static void strip_dssp(char *dsspfile,int nres,
bool bPhobres[],real t,
real *acc,FILE *fTArea,
t_matrix *mat,int average_area[])
{
static bool bFirst=TRUE;
static char *ssbuf;
FILE *tapeout;
static int xsize,frame;
char buf[STRLEN+1];
char SSTP;
int i,nr,iacc;
real iaccf,iaccb;
t_xpmelmt c;
tapeout=ffopen(dsspfile,"r");
/* Skip header */
do {
fgets2(buf,STRLEN,tapeout);
} while (strstr(buf,"KAPPA") == NULL);
if (bFirst) {
snew(ssbuf,nres+10);
}
iaccb=iaccf=0;
for(nr=0; (fgets2(buf,STRLEN,tapeout) != NULL); nr++) {
SSTP=buf[16]==' ' ? '~' : buf[16];
ssbuf[nr]=SSTP;
buf[39]='\0';
sscanf(&(buf[34]),"%d",&iacc);
acc[nr]=iacc;
average_area[nr]+=iacc;
if (bPhobres[nr])
iaccb+=iacc;
else
iaccf+=iacc;
}
ssbuf[nr]='\0';
if (bFirst) {
sprintf(mat->title,"Secondary structure");
mat->legend[0]=0;
sprintf(mat->label_x,"%s",time_label());
sprintf(mat->label_y,"Residue");
mat->bDiscrete=TRUE;
mat->ny=nr;
snew(mat->axis_y,nr);
for(i=0; i<nr; i++)
mat->axis_y[i]=i+1;
mat->axis_x=NULL;
mat->matrix=NULL;
xsize=0;
frame=0;
bFirst=FALSE;
}
if (frame>=xsize) {
xsize+=10;
srenew(mat->axis_x,xsize);
srenew(mat->matrix,xsize);
}
mat->axis_x[frame]=t;
snew(mat->matrix[frame],nr);
c.c2=0;
for(i=0; i<nr; i++) {
c.c1=ssbuf[i];
mat->matrix[frame][i] = max(0,searchcmap(mat->nmap,mat->map,c));
}
frame++;
mat->nx=frame;
if (fTArea)
fprintf(fTArea,"%10g %10g %10g\n",t,0.01*iaccb,0.01*iaccf);
fclose(tapeout);
}
static int strip_dssp(char *dsspfile, int nres,
gmx_bool bPhobres[], real t,
real *acc, FILE *fTArea,
t_matrix *mat, int average_area[],
const output_env_t oenv)
{
static gmx_bool bFirst = TRUE;
static char *ssbuf;
FILE *tapeout;
static int xsize, frame;
char buf[STRLEN+1];
char SSTP;
int i, nr, iacc, nresidues;
int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
real iaccf, iaccb;
t_xpmelmt c;
tapeout = gmx_ffopen(dsspfile, "r");
/* Skip header */
do
{
fgets2(buf, STRLEN, tapeout);
}
while (strstr(buf, "KAPPA") == NULL);
if (bFirst)
{
/* Since we also have empty lines in the dssp output (temp) file,
* and some line content is saved to the ssbuf variable,
* we need more memory than just nres elements. To be shure,
* we allocate 2*nres-1, since for each chain there is a
* separating line in the temp file. (At most each residue
* could have been defined as a separate chain.) */
snew(ssbuf, 2*nres-1);
}
iaccb = iaccf = 0;
nresidues = 0;
naccf = 0;
naccb = 0;
for (nr = 0; (fgets2(buf, STRLEN, tapeout) != NULL); nr++)
{
if (buf[13] == '!') /* Chain separator line has '!' at pos. 13 */
{
SSTP = '='; /* Chain separator sign '=' */
}
else
{
SSTP = buf[16] == ' ' ? '~' : buf[16];
}
ssbuf[nr] = SSTP;
buf[39] = '\0';
/* Only calculate solvent accessible area if needed */
if ((NULL != acc) && (buf[13] != '!'))
