buffer = xmalloc(strlen(g_prefix) + 9);
strcpy(buffer, g_prefix);
strcat(buffer, ".dG");
if (!(dGFile = fopen(buffer, "wt")))
{
perror(buffer);
return EXIT_FAILURE;
}
fputs("#T\t-RT ln Z\tZ\n", dGFile);
strcpy(buffer, g_prefix);
strcat(buffer, ".run");
if (!(file = fopen(buffer, "wt")))
{
perror(buffer);
return EXIT_FAILURE;
}
free(buffer);
now = time(NULL);
fprintf(file, "hybrid-min %s ran on %s and %s at %s\n", PACKAGE_VERSION, g_file1, g_file2, ctime(&now));
if (suffix)
fprintf(file, "suffix = %s\n", suffix);
else
{
fprintf(file, "NA = %s\n", NA ? "DNA" : "RNA");
fprintf(file, "tMin = %g\n", tMin);
fprintf(file, "tInc = %g\n", tInc);
fprintf(file, "tMax = %g\n", tMax);
fprintf(file, "[Na+] = %g\n", naConc);
fprintf(file, "[Mg++] = %g\n", mgConc);
}
if (g_allPairs)
fputs("all pairs\n", file);
fprintf(file, "maxloop = %d\n", g_maxLoop);
if (g_nodangle)
fprintf(file, "no dangle\n");
if (polymer)
fprintf(file, "polymer mode\n");
fprintf(file, "prefilter %d/%d\n", g_prefilter1, g_prefilter2);
if (noIsolate)
fputs("no isolated base pairs\n", file);
if (g_mfoldMax)
fprintf(file, "mfold mode: P=%d, W=%d, MAX=%d\n", g_mfoldP, g_mfoldW, g_mfoldMax);
fclose(file);
}
if (g_quiet)
{
g_file1 = g_file2 = xmalloc(1);
g_file1[0] = 0;
}
else if (!in1)
{
if (!(in1 = fopen(argv[optind], "rt")))
{
perror(argv[optind]);
return EXIT_FAILURE;
}
if (!(in2 = fopen(argv[optind + 1], "rt")))
{
perror(argv[optind + 1]);
return EXIT_FAILURE;
}
}
g_firstSeq = 1;
while (1)
{
if (g_quiet && !in1)
{
if (optind >= argc - 1)
break;
g_string1 = argv[optind];
g_string2 = argv[optind + 1];
optind += 2;
}
else
{
if (!input(in1, &g_name1, &g_string1) || !input(in2, &g_name2, &g_string2))
break;
if (!g_name1)
g_name1 = filename(g_file1);
if (!g_name2)
g_name2 = filename(g_file2);
}
g_len1 = strlen(g_string1);
g_len2 = strlen(g_string2);
/* convert sequence to numbers for speed */
g_seq1 = xrealloc(g_seq1, g_len1 + 2);
g_seq2 = xrealloc(g_seq2, g_len2 + 2);
for (i = 1; i <= g_len1; ++i)
g_seq1[i] = toNum(g_string1[i - 1]);
for (i = 1; i <= g_len2; ++i)
g_seq2[i] = toNum(g_string2[i - 1]);
g_seq1[0] = g_seq1[g_len1 + 1] = g_seq2[0] = g_seq2[g_len2 + 1] = 5;
if (g_mfoldMax > 0 && g_mfoldW < 0)
{
if (g_len1 + g_len2 < 30)
g_mfoldW = 0;
else if (g_len1 + g_len2 < 50)
g_mfoldW = 1;
else if (g_len1 + g_len2 < 120)
g_mfoldW = 2;
else if (g_len1 + g_len2 < 200)
g_mfoldW = 3;
else if (g_len1 + g_len2 < 300)
g_mfoldW = 5;
else if (g_len1 + g_len2 < 400)
g_mfoldW = 7;
else if (g_len1 + g_len2 < 500)
g_mfoldW = 8;
else if (g_len1 + g_len2 < 600)
g_mfoldW = 10;
else if (g_len1 + g_len2 < 700)
g_mfoldW = 11;
else if (g_len1 + g_len2 < 800)
g_mfoldW = 12;
else if (g_len1 + g_len2 < 1200)
