static gmx_bool parse_int(char **string, int *nr)
{
char *orig, c;
gmx_bool bRet;
orig = *string;
bRet = parse_int_char(string, nr, &c);
if (bRet && c != ' ')
{
*string = orig;
bRet = FALSE;
}
return bRet;
}
static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
t_blocka *block, char ***gn,
atom_id *nr, atom_id *index, char *gname)
{
static char **names, *ostring;
static gmx_bool bFirst = TRUE;
int j, n_names, sel_nr1;
atom_id i, nr1, *index1;
char c;
gmx_bool bRet, bCompl;
if (bFirst)
{
bFirst = FALSE;
snew(names, MAXNAMES);
for (i = 0; i < MAXNAMES; i++)
{
snew(names[i], NAME_LEN+1);
}
}
bRet = FALSE;
sel_nr1 = NOTSET;
while (*string[0] == ' ')
{
(*string)++;
}
if ((*string)[0] == '!')
{
bCompl = TRUE;
(*string)++;
while (*string[0] == ' ')
{
(*string)++;
}
}
else
{
bCompl = FALSE;
}
ostring = *string;
if (parse_int(string, &sel_nr1) ||
parse_string(string, &sel_nr1, block->nr, *gn))
{
if ((sel_nr1 >= 0) && (sel_nr1 < block->nr))
{
copy_group(sel_nr1, block, nr, index);
strcpy(gname, (*gn)[sel_nr1]);
printf("Copied index group %d '%s'\n", sel_nr1, (*gn)[sel_nr1]);
bRet = TRUE;
}
else
{
printf("Group %d does not exist\n", sel_nr1);
}
}
else if ((*string)[0] == 'a')
{
(*string)++;
if (check_have_atoms(atoms, ostring))
{
if (parse_int(string, &sel_nr1))
{
bRet = select_atomnumbers(string, atoms, sel_nr1, nr, index, gname);
}
else if (parse_names(string, &n_names, names))
{
bRet = select_atomnames(atoms, n_names, names, nr, index, FALSE);
make_gname(n_names, names, gname);
}
}
}
else if ((*string)[0] == 't')
{
(*string)++;
if (check_have_atoms(atoms, ostring) &&
parse_names(string, &n_names, names))
{
if (atoms->atomtype == NULL)
{
printf("Need a run input file to select atom types\n");
}
else
{
bRet = select_atomnames(atoms, n_names, names, nr, index, TRUE);
make_gname(n_names, names, gname);
}
}
}
else if (strncmp(*string, "res", 3) == 0)
{
(*string) += 3;
if (check_have_atoms(atoms, ostring) &&
parse_int(string, &sel_nr1) &&
(sel_nr1 >= 0) && (sel_nr1 < block->nr) )
{
bRet = atoms_from_residuenumbers(atoms,
sel_nr1, block, nr, index, (*gn)[sel_nr1]);
sprintf(gname, "atom_%s", (*gn)[sel_nr1]);
}
}
else if (strncmp(*string, "ri", 2) == 0)
{
(*string) += 2;
if (check_have_atoms(atoms, ostring) &&
parse_int_char(string, &sel_nr1, &c))
{
bRet = select_residueindices(string, atoms, sel_nr1, c, nr, index, gname);
}
}
else if ((*string)[0] == 'r')
{
(*string)++;
if (check_have_atoms(atoms, ostring))
{
if (parse_int_char(string, &sel_nr1, &c))
{
bRet = select_residuenumbers(string, atoms, sel_nr1, c, nr, index, gname);
}
else if (parse_names(string, &n_names, names))
{
bRet = select_residuenames(atoms, n_names, names, nr, index);
make_gname(n_names, names, gname);
}
}
}
else if (strncmp(*string, "chain", 5) == 0)
{
(*string) += 5;
if (check_have_atoms(atoms, ostring) &&
parse_names(string, &n_names, names))
{
bRet = select_chainnames(atoms, n_names, names, nr, index);
sprintf(gname, "ch%s", names[0]);
for (i = 1; i < n_names; i++)
{
strcat(gname, names[i]);
