int gmx_dih(int argc,char *argv[])
{
const char *desc[] = {
"g_dih can do two things. The default is to analyze dihedral transitions",
"by merely computing all the dihedral angles defined in your topology",
"for the whole trajectory. When a dihedral flips over to another minimum",
"an angle/time plot is made.[PAR]",
"The opther option is to discretize the dihedral space into a number of",
"bins, and group each conformation in dihedral space in the",
"appropriate bin. The output is then given as a number of dihedral",
"conformations sorted according to occupancy."
};
static int mult = -1;
static bool bSA = FALSE;
t_pargs pa[] = {
{ "-sa", FALSE, etBOOL, {&bSA},
"Perform cluster analysis in dihedral space instead of analysing dihedral transitions." },
{ "-mult", FALSE, etINT, {&mult},
"mulitiplicity for dihedral angles (by default read from topology)" }
};
FILE *out;
t_xrama *xr;
t_topology *top;
real **dih,*time;
real dd;
int i,nframes,maxframes=1000;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efOUT, NULL, NULL, ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (mult != -1)
fprintf(stderr,"Using %d for dihedral multiplicity rather than topology values\n",mult);
snew(xr,1);
init_rama(ftp2fn(efTRX,NFILE,fnm),
ftp2fn(efTPX,NFILE,fnm),xr,3);
top=read_top(ftp2fn(efTPX,NFILE,fnm),NULL);
/* Brute force malloc, may be too big... */
snew(dih,xr->ndih);
for(i=0; (i<xr->ndih); i++)
snew(dih[i],maxframes);
snew(time,maxframes);
fprintf(stderr,"\n");
nframes = 0;
while (new_data(xr)) {
for(i=0; (i<xr->ndih); i++) {
dd=xr->dih[i].ang*RAD2DEG;
while (dd < 0)
dd+=360;
while (dd > 360)
dd-=360;
dih[i][nframes]=dd;
}
time[nframes]=xr->t;
nframes++;
if (nframes > maxframes) {
maxframes += 1000;
for(i=0; (i<xr->ndih); i++)
srenew(dih[i],maxframes);
srenew(time,maxframes);
}
}
fprintf(stderr,"\nCalculated all dihedrals, now analysing...\n");
out=ftp2FILE(efOUT,NFILE,fnm,"w");
if (bSA) {
/* Cluster and structure analysis */
ana_cluster(out,xr,dih,time,top,nframes,mult);
}
else {
/* Analyse transitions... */
ana_trans(out,xr,dih,time,top,nframes);
}
fclose(out);
thanx(stderr);
return 0;
}
static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
int natom, t_atoms *atoms, rvec *xtps,
real *mass, rvec **xx, real *time,
int ifsize, atom_id *fitidx,
int iosize, atom_id *outidx,
char *trxfn, char *sizefn, char *transfn,
char *ntransfn, char *clustidfn, bool bAverage,
int write_ncl, int write_nst, real rmsmin,bool bFit,
FILE *log,t_rgb rlo,t_rgb rhi)
{
FILE *fp=NULL;
char buf[STRLEN],buf1[40],buf2[40],buf3[40],*trxsfn;
int trxout=0,trxsout=0;
int i,i1,cl,nstr,*structure,first=0,midstr;
bool *bWrite=NULL;
real r,clrmsd,midrmsd;
rvec *xav=NULL;
matrix zerobox;
clear_mat(zerobox);
ffprintf1(stderr,log,buf,"\nFound %d clusters\n\n",clust->ncl);
trxsfn=NULL;
if (trxfn) {
/* do we write all structures? */
if (write_ncl) {
trxsfn = parse_filename(trxfn, max(write_ncl,clust->ncl));
snew(bWrite,nf);
}
ffprintf2(stderr,log,buf,"Writing %s structure for each cluster to %s\n",
bAverage ? "average" : "middle", trxfn);
if (write_ncl) {
/* find out what we want to tell the user:
Writing [all structures|structures with rmsd > %g] for
{all|first %d} clusters {with more than %d structures} to %s */
if (rmsmin>0.0)
sprintf(buf1,"structures with rmsd > %g",rmsmin);
else
sprintf(buf1,"all structures");
buf2[0]=buf3[0]='\0';
if (write_ncl>=clust->ncl) {
if (write_nst==0)
sprintf(buf2,"all ");
} else
sprintf(buf2,"the first %d ",write_ncl);
if (write_nst)
