-/* molecule, Copyright (c) 2001-2006 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2012 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
/* Documentation on the PDB file format:
+ http://en.wikipedia.org/wiki/Protein_Data_Bank_%28file_format%29
+ http://www.wwpdb.org/docs.html
+ http://www.wwpdb.org/documentation/format32/v3.2.html
+ http://www.wwpdb.org/documentation/format32/sect9.html
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
Good source of PDB files:
http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
+ http://www.umass.edu/microbio/rasmol/whereget.htm
+ http://www.wwpdb.org/docs.html
*/
+#ifdef HAVE_GLBITMAP
+# define ATOM_FONT "-*-helvetica-medium-r-normal-*-180-*"
+#else
+# define ATOM_FONT "-*-helvetica-medium-r-normal-*-240-*"
+#endif
+
#define DEFAULTS "*delay: 10000 \n" \
"*showFPS: False \n" \
"*wireframe: False \n" \
- "*atomFont: -*-times-bold-r-normal-*-240-*\n" \
- "*titleFont: -*-times-bold-r-normal-*-180-*\n" \
+ "*atomFont: " ATOM_FONT "\n" \
+ "*atomFont2: -*-helvetica-bold-r-normal-*-80-*\n" \
+ "*titleFont: -*-helvetica-medium-r-normal-*-180-*\n" \
"*noLabelThreshold: 30 \n" \
"*wireframeThreshold: 150 \n" \
#define DEF_TITLES "True"
#define DEF_ATOMS "True"
#define DEF_BONDS "True"
-#define DEF_SHELLS "True"
+#define DEF_ESHELLS "True"
#define DEF_BBOX "False"
#define DEF_SHELL_ALPHA "0.3"
#define DEF_MOLECULE "(default)"
#define DEF_VERBOSE "False"
-#define SPHERE_SLICES 24 /* how densely to render spheres */
-#define SPHERE_STACKS 12
+#define SPHERE_SLICES 48 /* how densely to render spheres */
+#define SPHERE_STACKS 24
#define SMOOTH_TUBE /* whether to have smooth or faceted tubes */
# define TUBE_FACES 8
#endif
-#define SPHERE_SLICES_2 7
-#define SPHERE_STACKS_2 4
-#define TUBE_FACES_2 3
+#define SPHERE_SLICES_2 14
+#define SPHERE_STACKS_2 8
+#define TUBE_FACES_2 6
# ifdef __GNUC__
and their approximate size in angstroms.
*/
static const atom_data all_atom_data[] = {
- { "H", 1.17, 0.40, "#FFFFFF", "#B3B3B3", { 0, }},
+ { "H", 1.17, 0.40, "#FFFFFF", "#000000", { 0, }},
{ "C", 1.75, 0.58, "#999999", "#FFFFFF", { 0, }},
{ "CA", 1.80, 0.60, "#0000FF", "#ADD8E6", { 0, }},
- { "N", 1.55, 0.52, "#A2B5CD", "#836FFF", { 0, }},
+ { "N", 1.55, 0.52, "#A2B5CD", "#EE99FF", { 0, }},
{ "O", 1.40, 0.47, "#FF0000", "#FFB6C1", { 0, }},
{ "P", 1.28, 0.43, "#9370DB", "#DB7093", { 0, }},
{ "S", 1.80, 0.60, "#8B8B00", "#FFFF00", { 0, }},
GLuint molecule_dlist;
GLuint shell_dlist;
- XFontStruct *xfont1, *xfont2;
- GLuint font1_dlist, font2_dlist;
+# ifdef HAVE_GLBITMAP
+ XFontStruct *xfont1, *xfont2, *xfont3;
+ GLuint font1_dlist, font2_dlist, font3_dlist;
+# else
+ texture_font_data *font1_data, *font2_data, *font3_data;
+# endif
+
+
int polygon_count;
time_t draw_time;
{&do_wander, "wander", "Wander", DEF_WANDER, t_Bool},
{&do_atoms, "atoms", "Atoms", DEF_ATOMS, t_Bool},
{&do_bonds, "bonds", "Bonds", DEF_BONDS, t_Bool},
- {&do_shells, "eshells", "EShells", DEF_SHELLS, t_Bool},
+ {&do_shells, "eshells", "EShells", DEF_ESHELLS, t_Bool},
{&do_labels, "labels", "Labels", DEF_LABELS, t_Bool},
{&do_titles, "titles", "Titles", DEF_TITLES, t_Bool},
{&do_bbox, "bbox", "BBox", DEF_BBOX, t_Bool},
load_fonts (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
+# ifdef HAVE_GLBITMAP
load_font (mi->dpy, "atomFont", &mc->xfont1, &mc->font1_dlist);
- load_font (mi->dpy, "titleFont", &mc->xfont2, &mc->font2_dlist);
+ load_font (mi->dpy, "atomFont2", &mc->xfont2, &mc->font2_dlist);
+ load_font (mi->dpy, "titleFont", &mc->xfont3, &mc->font3_dlist);
+# else
+ mc->font1_data = load_texture_font (mi->dpy, "atomFont");
+ mc->font2_data = load_texture_font (mi->dpy, "atomFont2");
+ mc->font3_data = load_texture_font (mi->dpy, "titleFont");
+# endif
}
gl_color[3] = alpha;
+ /* If we're not drawing atoms, and the color is black, use white instead.
