-/* molecule, Copyright (c) 2001 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001, 2004 Jamie Zawinski <jwz@jwz.org>
* Draws molecules, based on coordinates from PDB (Protein Data Base) files.
*
* Permission to use, copy, modify, distribute, and sell this software and its
http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
*/
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <dirent.h>
#include <X11/Intrinsic.h>
#define PROGCLASS "Molecule"
static atom_data all_atom_data[] = {
{ "H", 1.17, 0, "White", "Grey70", { 0, }},
{ "C", 1.75, 0, "Grey60", "White", { 0, }},
+ { "CA", 1.80, 0, "Blue", "LightBlue", { 0, }},
{ "N", 1.55, 0, "LightSteelBlue3", "SlateBlue1", { 0, }},
{ "O", 1.40, 0, "Red", "LightPink", { 0, }},
{ "P", 1.28, 0, "MediumPurple", "PaleVioletRed", { 0, }},
};
static argtype vars[] = {
- {(caddr_t *) &molecule_str, "molecule", "Molecule", DEF_MOLECULE,t_String},
- {(caddr_t *) &timeout, "timeout","Seconds",DEF_TIMEOUT,t_Int},
- {(caddr_t *) &do_spin, "spin", "Spin", DEF_SPIN, t_String},
- {(caddr_t *) &do_wander, "wander", "Wander", DEF_WANDER, t_Bool},
- {(caddr_t *) &do_labels, "labels", "Labels", DEF_LABELS, t_Bool},
- {(caddr_t *) &do_titles, "titles", "Titles", DEF_TITLES, t_Bool},
- {(caddr_t *) &do_atoms, "atoms", "Atoms", DEF_ATOMS, t_Bool},
- {(caddr_t *) &do_bonds, "bonds", "Bonds", DEF_BONDS, t_Bool},
- {(caddr_t *) &do_bbox, "bbox", "BBox", DEF_BBOX, t_Bool},
+ {&molecule_str, "molecule", "Molecule", DEF_MOLECULE,t_String},
+ {&timeout, "timeout","Seconds",DEF_TIMEOUT,t_Int},
+ {&do_spin, "spin", "Spin", DEF_SPIN, t_String},
+ {&do_wander, "wander", "Wander", DEF_WANDER, t_Bool},
+ {&do_labels, "labels", "Labels", DEF_LABELS, t_Bool},
+ {&do_titles, "titles", "Titles", DEF_TITLES, t_Bool},
+ {&do_atoms, "atoms", "Atoms", DEF_ATOMS, t_Bool},
+ {&do_bonds, "bonds", "Bonds", DEF_BONDS, t_Bool},
+ {&do_bbox, "bbox", "BBox", DEF_BBOX, t_Bool},
};
ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
for (i = 0; i < countof(all_atom_data); i++)
{
d = &all_atom_data[i];
- if (!strcmp (n, all_atom_data[i].name))
+ if (!strcasecmp (n, all_atom_data[i].name))
break;
}
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss-- = 0;
+ ss = name + 1;
+ while(*ss)
+ {
+ *ss = tolower(*ss);
+ ss++;
+ }
sscanf (s + 32, " %f %f %f ", &x, &y, &z);
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
+ Bool verbose_p = False;
+ int i;
if (!molecule_str || !*molecule_str ||
!strcmp(molecule_str, "(default)")) /* do the builtins */
{
- int i;
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);
- generate_molecule_formula (&mc->molecules[i]);
- insert_vertical_whitespace ((char *) mc->molecules[i].label);
}
}
else /* Load a file */
{
- int i = 0;
- mc->nmolecules = 1;
- mc->molecules = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
- parse_pdb_file (&mc->molecules[i], molecule_str);
- generate_molecule_formula (&mc->molecules[i]);
- insert_vertical_whitespace ((char *) mc->molecules[i].label);
+ /* 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;
+
+ 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);
+ exit (1);
+ }
+ }
+ 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);
+ }
- if ((wire || !do_atoms) &&
- !do_labels &&
- mc->molecules[i].nbonds == 0)
+ mc->nmolecules = nfiles;
+ mc->molecules = (molecule *) calloc (sizeof (molecule), mc->nmolecules);
+ for (i = 0; i < mc->nmolecules; i++)
{
- /* 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: no bonds: turning -label on.\n", progname);
- do_labels = 1;
+ if (verbose_p)
+ fprintf (stderr, "%s: reading %s\n", progname, files[i]);
+ parse_pdb_file (&mc->molecules[i], files[i]);
+
+ if ((wire || !do_atoms) &&
+ !do_labels &&
+ mc->molecules[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... */
+ fprintf (stderr, "%s: %s: no bonds: turning -label on.\n",
+ progname, files[i]);
+ do_labels = 1;
+ }
+
+ free (files[i]);
+ files[i] = 0;
}
+
+ free (files);
+ files = 0;
+ }
+
+ for (i = 0; i < mc->nmolecules; i++)
+ {
+ generate_molecule_formula (&mc->molecules[i]);
+ insert_vertical_whitespace ((char *) mc->molecules[i].label);
}
}
projects / xscreensaver / blobdiff