}
}
}
if (bRet && bCompl)
{
snew(index1, natoms-*nr);
nr1 = 0;
for (i = 0; i < natoms; i++)
{
j = 0;
while ((j < *nr) && (index[j] != i))
{
j++;
}
if (j == *nr)
{
if (nr1 >= natoms-*nr)
{
printf("There are double atoms in your index group\n");
break;
}
index1[nr1] = i;
nr1++;
}
}
*nr = nr1;
for (i = 0; i < nr1; i++)
{
index[i] = index1[i];
}
sfree(index1);
for (i = strlen(gname)+1; i > 0; i--)
{
gname[i] = gname[i-1];
}
gname[0] = '!';
printf("Complemented group: %d atoms\n", *nr);
}
return bRet;
}
static int select_residueindices(char **string, t_atoms *atoms,
atom_id n1, char c,
atom_id *nr, atom_id *index, char *gname)
{
/*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/
/*resind+1 for 1-indexing*/
char buf[STRLEN];
int i, j, up;
t_resinfo *ri;
*nr = 0;
while ((*string)[0] == ' ')
{
(*string)++;
}
if ((*string)[0] == '-')
{
/* Residue number range selection */
if (c != ' ')
{
printf("Error: residue insertion codes can not be used with residue range selection\n");
return 0;
}
(*string)++;
parse_int(string, &up);
for (i = 0; i < atoms->nr; i++)
{
ri = &atoms->resinfo[atoms->atom[i].resind];
for (j = n1; (j <= up); j++)
{
if (atoms->atom[i].resind+1 == j && (c == ' ' || ri->ic == c))
{
index[*nr] = i;
(*nr)++;
}
}
}
printf("Found %d atom%s with resind.+1 in range %d-%d\n",
*nr, (*nr == 1) ? "" : "s", n1, up);
if (n1 == up)
{
sprintf(buf, "r_%d", n1);
}
else
{
sprintf(buf, "r_%d-%d", n1, up);
}
strcpy(gname, buf);
}
else
{
/* Individual residue number/insertion code selection */
j = n1;
sprintf(gname, "r");
do
{
for (i = 0; i < atoms->nr; i++)
{
ri = &atoms->resinfo[atoms->atom[i].resind];
if (atoms->atom[i].resind+1 == j && ri->ic == c)
{
index[*nr] = i;
(*nr)++;
}
}
sprintf(buf, "_%d", j);
strcat(gname, buf);
}
while (parse_int_char(string, &j, &c));
}
return *nr;
}
static int select_residuenumbers(char **string, const t_atoms *atoms,
int n1, char c,
int *nr, int *index, char *gname)
{
char buf[STRLEN];
int i, j, up;
t_resinfo *ri;
*nr = 0;
while ((*string)[0] == ' ')
{
(*string)++;
}
if ((*string)[0] == '-')
{
/* Residue number range selection */
if (c != ' ')
{
printf("Error: residue insertion codes can not be used with residue range selection\n");
return 0;
}
(*string)++;
parse_int(string, &up);
for (i = 0; i < atoms->nr; i++)
{
ri = &atoms->resinfo[atoms->atom[i].resind];
for (j = n1; (j <= up); j++)
{
if (ri->nr == j && (c == ' ' || ri->ic == c))
{
index[*nr] = i;
(*nr)++;
}
}
}
printf("Found %d atom%s with res.nr. in range %d-%d\n",
*nr, (*nr == 1) ? "" : "s", n1, up);
if (n1 == up)
{
sprintf(buf, "r_%d", n1);
}
else
{
sprintf(buf, "r_%d-%d", n1, up);
}
std::strcpy(gname, buf);
}
else
{
/* Individual residue number/insertion code selection */
j = n1;
sprintf(gname, "r");
do
{
for (i = 0; i < atoms->nr; i++)
{
ri = &atoms->resinfo[atoms->atom[i].resind];
if (ri->nr == j && ri->ic == c)
{
index[*nr] = i;
(*nr)++;
}
}
sprintf(buf, "_%d", j);
std::strcat(gname, buf);
}
while (parse_int_char(string, &j, &c));
}
return *nr;
}