g_mfoldW = 15;
else if (g_len1 + g_len2 < 2000)
g_mfoldW = 20;
else
g_mfoldW = 25;
}
lprime = recalloc2(lprime, g_len1, g_len2);
if (g_mfoldMax)
rprime = recalloc2(rprime, g_len1, g_len2);
#if ENABLE_FORCE
g_ssok1 = xrealloc(g_ssok1, (g_len1 + 2) * (g_len1 + 2));
g_ssok2 = xrealloc(g_ssok2, (g_len2 + 2) * (g_len2 + 2));
for (i = 0; i <= g_len1 + 1; ++i)
for (j = 0; j <= g_len1 + 1; ++j)
ssOK1(i, j) = 1;
for (i = 0; i <= g_len2 + 1; ++i)
for (j = 0; j <= g_len2 + 1; ++j)
ssOK2(i, j) = 1;
#endif
for (t = tMin; t <= tMax; t += tInc)
{
tRatio = (t + 273.15) / 310.15;
RT = R * (t + 273.15);
if (!suffix && (!g_oneTemp || g_firstSeq))
{
combineStack(stackEnergies, stackEnthalpies, tRatio, g_stack);
if (!g_nodangle)
combineDangle(dangleEnergies3, dangleEnergies5, dangleEnthalpies3, dangleEnthalpies5, tRatio, g_dangle3, g_dangle5);
combineLoop(interiorLoopEnergies, bulgeLoopEnergies, hairpinLoopEnergies, interiorLoopEnthalpies, bulgeLoopEnthalpies, hairpinLoopEnthalpies, tRatio, g_interiorLoop, g_bulgeLoop, g_hairpinLoop);
combineSint2(sint2Energies, sint2Enthalpies, tRatio, g_sint2);
combineAsint1x2(asint1x2Energies, asint1x2Enthalpies, tRatio, g_asint1x2);
combineSint4(sint4Energies, sint4Enthalpies, tRatio, g_sint4);
combineTstack(tstackiEnergies, tstackiEnthalpies, tRatio, g_tstacki);
combineTstack(tstacki23Energies, tstacki23Enthalpies, tRatio, g_tstacki23);
if (!g_nodangle)
combineTstack2(tstackeEnergies, tstackeEnthalpies, tRatio, g_tstacke);
combineMisc(miscEnergies, miscEnthalpies, tRatio, g_misc);
}
makeAUPenalty(g_misc, g_aup, 0);
makeAUPenaltyH(miscEnthalpies, g_aupH, 0);
/* if (!g_zip)
minZeroDangle(g_dangle3, g_dangle5); */
g_homodimer = (g_len1 != g_len2 || seqcmp(g_seq1, g_seq2, g_len1 + 2)) ? 0.0 : floor(RT * log(2.0) * PRECISION + 0.5);
if (!g_quiet)
printf("Calculating for %s and %s, t = %g\n", g_name1, g_name2, t);
initializeMatrices(RT);
limitBasePairs();
prohibit();
#if ENABLE_FORCE
force();
#endif
if (g_prefilter1 > 1 && !g_allPairs)
prefilter();
if (noIsolate)
{
fillMatrixL_noI(RT);
if (g_mfoldMax)
fillMatrixR_noI(RT);
}
else
{
fillMatrixL(RT);
if (g_mfoldMax)
fillMatrixR(RT);
}
Eleft = INFINITY;
if (noIsolate)
{
for (i = 1; i < g_len1; ++i)
for (j = g_len2; j > 1; --j)
if (Lprime(i, j) + Es(i, j) + R0(i + 1, j - 1) < Eleft)
{
Eleft = Lprime(i, j) + Es(i, j) + R0(i + 1, j - 1);
bestI = i;
bestJ = j;
}
}
else
{
for (i = 1; i <= g_len1; ++i)
for (j = g_len2; j >= 1; --j)
if (Lprime(i, j) + R0(i, j) < Eleft)
{
Eleft = Lprime(i, j) + R0(i, j);
bestI = i;
bestJ = j;
}
}
if (!isFinite(Eleft))
bestI = bestJ = 1;
/*Eright = INFINITY;
if (noIsolate)
{
for (j = 2; j <= g_len2; ++j)
for (i = g_len1 - 1; i >= 1; --i)
