void print_bondeds(FILE *out, int natoms, directive d,
int ftype, int fsubtype, t_params plist[])
{
t_symtab stab;
gpp_atomtype_t atype;
t_param *param;
t_atom *a;
int i;
atype = init_atomtype();
snew(a, 1);
snew(param, 1);
open_symtab(&stab);
for (i = 0; (i < natoms); i++)
{
char buf[12];
sprintf(buf, "%4d", (i+1));
add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
}
print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
done_symtab(&stab);
sfree(a);
sfree(param);
done_atomtype(atype);
}
gpp_atomtype_t read_atype(const char *ffdir, t_symtab *tab)
{
int nfile, f;
char **file;
FILE *in;
char buf[STRLEN], name[STRLEN];
double m;
int nratt = 0;
gpp_atomtype_t at;
t_atom *a;
t_param *nb;
nfile = fflib_search_file_end(ffdir, ".atp", TRUE, &file);
at = init_atomtype();
snew(a, 1);
snew(nb, 1);
for (f = 0; f < nfile; f++)
{
in = fflib_open(file[f]);
while (!feof(in))
{
/* Skip blank or comment-only lines */
do
{
if (fgets2(buf, STRLEN, in) != NULL)
{
strip_comment(buf);
trim(buf);
}
}
while (!feof(in) && strlen(buf) == 0);
if (sscanf(buf, "%s%lf", name, &m) == 2)
{
a->m = m;
add_atomtype(at, tab, a, name, nb, 0, 0.0, 0.0, 0.0, 0, 0.0, 0.0 );
fprintf(stderr, "\rAtomtype %d", ++nratt);
fflush(stderr);
}
else
{
fprintf(stderr, "\nInvalid format: %s\n", buf);
}
}
gmx_ffclose(in);
sfree(file[f]);
}
fprintf(stderr, "\n");
sfree(file);
return at;
}
int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
gpp_atomtype_t atype, int *nbonds, t_params *bonds)
{
int cur = 0;
#define prev (1-cur)
int i, j, k, m, n, nresolved, nb, maxbond, ai, aj, best, im, nqual[2][ematchNR];
int *bbb, *n_mask, *m_mask, **match, **quality;
char *aname_i, *aname_m, *aname_n, *type;
double qq, mm;
t_param *param;
snew(param, 1);
maxbond = 0;
for (i = 0; (i < atoms->nr); i++)
{
maxbond = max(maxbond, nbonds[i]);
}
if (debug)
{
fprintf(debug, "Max number of bonds per atom is %d\n", maxbond);
}
snew(bbb, maxbond);
snew(n_mask, maxbond);
snew(m_mask, maxbond);
snew(match, maxbond);
for (i = 0; (i < maxbond); i++)
{
snew(match[i], maxbond);
}
nresolved = 0;
for (i = 0; (i < atoms->nr); i++)
{
aname_i = *atoms->atomname[i];
nb = 0;
for (j = 0; (j < bonds->nr); j++)
{
ai = bonds->param[j].AI;
aj = bonds->param[j].AJ;
if (ai == i)
{
bbb[nb++] = aj;
}
else if (aj == i)
{
bbb[nb++] = ai;
}
}
if (nb != nbonds[i])
{
gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d",
nb, i, nbonds[i]);
}
if (debug)
{
fprintf(debug, "%4s has bonds to", aname_i);
for (j = 0; (j < nb); j++)
{
fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
}
fprintf(debug, "\n");
}
best = -1;
for (k = 0; (k < ematchNR); k++)
{
nqual[prev][k] = 0;
}
/* First check for names */
for (k = 0; (k < nnm); k++)
{
if (nm2t[k].nbonds == nb)
{
im = match_str(*atoms->atomname[i], nm2t[k].elem);
if (im > ematchWild)
{
for (j = 0; (j < ematchNR); j++)
{
nqual[cur][j] = 0;
}
/* Fill a matrix with matching quality */
for (m = 0; (m < nb); m++)
{
aname_m = *atoms->atomname[bbb[m]];
for (n = 0; (n < nb); n++)
{
aname_n = nm2t[k].bond[n];
match[m][n] = match_str(aname_m, aname_n);
}
}
/* Now pick the best matches */
for (m = 0; (m < nb); m++)
{
n_mask[m] = 0;
m_mask[m] = 0;
}
for (j = ematchNR-1; (j > 0); j--)
{
for (m = 0; (m < nb); m++)
{
for (n = 0; (n < nb); n++)
{
if ((n_mask[n] == 0) &&
(m_mask[m] == 0) &&
(match[m][n] == j))
{
n_mask[n] = 1;
m_mask[m] = 1;
nqual[cur][j]++;
}
}
}
}
if ((nqual[cur][ematchExact]+
nqual[cur][ematchElem]+
nqual[cur][ematchWild]) == nb)
{
if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
(nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
(nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
(nqual[cur][ematchWild] > nqual[prev][ematchWild])))
{
best = k;
cur = prev;
}
}
}
}
}
if (best != -1)
{
int atomnr = 0;
real alpha = 0;
qq = nm2t[best].q;
mm = nm2t[best].m;
type = nm2t[best].type;
if ((k = get_atomtype_type(type, atype)) == NOTSET)
{
atoms->atom[i].qB = alpha;
atoms->atom[i].m = atoms->atom[i].mB = mm;
k = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
}
atoms->atom[i].type = k;
atoms->atom[i].typeB = k;
atoms->atom[i].q = qq;
atoms->atom[i].qB = qq;
atoms->atom[i].m = mm;
atoms->atom[i].mB = mm;
nresolved++;
}
else
{
fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
*atoms->atomname[i], i+1, nb);
}
}
sfree(bbb);
sfree(n_mask);
sfree(m_mask);
sfree(param);
return nresolved;
}
