/* Construct the molecule data from either: the builtins; or from
the (one) .pdb file specified with -molecule.
*/
static void
load_molecules (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = cur_wire;
if (!molecule_str || !*molecule_str ||
!strcmp(molecule_str, "(default)")) /* do the builtins */
{
int i;
mc->nmolecules = countof(builtin_pdb_data);
if (!mols) {
mols = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
for (i = 0; i < mc->nmolecules; i++)
{
char name[100];
(void) sprintf (name, "<builtin-%d>", i);
parse_pdb_data (&mols[i], builtin_pdb_data[i], name, 1);
generate_molecule_formula (&mols[i]);
insert_vertical_whitespace ((char *) mols[i].label);
}
}
mc->molecules = mols;
}
else /* Load a file */
{
int i = 0;
mc->nmolecules = 1;
if (!mols) {
mols = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
parse_pdb_file (&mols[i], molecule_str);
generate_molecule_formula (&mols[i]);
insert_vertical_whitespace ((char *) mols[i].label);
if ((wire || !do_atoms) &&
!do_labels &&
mols[i].nbonds == 0)
{
/* If we're not drawing atoms (e.g., wireframe mode), and
there is no bond info, then make sure labels are turned on,
or we'll be looking at a black screen... */
(void) fprintf (stderr, "molecule: no bonds: turning -label on.\n");
do_labels = 1;
}
}
mc->molecules = mols;
}
}
/* Construct the molecule data from either: the builtins; or from
the (one) .pdb file specified with -molecule.
*/
static void
load_molecules (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
int i;
mc->nmolecules = 0;
if (molecule_str && *molecule_str &&
strcmp(molecule_str, "(default)")) /* try external PDB files */
{
/* The -molecule option can point to a .pdb file, or to
a directory of them.
*/
struct stat st;
int nfiles = 0;
int list_size = 0;
char **files = 0;
int molecule_ctr;
if (!stat (molecule_str, &st) &&
S_ISDIR (st.st_mode))
{
char buf [255];
DIR *pdb_dir;
struct dirent *dentry;
pdb_dir = opendir (molecule_str);
if (! pdb_dir)
{
sprintf (buf, "%.100s: %.100s", progname, molecule_str);
perror (buf);
exit (1);
}
if (verbose_p)
fprintf (stderr, "%s: directory %s\n", progname, molecule_str);
nfiles = 0;
list_size = 100;
files = (char **) calloc (sizeof(*files), list_size);
while ((dentry = readdir (pdb_dir)))
{
int L = strlen (dentry->d_name);
if (L > 4 && !strcasecmp (dentry->d_name + L - 4, ".pdb"))
{
char *fn;
if (nfiles >= list_size-1)
{
list_size = (list_size + 10) * 1.2;
files = (char **)
realloc (files, list_size * sizeof(*files));
if (!files)
{
OOM:
fprintf (stderr, "%s: out of memory (%d files)\n",
progname, nfiles);
exit (1);
}
}
fn = (char *) malloc (strlen (molecule_str) + L + 10);
if (!fn) goto OOM;
strcpy (fn, molecule_str);
if (fn[strlen(fn)-1] != '/') strcat (fn, "/");
strcat (fn, dentry->d_name);
files[nfiles++] = fn;
if (verbose_p)
fprintf (stderr, "%s: file %s\n", progname, fn);
}
}
closedir (pdb_dir);
if (nfiles == 0)
fprintf (stderr, "%s: no .pdb files in directory %s\n",
progname, molecule_str);
}
else
{
files = (char **) malloc (sizeof (*files));
nfiles = 1;
files[0] = strdup (molecule_str);
if (verbose_p)
fprintf (stderr, "%s: file %s\n", progname, molecule_str);
}
mc->nmolecules = nfiles;
mc->molecules = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
molecule_ctr = 0;
for (i = 0; i < mc->nmolecules; i++)
{
if (verbose_p)
fprintf (stderr, "%s: reading %s\n", progname, files[i]);
if (!parse_pdb_file (&mc->molecules[molecule_ctr], files[i]))
{
if ((wire || !do_atoms) &&
!do_labels &&
mc->molecules[molecule_ctr].nbonds == 0)
{
/* If we're not drawing atoms (e.g., wireframe mode), and
there is no bond info, then make sure labels are turned
on, or we'll be looking at a black screen... */
fprintf (stderr, "%s: %s: no bonds: turning -label on.\n",
progname, files[i]);
do_labels = 1;
}
free (files[i]);
files[i] = 0;
molecule_ctr++;
}
}
free (files);
files = 0;
mc->nmolecules = molecule_ctr;
}
if (mc->nmolecules == 0) /* do the builtins if no files */
{
mc->nmolecules = countof(builtin_pdb_data);
mc->molecules = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
for (i = 0; i < mc->nmolecules; i++)
{
char name[100];
sprintf (name, "<builtin-%d>", i);
if (verbose_p) fprintf (stderr, "%s: reading %s\n", progname, name);
parse_pdb_data (&mc->molecules[i], builtin_pdb_data[i], name, 1);
}
}
for (i = 0; i < mc->nmolecules; i++)
{
generate_molecule_formula (&mc->molecules[i]);
insert_vertical_whitespace ((char *) mc->molecules[i].label);
}
}