{
sscanf(&(buf[34]), "%d", &iacc);
acc[nr] = iacc;
/* average_area and bPhobres are counted from 0...nres-1 */
average_area[nresidues] += iacc;
if (bPhobres[nresidues])
{
naccb++;
iaccb += iacc;
}
else
{
naccf++;
iaccf += iacc;
}
/* Keep track of the residue number (do not count chain separator lines '!') */
nresidues++;
}
}
ssbuf[nr] = '\0';
if (bFirst)
{
if (0 != acc)
{
fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n", naccb, naccf);
}
sprintf(mat->title, "Secondary structure");
mat->legend[0] = 0;
sprintf(mat->label_x, "%s", output_env_get_time_label(oenv));
sprintf(mat->label_y, "Residue");
mat->bDiscrete = TRUE;
mat->ny = nr;
snew(mat->axis_y, nr);
for (i = 0; i < nr; i++)
{
mat->axis_y[i] = i+1;
}
mat->axis_x = NULL;
mat->matrix = NULL;
xsize = 0;
frame = 0;
bFirst = FALSE;
}
if (frame >= xsize)
{
xsize += 10;
srenew(mat->axis_x, xsize);
srenew(mat->matrix, xsize);
}
mat->axis_x[frame] = t;
snew(mat->matrix[frame], nr);
c.c2 = 0;
for (i = 0; i < nr; i++)
{
c.c1 = ssbuf[i];
mat->matrix[frame][i] = max(0, searchcmap(mat->nmap, mat->map, c));
}
frame++;
mat->nx = frame;
if (fTArea)
{
fprintf(fTArea, "%10g %10g %10g\n", t, 0.01*iaccb, 0.01*iaccf);
}
gmx_ffclose(tapeout);
/* Return the number of lines found in the dssp file (i.e. number
* of redidues plus chain separator lines).
* This is the number of y elements needed for the area xpm file */
return nr;
}
void read_xpm_entry(FILE *in,t_matrix *mm)
{
t_mapping *map;
char *line=NULL,*str,buf[256];
int i,m,col_len,nch,n_axis_x,n_axis_y,llmax;
unsigned int r,g,b;
double u;
bool bGetOnWithIt;
t_xpmelmt c;
mm->flags=0;
mm->title[0]=0;
mm->legend[0]=0;
mm->label_x[0]=0;
mm->label_y[0]=0;
mm->matrix=NULL;
mm->axis_x=NULL;
mm->axis_y=NULL;
mm->bDiscrete=FALSE;
llmax = STRLEN;
while (fgetline(&line,llmax,in) && (strncmp(line,"static",6) != 0)) {
parsestring(line,"title",(mm->title));
parsestring(line,"legend",(mm->legend));
parsestring(line,"x-label",(mm->label_x));
parsestring(line,"y-label",(mm->label_y));
parsestring(line,"type",buf);
}
if (buf[0] && (strcasecmp(buf,"Discrete")==0))
mm->bDiscrete=TRUE;
if (debug)
fprintf(debug,"%s %s %s %s\n",
mm->title,mm->legend,mm->label_x,mm->label_y);
if (strncmp(line,"static",6) != 0)
gmx_input("Invalid XPixMap");
/* Read sizes */
bGetOnWithIt=FALSE;
while (!bGetOnWithIt && fgetline(&line,llmax,in)) {
while (( line[0] != '\"' ) && ( line[0] != '\0' ))
line++;
if ( line[0] == '\"' ) {
line2string(&line);
sscanf(line,"%d %d %d %d",&(mm->nx),&(mm->ny),&(mm->nmap),&nch);
if (nch > 2)
gmx_fatal(FARGS,"Sorry can only read xpm's with at most 2 caracters per pixel\n");
llmax = max(STRLEN,mm->nx+10);
bGetOnWithIt=TRUE;
}
}
if (debug)