if (L0(i, j) + Es(i, j, 0) + Rprime(i + 1, j - 1) < Eright)
Eright = L0(i, j) + Es(i, j, 0) + Rprime(i + 1, j - 1);
}
else
{
for (j = 1; j <= g_len2; ++j)
for (i = g_len1; i >= 1; --i)
if (L0(i, j) + Rprime(i, j) < Eright)
Eright = L0(i, j) + Rprime(i, j);
}
if (2 * fabs(Eleft - Eright) / (Eleft + Eright) > 1e-12)
fprintf(stderr, "Warning: L(m, 1) = %g but R(1, n) = %g.\n", Eleft, Eright);*/
if (g_quiet)
printf("%g", (double) (g_misc[5] + Eleft + g_homodimer) / PRECISION);
else
fprintf(dGFile, "%g\t%g\t%g\n", t, (double) (g_misc[5] + Eleft + g_homodimer) / PRECISION, exp((double) -(g_misc[5] + Eleft + g_homodimer) / PRECISION / RT));
if (!skipTraceback)
{
int *bp1, *bp2, *upst1, *upst2, *dnst1, *dnst2;
bp1 = xcalloc(g_len1, sizeof(int));
bp2 = xcalloc(g_len2, sizeof(int));
upst1 = xcalloc(g_len1, sizeof(int));
upst2 = xcalloc(g_len2, sizeof(int));
dnst1 = xcalloc(g_len1, sizeof(int));
dnst2 = xcalloc(g_len2, sizeof(int));
for (i = 0; i < g_len1; ++i)
bp1[i] = upst1[i] = dnst1[i] = 0;
for (j = 0; j < g_len2; ++j)
bp2[j] = upst2[j] = dnst2[j] = 0;
if (g_mfoldMax)
{
char** found;
int structures, *pnum1, *pnum2;
ENERGY cutoff;
pnum1 = xcalloc(g_len1, sizeof(int));
pnum2 = xcalloc(g_len2, sizeof(int));
for (i = 1; i <= g_len1; ++i)
pnum1[i - 1] = 0;
for (j = 1; j <= g_len2; ++j)
pnum2[j - 1] = 0;
cutoff = (Eleft + g_misc[5] + g_homodimer) * (1.0 - g_mfoldP / 100.0);
if (cutoff > Eleft + g_misc[5] + g_homodimer + 12 * PRECISION)
cutoff = Eleft + g_misc[5] + g_homodimer + 12 * PRECISION;
else if (cutoff < Eleft + g_misc[5] + g_homodimer + 1 * PRECISION)
cutoff = Eleft + g_misc[5] + g_homodimer + 1 * PRECISION;
if (noIsolate)
makePairList_noI(cutoff, pnum1, pnum2);
else
makePairList(cutoff, pnum1, pnum2);
writePnum(pnum1, pnum2, t);
free(pnum1);
free(pnum2);
writeBoxPlot(t);
found = xcalloc(g_len1, sizeof(char*));
for (i = 1; i <= g_len1; ++i)
{
found[i - 1] = xmalloc(g_len2);
for (j = 1; j <= g_len2; ++j)
found[i - 1][j - 1] = 0;
}
sortPairList();
structures = 0;
do {
if (noIsolate)
{
traceback_noI(pairList->i, pairList->j, RT, bp1, bp2, upst1, upst2, dnst1, dnst2, NULL);
traceback_rev_noI(pairList->i + 1, pairList->j - 1, RT, bp1, bp2, upst1, upst2, dnst1, dnst2);
}
else
{
traceback(pairList->i, pairList->j, RT, bp1, bp2, upst1, upst2, dnst1, dnst2, NULL);
traceback_rev(pairList->i, pairList->j, RT, bp1, bp2, upst1, upst2, dnst1, dnst2);
}
if (unique(bp1, found) >= g_mfoldW)
{
writeStructure(bp1, bp2, upst1, upst2, dnst1, dnst2, t, pairList->E, NULL);
g_firstSeq = 0;
}
/* if (structures == 0)
writePlotExt(bp1, bp2, t, pairList->E); */
for (i = 1; i <= g_len1; ++i)
if (bp1[i - 1])
{
int ii, jj;
