-/* 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"
#define DEF_BONDS "True"
#define DEF_BBOX "False"
#define DEF_MOLECULE "(default)"
+#define DEF_VERBOSE "False"
#define DEFAULTS "*delay: 10000 \n" \
"*timeout: " DEF_TIMEOUT "\n" \
"*showFPS: False \n" \
"*wireframe: False \n" \
+ "*verbose: " DEF_VERBOSE "\n" \
"*molecule: " DEF_MOLECULE "\n" \
"*spin: " DEF_SPIN "\n" \
"*wander: " DEF_WANDER "\n" \
#include "colors.h"
#include "sphere.h"
#include "tube.h"
+#include "glxfonts.h"
#include "rotator.h"
#include "gltrackball.h"
#include <sys/time.h>
#include <GL/glu.h>
-#define SPHERE_SLICES 16 /* how densely to render spheres */
-#define SPHERE_STACKS 10
+#define SPHERE_SLICES 24 /* how densely to render spheres */
+#define SPHERE_STACKS 12
#define SMOOTH_TUBE /* whether to have smooth or faceted tubes */
#define TUBE_FACES_2 3
+# ifdef __GNUC__
+ __extension__ /* don't warn about "string length is greater than the length
+ ISO C89 compilers are required to support" when includng
+ the following data file... */
+# endif
const char * const builtin_pdb_data[] = {
# include "molecules.h"
};
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, }},
int nmolecules;
molecule *molecules;
+ int mode; /* 0 = normal, 1 = out, 2 = in */
+ int mode_tick;
+
GLuint molecule_dlist;
XFontStruct *xfont1, *xfont2;
static Bool do_atoms;
static Bool do_bonds;
static Bool do_bbox;
+static Bool verbose_p;
static Bool orig_do_labels, orig_do_bonds, orig_wire; /* saved to reset */
{ "+atoms", ".atoms", XrmoptionNoArg, "False" },
{ "-bonds", ".bonds", XrmoptionNoArg, "True" },
{ "+bonds", ".bonds", XrmoptionNoArg, "False" },
- { "-bbox", ".bbox", XrmoptionNoArg, "True" },
- { "+bbox", ".bbox", XrmoptionNoArg, "False" },
+ { "-bbox", ".bbox", XrmoptionNoArg, "True" },
+ { "+bbox", ".bbox", XrmoptionNoArg, "False" },
+ { "-verbose",".verbose",XrmoptionNoArg, "True" },
};
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},
+ {&verbose_p, "verbose","Verbose",DEF_VERBOSE,t_Bool},
};
ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
}
-static void
-load_font (ModeInfo *mi, char *res, XFontStruct **fontP, GLuint *dlistP)
-{
- const char *font = get_string_resource (res, "Font");
- XFontStruct *f;
- Font id;
- int first, last;
-
- if (!font) font = "-*-times-bold-r-normal-*-180-*";
-
- f = XLoadQueryFont(mi->dpy, font);
- if (!f) f = XLoadQueryFont(mi->dpy, "fixed");
-
- id = f->fid;
- first = f->min_char_or_byte2;
- last = f->max_char_or_byte2;
-
- clear_gl_error ();
- *dlistP = glGenLists ((GLuint) last+1);
- check_gl_error ("glGenLists");
- glXUseXFont(id, first, last-first+1, *dlistP + first);
- check_gl_error ("glXUseXFont");
-
- *fontP = f;
-}
-
-
static void
load_fonts (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- load_font (mi, "atomFont", &mc->xfont1, &mc->font1_dlist);
- load_font (mi, "titleFont", &mc->xfont2, &mc->font2_dlist);
-}
-
-
-static int
-string_width (XFontStruct *f, const char *c)
-{
- int w = 0;
- while (*c)
- {
- int cc = *((unsigned char *) c);
- w += (f->per_char
- ? f->per_char[cc-f->min_char_or_byte2].rbearing
- : f->min_bounds.rbearing);
- c++;
- }
- return w;
+ load_font (mi->dpy, "atomFont", &mc->xfont1, &mc->font1_dlist);
+ load_font (mi->dpy, "titleFont", &mc->xfont2, &mc->font2_dlist);
}
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;
}
}
-static void
-print_title_string (ModeInfo *mi, const char *string,
- GLfloat x, GLfloat y, XFontStruct *font)
-{
- molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- GLfloat line_height = font->ascent + font->descent;
- GLfloat sub_shift = (line_height * 0.3);
-
- y -= line_height;
-
- glPushAttrib (GL_TRANSFORM_BIT | /* for matrix contents */
- GL_ENABLE_BIT); /* for various glDisable calls */
- glDisable (GL_LIGHTING);
- glDisable (GL_DEPTH_TEST);
- {
- glMatrixMode(GL_PROJECTION);
- glPushMatrix();
- {
- glLoadIdentity();
