void done_mat(t_mat **m)
{
done_matrix((*m)->n1, &((*m)->mat));
sfree((*m)->m_ind);
sfree((*m)->erow);
sfree(*m);
*m = NULL;
}
static void jarvis_patrick(int n1,real **mat,int M,int P,
real rmsdcut,t_clusters *clust)
{
t_dist *row;
t_clustid *c;
int **nnb;
int i,j,k,cid,diff,max;
bool bChange;
real **mcpy=NULL;
if (rmsdcut < 0)
rmsdcut = 10000;
/* First we sort the entries in the RMSD matrix row by row.
* This gives us the nearest neighbor list.
*/
snew(nnb,n1);
snew(row,n1);
for(i=0; (i<n1); i++) {
for(j=0; (j<n1); j++) {
row[j].j = j;
row[j].dist = mat[i][j];
}
qsort(row,n1,sizeof(row[0]),rms_dist_comp);
if (M>0) {
/* Put the M nearest neighbors in the list */
snew(nnb[i],M+1);
for(j=k=0; (k<M) && (j<n1) && (mat[i][row[j].j] < rmsdcut); j++)
if (row[j].j != i) {
nnb[i][k] = row[j].j;
k++;
}
nnb[i][k] = -1;
} else {
/* Put all neighbors nearer than rmsdcut in the list */
max=0;
k=0;
for(j=0; (j<n1) && (mat[i][row[j].j] < rmsdcut); j++)
if (row[j].j != i) {
if (k >= max) {
max += 10;
srenew(nnb[i],max);
}
nnb[i][k] = row[j].j;
k++;
}
if (k == max)
srenew(nnb[i],max+1);
nnb[i][k] = -1;
}
}
sfree(row);
if (debug) {
fprintf(debug,"Nearest neighborlist. M = %d, P = %d\n",M,P);
for(i=0; (i<n1); i++) {
fprintf(debug,"i:%5d nbs:",i);
for(j=0; nnb[i][j]>=0; j++)
fprintf(debug,"%5d[%5.3f]",nnb[i][j],mat[i][nnb[i][j]]);
fprintf(debug,"\n");
}
}
c = new_clustid(n1);
fprintf(stderr,"Linking structures ");
/* Use mcpy for temporary storage of booleans */
mcpy = mk_matrix(n1,n1,FALSE);
for(i=0; i<n1; i++)
for(j=i+1; j<n1; j++)
mcpy[i][j] = jp_same(nnb,i,j,P);
do {
fprintf(stderr,"*");
bChange=FALSE;
for(i=0; i<n1; i++) {
for(j=i+1; j<n1; j++)
if (mcpy[i][j]) {
diff = c[j].clust - c[i].clust;
if (diff) {
bChange = TRUE;
if (diff > 0)
c[j].clust = c[i].clust;
else
c[i].clust = c[j].clust;
}
}
}
} while (bChange);
fprintf(stderr,"\nSorting and renumbering clusters\n");
/* Sort on cluster number */
qsort(c,n1,sizeof(c[0]),clust_id_comp);
/* Renumber clusters */
cid = 1;
for(k=1; k<n1; k++) {
if (c[k].clust != c[k-1].clust) {
c[k-1].clust = cid;
cid ++;
} else
c[k-1].clust = cid;
}
c[k-1].clust = cid;
clust->ncl = cid;
for(k=0; k<n1; k++)
clust->cl[c[k].conf] = c[k].clust;
if (debug)
for(k=0; (k<n1); k++)
fprintf(debug,"Cluster index for conformation %d: %d\n",
c[k].conf,c[k].clust);
/* Again, I don't see the point in this... (AF) */
/* for(i=0; (i<n1); i++) { */
/* for(j=0; (j<n1); j++) */
/* mcpy[c[i].conf][c[j].conf] = mat[i][j]; */
/* } */
/* for(i=0; (i<n1); i++) { */
/* for(j=0; (j<n1); j++) */
/* mat[i][j] = mcpy[i][j]; */
/* } */
done_matrix(n1,&mcpy);
sfree(c);
for(i=0; (i<n1); i++)
sfree(nnb[i]);
sfree(nnb);
}