for (ii = i > g_mfoldW ? i - g_mfoldW : 1; ii <= i + g_mfoldW && ii <= g_len1; ++ii)
for (jj = bp1[i - 1] > g_mfoldW ? bp1[i - 1] - g_mfoldW : 1; jj <= bp1[i - 1] + g_mfoldW && jj <= g_len2; ++jj)
++found[ii - 1][jj - 1];
}
++structures;
for (i = 0; i < g_len1; ++i)
bp1[i] = upst1[i] = dnst1[i] = 0;
for (j = 0; j < g_len2; ++j)
bp2[j] = upst2[j] = dnst2[j] = 0;
while (pairList && found[pairList->i - 1][pairList->j - 1])
{
struct pairListNode* newTop;
newTop = pairList->next;
free(pairList);
pairList = newTop;
}
} while (pairList && structures < g_mfoldMax);
for (i = 1; i <= g_len1; ++i)
free(found[i - 1]);
free(found);
}
else
{
double enthalpy;
enthalpy = 0.0;
if (isFinite(Lprime(bestI, bestJ)))
{
if (noIsolate)
traceback_noI(bestI, bestJ, RT, bp1, bp2, upst1, upst2, dnst1, dnst2, suffix ? NULL : &enthalpy);
else
traceback(bestI, bestJ, RT, bp1, bp2, upst1, upst2, dnst1, dnst2, suffix ? NULL : &enthalpy);
if (!suffix)
enthalpy += auPenaltyH(g_seq1[bestI], g_seq2[bestJ]) + miscEnthalpies[5];
if (!g_nodangle)
{
if (bestI < g_len1 && bestJ > 1 &&
(g_zip || (g_tstacke[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]][g_seq2[bestJ - 1]] <= g_dangle3[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]] &&
g_tstacke[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]][g_seq2[bestJ - 1]] <= g_dangle5[g_seq1[bestI]][g_seq2[bestJ]][g_seq2[bestJ - 1]] &&
g_tstacke[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]][g_seq2[bestJ - 1]] <= 0.0)))
{
upst1[bestI] = bestI;
dnst1[bestI - 1] = bestI + 1;
upst2[bestJ - 1] = bestJ - 1;
dnst2[bestJ - 2] = bestJ;
if (!suffix)
enthalpy += tstackeEnthalpies[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]][g_seq2[bestJ - 1]];
}
else if (bestI < g_len1 &&
g_dangle3[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]] <= g_dangle5[g_seq1[bestI]][g_seq2[bestJ]][g_seq2[bestJ - 1]] &&
g_dangle3[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]] <= 0.0)
{
upst1[bestI] = bestI;
dnst1[bestI - 1] = bestI + 1;
if (!suffix)
enthalpy += dangleEnthalpies3[g_seq1[bestI]][g_seq2[bestJ]][g_seq1[bestI + 1]];
}
else if (bestJ > 1 && g_dangle5[g_seq1[bestI]][g_seq2[bestJ]][g_seq2[bestJ - 1]] <= 0.0)
{
upst2[bestJ - 1] = bestJ - 1;
dnst2[bestJ - 2] = bestJ;
if (!suffix)
enthalpy += dangleEnthalpies5[g_seq1[bestI]][g_seq2[bestJ]][g_seq2[bestJ - 1]];
}
}
}
if (g_quiet)
{
if (suffix)
puts("");
else
printf("\t%g\t%g\n", enthalpy, 1000.0 * (enthalpy - (double) (g_misc[5] + Eleft + g_homodimer) / PRECISION) / (273.15 + t));
fflush(stdout);
}
else
{
writeStructure(bp1, bp2, upst1, upst2, dnst1, dnst2, t, Eleft, suffix ? NULL : &enthalpy);
if (g_firstSeq)
writePlotExt(bp1, bp2, t, Eleft);
}
}
free(bp1);
free(bp2);