fprintf(debug,"mm->nx %d mm->ny %d mm->nmap %d nch %d\n",
mm->nx,mm->ny,mm->nmap,nch);
/* Read color map */
snew(map,mm->nmap);
m=0;
while ((m < mm->nmap) && fgetline(&line,llmax,in)) {
line=strchr(line,'\"');
if (line) {
line++;
/* Read xpm color map entry */
map[m].code.c1 = line[0];
if (nch==1)
map[m].code.c2 = 0;
else
map[m].code.c2 = line[1];
line += nch;
str = strchr(line,'#');
if (str) {
str++;
col_len = 0;
while (isxdigit(str[col_len]))
col_len++;
if (col_len==6) {
sscanf(line,"%*s #%2x%2x%2x",&r,&g,&b);
map[m].rgb.r=r/255.0;
map[m].rgb.g=g/255.0;
map[m].rgb.b=b/255.0;
} else if (col_len==12) {
sscanf(line,"%*s #%4x%4x%4x",&r,&g,&b);
map[m].rgb.r=r/65535.0;
map[m].rgb.g=g/65535.0;
map[m].rgb.b=b/65535.0;
} else
gmx_file("Unsupported or invalid colormap in X PixMap");
} else {
str = strchr(line,'c');
if (str)
str += 2;
else
gmx_file("Unsupported or invalid colormap in X PixMap");
fprintf(stderr,"Using white for color \"%s",str);
map[m].rgb.r = 1;
map[m].rgb.g = 1;
map[m].rgb.b = 1;
}
line=strchr(line,'\"');
line++;
line2string(&line);
map[m].desc = strdup(line);
m++;
}
}
if ( m != mm->nmap )
gmx_fatal(FARGS,"Number of read colors map entries (%d) does not match the number in the header (%d)",m,mm->nmap);
mm->map = map;
/* Read axes, if there are any */
n_axis_x=0;
n_axis_y=0;
bGetOnWithIt=FALSE;
do {
if (strstr(line,"x-axis")) {
line=strstr(line,"x-axis");
skipstr(&line);
if (mm->axis_x==NULL)
snew(mm->axis_x,mm->nx + 1);
while (sscanf(line,"%lf",&u)==1) {
if (n_axis_x > mm->nx) {
gmx_fatal(FARGS,"Too many x-axis labels in xpm (max %d)",mm->nx);
} else if (n_axis_x == mm->nx) {
mm->flags |= MAT_SPATIAL_X;
}
mm->axis_x[n_axis_x] = u;
n_axis_x++;
skipstr(&line);
}
}
else if (strstr(line,"y-axis")) {
line=strstr(line,"y-axis");
skipstr(&line);
if (mm->axis_y==NULL)
snew(mm->axis_y,mm->ny + 1);
while (sscanf(line,"%lf",&u)==1) {
if (n_axis_y > mm->ny) {
gmx_file("Too many y-axis labels in xpm");
} else if (n_axis_y == mm->ny) {
mm->flags |= MAT_SPATIAL_Y;
}
mm->axis_y[n_axis_y] = u;
n_axis_y++;
skipstr(&line);
}
}
} while ((line[0] != '\"') && fgetline(&line,llmax,in));
/* Read matrix */
snew(mm->matrix,mm->nx);
for(i=0; i<mm->nx; i++)
snew(mm->matrix[i],mm->ny);
m=mm->ny-1;
do {
if(m%(1+mm->ny/100)==0)
fprintf(stderr,"%3d%%\b\b\b\b",(100*(mm->ny-m))/mm->ny);
while ((line[0] != '\"') && (line[0] != '\0'))
line++;
if (line[0] != '\"')
gmx_fatal(FARGS,"Not enough caracters in row %d of the matrix\n",m+1);
else {
line++;
for(i=0; i<mm->nx; i++) {
c.c1=line[nch*i];
if (nch==1)
c.c2=0;
else
c.c2=line[nch*i+1];
mm->matrix[i][m]=searchcmap(mm->nmap,mm->map,c);
}
m--;
}
} while ((m>=0) && fgetline(&line,llmax,in));
if (m>=0)
gmx_incons("Not enough rows in the matrix");
}