-
- glMatrixMode(GL_MODELVIEW);
- glPushMatrix();
- {
- int i;
- int x2 = x;
- Bool sub_p = False;
- glLoadIdentity();
-
- gluOrtho2D (0, mi->xgwa.width, 0, mi->xgwa.height);
-
- set_atom_color (mi, 0, True);
-
- glRasterPos2f (x, y);
- for (i = 0; i < strlen(string); i++)
- {
- char c = string[i];
- if (c == '\n')
- {
- glRasterPos2f (x, (y -= line_height));
- x2 = x;
- }
- else if (c == '(' && (isdigit (string[i+1])))
- {
- sub_p = True;
- glRasterPos2f (x2, (y -= sub_shift));
- }
- else if (c == ')' && sub_p)
- {
- sub_p = False;
- glRasterPos2f (x2, (y += sub_shift));
- }
- else
- {
- glCallList (mc->font2_dlist + (int)(c));
- x2 += (font->per_char
- ? font->per_char[c - font->min_char_or_byte2].width
- : font->min_bounds.width);
- }
- }
- }
- glPopMatrix();
- }
- glMatrixMode(GL_PROJECTION);
- glPopMatrix();
- }
- glPopAttrib();
-
- glMatrixMode(GL_MODELVIEW);
-}
-
/* Constructs the GL shapes of the current molecule
*/
tube (from->x, from->y, from->z,
to->x, to->y, to->z,
thickness, cap_size,
- faces, smooth, wire);
+ faces, smooth, False, wire);
}
}
draw_bounding_box (mi);
if (do_titles && m->label && *m->label)
- print_title_string (mi, m->label,
- 10, mi->xgwa.height - 10,
- mc->xfont2);
+ {
+ set_atom_color (mi, 0, True);
+ print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ m->label);
+ }
}
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",
}
-static void
+static int
parse_pdb_file (molecule *m, const char *name)
{
FILE *in;
char *buf = (char *) malloc(1024 + strlen(name));
sprintf(buf, "%s: error reading \"%s\"", progname, name);
perror(buf);
- exit (1);
+ return -1;
}
buf = (char *) malloc (buf_size);
{
fprintf (stderr, "%s: file %s contains no atomic coordinates!\n",
progname, name);
- exit (1);
+ return -1;
}
if (!m->nbonds && do_bonds)
progname, name);
do_bonds = 0;
}
+
+ return 0;
}
free (counts[i].atom);
s += strlen (s);
if (counts[i].count > 1)
- sprintf (s, "(%d)", counts[i].count);
+ sprintf (s, "[%d]", counts[i].count); /* use [] to get subscripts */
s += strlen (s);
i++;
}
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
+ int i;
- if (!molecule_str || !*molecule_str ||
- !strcmp(molecule_str, "(default)")) /* do the builtins */
+ 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 */
{
- 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 */
+
+ for (i = 0; i < mc->nmolecules; i++)
{
- 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);
-
- 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: no bonds: turning -label on.\n", progname);
- do_labels = 1;
- }
}
}
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
const char *s = "Constructing molecules...";
- print_title_string (mi, s,
- mi->xgwa.width - (string_width (mc->xfont2, s) + 40),
- 10 + mc->xfont2->ascent + mc->xfont2->descent,
- mc->xfont2);
+ print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ s);
glFinish();
glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
}
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
if (event->xany.type == ButtonPress &&
- event->xbutton.button & Button1)
+ event->xbutton.button == Button1)
{
mc->button_down_p = True;
gltrackball_start (mc->trackball,
return True;
}
else if (event->xany.type == ButtonRelease &&
- event->xbutton.button & Button1)
+ event->xbutton.button == Button1)
{
mc->button_down_p = False;
return True;
}
+ else if (event->xany.type == ButtonPress &&
+ (event->xbutton.button == Button4 ||
+ event->xbutton.button == Button5))
+ {
+ gltrackball_mousewheel (mc->trackball, event->xbutton.button, 10,
+ !!event->xbutton.state);
+ return True;
+ }
+ else if (event->xany.type == KeyPress)
+ {
+ KeySym keysym;
+ char c = 0;
+ XLookupString (&event->xkey, &c, 1, &keysym, 0);
+
+ if (c == ' ' || c == '\t' || c == '\r' || c == '\n')
+ {
+ GLfloat speed = 4.0;
+ mc->mode = 1;
+ mc->mode_tick = 10 * speed;
+ return True;
+ }
+ }