free(upst1);
free(upst2);
free(dnst1);
free(dnst2);
}
else if (g_quiet)
{
puts("");
fflush(stdout);
}
}
g_firstSeq = 0;
}
if (!g_quiet)
{
fclose(in1);
fclose(in2);
fclose(dGFile);
}
return EXIT_SUCCESS;
}
void initializeMatrices(double RT)
{
/* initialize L', R' to +infinity for illegal pairs, 0 otherwise */
int i, j;
for (i = 1; i <= g_len1; ++i)
for (j = g_len2; j >= 1; --j)
if (basePairIndex(g_seq1[i], g_seq2[j]) == 6 && !g_allPairs)
{
Lprime(i, j) = INFINITY;
if (rprime)
Rprime(i, j) = INFINITY;
}
else
{
Lprime(i, j) = 0.0;
if (rprime)
Rprime(i, j) = 0.0;
}
}
void limitBasePairs()
{
if (g_bpFile)
{
int i, j, k;
FILE* bp;
for (i = 1; i <= g_len1; ++i)
for (j = 1; j <= g_len2; ++j)
{
Lprime(i, j) = INFINITY;
if (rprime)
Rprime(i, j) = INFINITY;
}
if (!(bp = fopen(g_bpFile, "rt")))
{
perror(g_bpFile);
exit(EXIT_FAILURE);
}
while (fscanf(bp, "%d%d%d", &i, &j, &k) == 3)
for (--k; k >= 0; --k)
{
Lprime(i + k, j - k) = 0;
if (rprime)
Rprime(i + k, j - k) = 0;
}
fclose(bp);
}
}
void prohibit()
{
int i, j, k;
struct constraintListNode* top;
top = prohibitList;
while (top)
{
if (top->i >= 1 && top->i <= g_len1 && top->j >= 1 && top->j <= g_len1 &&
top->k >= 1 && top->k <= g_len2 && top->l >= 1 && top->l <= g_len2)
for (i = top->i; i <= top->j; ++i)
for (j = top->k; j <= top->l; ++j)
{
Lprime(i, j) = INFINITY;
if (rprime)
Rprime(j, i) = INFINITY;
}
else if (top->i >= 1 && top->i <= g_len1 && top->j >= 1 && top->j <= g_len2)
for (k = 0; k < top->k; ++k)
{
Lprime(top->i + k, top->j - k) = INFINITY;
if (rprime)
Rprime(top->i + k, top->j - k) = INFINITY;
}
else if (top->i >= 1 && top->i <= g_len1 && top->j == 0)
for (k = 0; k < top->k; ++k)
for (j = 1; j <= g_len2; ++j)
{
Lprime(top->i + k, j) = INFINITY;
if (rprime)
Rprime(top->i + k, j) = INFINITY;
}
else if (top->j >= 1 && top->j <= g_len2 && top->i == 0)
for (k = 0; k < top->k; ++k)
for (i = 1; i <= g_len1; ++i)
{
Lprime(i, top->j + k) = INFINITY;
if (rprime)
Rprime(i, top->j + k) = INFINITY;
}
top = top->next;
}
}
#if ENABLE_FORCE
void force()
{
int i, j, k;
struct constraintListNode* top;
top = forceList;
while (top)
{
if (top->i >= 1 && top->i <= g_len1)
for (i = 0; i <= g_len1 + 1; ++i)
for (j = i; j <= g_len1 + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->i + k && top->i + k <= j)
ssOK1(i, j) = 0;
if (top->j >= 1 && top->j <= g_len2)
{
if (top->i == 0)
{
for (i = 0; i <= g_len2 + 1; ++i)
for (j = i; j <= g_len2 + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->j + k && top->j + k <= j)
ssOK2(i, j) = 0;
}
else
{
for (i = 0; i <= g_len2 + 1; ++i)
for (j = i; j <= g_len2 + 1; ++j)
for (k = 0; k < top->k; ++k)
if (i <= top->j - k && top->j - k <= j)
ssOK2(i, j) = 0;
}