void mk_bonds(int nnm, t_nm2type nmt[],
t_atoms *atoms, rvec x[], t_params *bond, int nbond[],
gmx_bool bPBC, matrix box)
{
t_param b;
int i, j;
t_pbc pbc;
rvec dx;
real dx2;
for (i = 0; (i < MAXATOMLIST); i++)
{
b.a[i] = -1;
}
for (i = 0; (i < MAXFORCEPARAM); i++)
{
b.c[i] = 0.0;
}
if (bPBC)
{
set_pbc(&pbc, -1, box);
}
for (i = 0; (i < atoms->nr); i++)
{
if ((i % 10) == 0)
{
fprintf(stderr, "\ratom %d", i);
}
for (j = i+1; (j < atoms->nr); j++)
{
if (bPBC)
{
pbc_dx(&pbc, x[i], x[j], dx);
}
else
{
rvec_sub(x[i], x[j], dx);
}
dx2 = iprod(dx, dx);
if (is_bond(nnm, nmt, *atoms->atomname[i], *atoms->atomname[j],
sqrt(dx2)))
{
b.AI = i;
b.AJ = j;
b.C0 = sqrt(dx2);
add_param_to_list (bond, &b);
nbond[i]++;
nbond[j]++;
if (debug)
{
fprintf(debug, "Bonding atoms %s-%d and %s-%d\n",
*atoms->atomname[i], i+1, *atoms->atomname[j], j+1);
}
}
}
}
fprintf(stderr, "\ratom %d\n", i);
}
int mk_specbonds(t_atoms *pdba,rvec x[],gmx_bool bInteractive,
t_ssbond **specbonds,gmx_bool bVerbose)
{
t_specbond *sb=NULL;
t_ssbond *bonds=NULL;
int nsb;
int nspec,nbonds;
int *specp,*sgp;
gmx_bool bDoit,bSwap;
int i,j,b,e,e2;
int ai,aj,index_sb;
real **d;
char buf[10];
nbonds = 0;
sb = get_specbonds(&nsb);
if (nsb > 0) {
snew(specp,pdba->nr);
snew(sgp,pdba->nr);
nspec = 0;
for(i=0; (i<pdba->nr); i++) {
/* Check if this atom is special and if it is not a double atom
* in the input that still needs to be removed.
*/
if (is_special(nsb,sb,*pdba->resinfo[pdba->atom[i].resind].name,
*pdba->atomname[i]) &&
!(nspec > 0 &&
pdba->atom[sgp[nspec-1]].resind == pdba->atom[i].resind &&
gmx_strcasecmp(*pdba->atomname[sgp[nspec-1]],
*pdba->atomname[i]) == 0)) {
specp[nspec] = pdba->atom[i].resind;
sgp[nspec] = i;
nspec++;
}
}
/* distance matrix d[nspec][nspec] */
snew(d,nspec);
for(i=0; (i<nspec); i++)
snew(d[i],nspec);
for(i=0; (i<nspec); i++) {
ai=sgp[i];
for(j=0; (j<nspec); j++) {
aj=sgp[j];
d[i][j]=sqrt(distance2(x[ai],x[aj]));
}
}
if (nspec > 1) {
#define MAXCOL 7
fprintf(stderr,"Special Atom Distance matrix:\n");
for(b=0; (b<nspec); b+=MAXCOL) {
/* print resname/number column headings */
fprintf(stderr,"%8s%8s","","");
e=min(b+MAXCOL, nspec-1);
for(i=b; (i<e); i++) {
sprintf(buf,"%s%d",*pdba->resinfo[pdba->atom[sgp[i]].resind].name,
pdba->resinfo[specp[i]].nr);
fprintf(stderr,"%8s",buf);
}
fprintf(stderr,"\n");
/* print atomname/number column headings */
fprintf(stderr,"%8s%8s","","");
e=min(b+MAXCOL, nspec-1);
for(i=b; (i<e); i++) {
sprintf(buf,"%s%d",*pdba->atomname[sgp[i]], sgp[i]+1);
fprintf(stderr,"%8s",buf);
}
fprintf(stderr,"\n");
/* print matrix */
e=min(b+MAXCOL, nspec);
for(i=b+1; (i<nspec); i++) {
sprintf(buf,"%s%d",*pdba->resinfo[pdba->atom[sgp[i]].resind].name,
pdba->resinfo[specp[i]].nr);
fprintf(stderr,"%8s",buf);
sprintf(buf,"%s%d", *pdba->atomname[sgp[i]], sgp[i]+1);
fprintf(stderr,"%8s",buf);
e2=min(i,e);
for(j=b; (j<e2); j++)
fprintf(stderr," %7.3f",d[i][j]);
fprintf(stderr,"\n");
}
}
}
snew(bonds,nspec);
for(i=0; (i<nspec); i++) {
ai = sgp[i];
for(j=i+1; (j<nspec); j++) {
aj = sgp[j];
if (is_bond(nsb,sb,pdba,ai,aj,d[i][j],&index_sb,&bSwap)) {
fprintf(stderr,"%s %s-%d %s-%d and %s-%d %s-%d%s",
bInteractive ? "Link" : "Linking",
*pdba->resinfo[pdba->atom[ai].resind].name,
pdba->resinfo[specp[i]].nr,
*pdba->atomname[ai], ai+1,
*pdba->resinfo[pdba->atom[aj].resind].name,
pdba->resinfo[specp[j]].nr,
*pdba->atomname[aj], aj+1,
bInteractive ? " (y/n) ?" : "...\n");
bDoit=bInteractive ? yesno() : TRUE;
if (bDoit) {
/* Store the residue numbers in the bonds array */
bonds[nbonds].res1 = specp[i];
bonds[nbonds].res2 = specp[j];
bonds[nbonds].a1 = strdup(*pdba->atomname[ai]);
bonds[nbonds].a2 = strdup(*pdba->atomname[aj]);
/* rename residues */
if (bSwap) {
rename_1res(pdba,specp[i],sb[index_sb].newres2,bVerbose);
rename_1res(pdba,specp[j],sb[index_sb].newres1,bVerbose);
}
else {
rename_1res(pdba,specp[i],sb[index_sb].newres1,bVerbose);
rename_1res(pdba,specp[j],sb[index_sb].newres2,bVerbose);
}
nbonds++;
}
}
}
}
for(i=0; (i<nspec); i++)
sfree(d[i]);
sfree(d);
sfree(sgp);
sfree(specp);
done_specbonds(nsb,sb);
sfree(sb);
}
*specbonds=bonds;
return nbonds;
}