sprintf(buf3," with more than %d structures",write_nst);
sprintf(buf,"Writing %s for %sclusters%s to %s\n",buf1,buf2,buf3,trxsfn);
ffprintf(stderr,log,buf);
}
/* Prepare a reference structure for the orientation of the clusters */
if (bFit)
reset_x(ifsize,fitidx,natom,NULL,xtps,mass);
trxout = open_trx(trxfn,"w");
/* Calculate the average structure in each cluster, *
* all structures are fitted to the first struture of the cluster */
snew(xav,natom);
}
if (transfn || ntransfn)
ana_trans(clust, nf, transfn, ntransfn, log,rlo,rhi);
if (clustidfn) {
fp=xvgropen(clustidfn,"Clusters",xvgr_tlabel(),"Cluster #");
fprintf(fp,"@ s0 symbol 2\n");
fprintf(fp,"@ s0 symbol size 0.2\n");
fprintf(fp,"@ s0 linestyle 0\n");
for(i=0; i<nf; i++)
fprintf(fp,"%8g %8d\n",time[i],clust->cl[i]);
ffclose(fp);
}
if (sizefn) {
fp=xvgropen(sizefn,"Cluster Sizes","Cluster #","# Structures");
fprintf(fp,"@g%d type %s\n",0,"bar");
}
snew(structure,nf);
fprintf(log,"\n%3s | %3s %4s | %6s %4s | cluster members\n",
"cl.","#st","rmsd","middle","rmsd");
for(cl=1; cl<=clust->ncl; cl++) {
/* prepare structures (fit, middle, average) */
if (xav)
for(i=0; i<natom;i++)
clear_rvec(xav[i]);
nstr=0;
for(i1=0; i1<nf; i1++)
if (clust->cl[i1] == cl) {
structure[nstr] = i1;
nstr++;
if (trxfn && (bAverage || write_ncl) ) {
if (bFit)
reset_x(ifsize,fitidx,natom,NULL,xx[i1],mass);
if (nstr == 1)
first = i1;
else if (bFit)
do_fit(natom,mass,xx[first],xx[i1]);
if (xav)
for(i=0; i<natom; i++)
rvec_inc(xav[i],xx[i1][i]);
}
}
if (sizefn)
fprintf(fp,"%8d %8d\n",cl,nstr);
clrmsd = 0;
midstr = 0;
midrmsd = 10000;
for(i1=0; i1<nstr; i1++) {
r = 0;
if (nstr > 1) {
for(i=0; i<nstr; i++)
if (i < i1)
r += rmsd[structure[i]][structure[i1]];
else
r += rmsd[structure[i1]][structure[i]];
r /= (nstr - 1);
}
if ( r < midrmsd ) {
midstr = structure[i1];
midrmsd = r;
}
clrmsd += r;
}
clrmsd /= nstr;
/* dump cluster info to logfile */
if (nstr > 1) {
sprintf(buf1,"%5.3f",clrmsd);
if (buf1[0] == '0')
buf1[0] = ' ';
sprintf(buf2,"%5.3f",midrmsd);
if (buf2[0] == '0')
buf2[0] = ' ';
} else {
sprintf(buf1,"%5s","");
sprintf(buf2,"%5s","");
}
fprintf(log,"%3d | %3d%s | %6g%s |",cl,nstr,buf1,time[midstr],buf2);
for(i=0; i<nstr; i++) {
if ((i % 7 == 0) && i)
sprintf(buf,"\n%3s | %3s %4s | %6s %4s |","","","","","");
else
buf[0] = '\0';
i1 = structure[i];
fprintf(log,"%s %6g",buf,time[i1]);
}
fprintf(log,"\n");
/* write structures to trajectory file(s) */
if (trxfn) {
if (write_ncl)
for(i=0; i<nstr; i++)
bWrite[i]=FALSE;
if ( cl < write_ncl+1 && nstr > write_nst ) {
/* Dump all structures for this cluster */
/* generate numbered filename (there is a %d in trxfn!) */
sprintf(buf,trxsfn,cl);
trxsout = open_trx(buf,"w");
for(i=0; i<nstr; i++) {
bWrite[i] = TRUE;
if (rmsmin>0.0)
for(i1=0; i1<i && bWrite[i]; i1++)
if (bWrite[i1])
bWrite[i] = rmsd[structure[i1]][structure[i]] > rmsmin;
if (bWrite[i])
write_trx(trxsout,iosize,outidx,atoms,i,time[structure[i]],zerobox,
xx[structure[i]],NULL);
}
close_trx(trxsout);
}
/* Dump the average structure for this cluster */
if (bAverage) {
for(i=0; i<natom; i++)
svmul(1.0/nstr,xav[i],xav[i]);
} else {
for(i=0; i<natom; i++)
copy_rvec(xx[midstr][i],xav[i]);
if (bFit)
reset_x(ifsize,fitidx,natom,NULL,xav,mass);
}
if (bFit)
do_fit(natom,mass,xtps,xav);
r = cl;
write_trx(trxout,iosize,outidx,atoms,cl,time[midstr],zerobox,xav,NULL);
}
}
/* clean up */
if (trxfn) {
close_trx(trxout);
sfree(xav);
if (write_ncl)
sfree(bWrite);
}
sfree(structure);
if (trxsfn)
sfree(trxsfn);
}