else if (event->xany.type == MotionNotify &&
mc->button_down_p)
{
{
Bool spinx=False, spiny=False, spinz=False;
- double spin_speed = 2.0;
- double wander_speed = 0.03;
+ double spin_speed = 0.5;
+ double spin_accel = 0.3;
+ double wander_speed = 0.01;
char *s = do_spin;
while (*s)
mc->rot = make_rotator (spinx ? spin_speed : 0,
spiny ? spin_speed : 0,
spinz ? spin_speed : 0,
- 1.0,
+ spin_accel,
do_wander ? wander_speed : 0,
(spinx && spiny && spinz));
mc->trackball = gltrackball_init ();
"NoLabelThreshold");
mc->wireframe_threshold = get_float_resource ("wireframeThreshold",
"WireframeThreshold");
+ mc->mode = 0;
if (wire)
do_bonds = 1;
}
+static void
+pick_new_molecule (ModeInfo *mi, time_t last)
+{
+ molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
+
+ if (mc->nmolecules == 1)
+ {
+ if (last != 0) return;
+ mc->which = 0;
+ }
+ else if (last == 0)
+ {
+ mc->which = random() % mc->nmolecules;
+ }
+ else
+ {
+ int n = mc->which;
+ while (n == mc->which)
+ n = random() % mc->nmolecules;
+ mc->which = n;
+ }
+
+ if (verbose_p)
+ {
+ char *name = strdup (mc->molecules[mc->which].label);
+ char *s = strpbrk (name, "\r\n");
+ if (s) *s = 0;
+ fprintf (stderr, "%s: drawing %s (%d)\n", progname, name, mc->which);
+ free (name);
+ }
+
+ glNewList (mc->molecule_dlist, GL_COMPILE);
+ ensure_bounding_box_visible (mi);
+
+ do_labels = orig_do_labels;
+ do_bonds = orig_do_bonds;
+ MI_IS_WIREFRAME(mi) = orig_wire;
+
+ if (mc->molecule_size > mc->no_label_threshold)
+ do_labels = 0;
+ if (mc->molecule_size > mc->wireframe_threshold)
+ MI_IS_WIREFRAME(mi) = 1;
+
+ if (MI_IS_WIREFRAME(mi))
+ do_bonds = 1;
+
+ build_molecule (mi);
+ glEndList();
+}
+
+
void
draw_molecule (ModeInfo *mi)
{
static time_t last = 0;
time_t now = time ((time_t *) 0);
+ GLfloat speed = 4.0; /* speed at which the zoom out/in happens */
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
Display *dpy = MI_DISPLAY(mi);
if (!mc->glx_context)
return;
- if (last + timeout <= now && /* randomize molecules every -timeout seconds */
- !mc->button_down_p)
+ if (last == 0)
{
- if (mc->nmolecules == 1)
- {
- if (last != 0) goto SKIP;
- mc->which = 0;
- }
- else if (last == 0)
+ pick_new_molecule (mi, last);
+ last = now;
+ }
+ else if (mc->mode == 0)
+ {
+ static int tick = 0;
+ if (tick++ > 10)
{
- mc->which = random() % mc->nmolecules;
+ time_t now = time((time_t *) 0);
+ if (last == 0) last = now;
+ tick = 0;
+
+ if (!mc->button_down_p &&
+ mc->nmolecules > 1 &&
+ last + timeout <= now)
+ {
+ /* randomize molecules every -timeout seconds */
+ mc->mode = 1; /* go out */
+ mc->mode_tick = 10 * speed;
+ last = now;
+ }
}
- else
+ }
+ else if (mc->mode == 1) /* out */
+ {
+ if (--mc->mode_tick <= 0)
{
- int n = mc->which;
- while (n == mc->which)
- n = random() % mc->nmolecules;
- mc->which = n;
+ mc->mode_tick = 10 * speed;
+ mc->mode = 2; /* go in */
+ pick_new_molecule (mi, last);
+ last = now;
}
-
- last = now;
-
-
- glNewList (mc->molecule_dlist, GL_COMPILE);
- ensure_bounding_box_visible (mi);
-
- do_labels = orig_do_labels;
- do_bonds = orig_do_bonds;
- MI_IS_WIREFRAME(mi) = orig_wire;
-
- if (mc->molecule_size > mc->no_label_threshold)
- do_labels = 0;
- if (mc->molecule_size > mc->wireframe_threshold)
- MI_IS_WIREFRAME(mi) = 1;
-
- if (MI_IS_WIREFRAME(mi))
- do_bonds = 1;
-
- build_molecule (mi);
- glEndList();
}
- SKIP:
+ else if (mc->mode == 2) /* in */
+ {
+ if (--mc->mode_tick <= 0)
+ mc->mode = 0; /* normal */
+ }
+ else
+ abort();
glPushMatrix ();
glScalef(1.1, 1.1, 1.1);
}
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+
+ if (mc->mode != 0)
+ {
+ GLfloat s = (mc->mode == 1
+ ? mc->mode_tick / (10 * speed)
+ : ((10 * speed) - mc->mode_tick + 1) / (10 * speed));
+ glScalef (s, s, s);
+ }
+
glCallList (mc->molecule_dlist);
- draw_labels (mi);
+
+ if (mc->mode == 0)
+ draw_labels (mi);
glPopMatrix ();
projects / xscreensaver / blobdiff