+ This is a kludge so that H can have black text over its white ball,
+ but the text still shows up if balls are off.
+ */
+ if (font_p && !do_atoms &&
+ gl_color[0] == 0 && gl_color[1] == 0 && gl_color[2] == 0)
+ {
+ gl_color[0] = gl_color[1] = gl_color[2] = 1;
+ }
+
if (font_p)
glColor4f (gl_color[0], gl_color[1], gl_color[2], gl_color[3]);
else
glVertex3f(x2, y2, z2); glVertex3f(x2, y2, z1);
glEnd();
- glPushAttrib (GL_LIGHTING);
glDisable (GL_LIGHTING);
glColor3f (c2[0], c2[1], c2[2]);
glVertex3f(0, 0, z1); glVertex3f(0, 0, z2);
glEnd();
- glPopAttrib();
+ if (!wire)
+ glEnable (GL_LIGHTING);
}
if (thickness > 0.3)
thickness = 0.3;
- tube (from->x, from->y, from->z,
- to->x, to->y, to->z,
- thickness, cap_size,
- faces, smooth, (!do_atoms || do_shells), wire);
- polys += faces;
+ polys += tube (from->x, from->y, from->z,
+ to->x, to->y, to->z,
+ thickness, cap_size,
+ faces, smooth, (!do_atoms || do_shells), wire);
}
}
else if (!strncmp (s, "ATOM ", 7))
{
int id;
+ const char *end = strchr (s, '\n');
+ int L = end - s;
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
if (1 != sscanf (s+7, " %d ", &id))
parse_error (filename, line, s);
+ /* Use the "atom name" field if that is all that is available. */
strncpy (name, s+12, 3);
+
+ /* But prefer the "element" field. */
+ if (L > 77 && !isspace(s[77])) {
+ /* fprintf(stderr, " \"%s\" -> ", name); */
+ name[0] = s[76];
+ name[1] = s[77];
+ name[2] = 0;
+ /* fprintf(stderr, "\"%s\"\n", name); */
+ }
+
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
const char *s = "Constructing molecules...";
- print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ print_gl_string (mi->dpy,
+# ifdef HAVE_GLBITMAP
+ mc->xfont3, mc->font3_dlist,
+# else
+ mc->font3_data,
+# endif
mi->xgwa.width, mi->xgwa.height,
10, mi->xgwa.height - 10,
- s);
+ s, False);
glFinish();
glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
}
}
else if (event->xany.type == ButtonPress &&
(event->xbutton.button == Button4 ||
- event->xbutton.button == Button5))
+ event->xbutton.button == Button5 ||
+ event->xbutton.button == Button6 ||
+ event->xbutton.button == Button7))
{
gltrackball_mousewheel (mc->trackball, event->xbutton.button, 10,
!!event->xbutton.state);
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
molecule *m = &mc->molecules[mc->which];
- int i, j;
+# ifdef HAVE_GLBITMAP
+ XFontStruct *xfont = (mc->scale_down ? mc->xfont2 : mc->xfont1);
+ GLuint font_dlist = (mc->scale_down ? mc->font2_dlist : mc->font1_dlist);
+# else
+ texture_font_data *font_data = mc->font1_data; /* don't scale down */
+# endif
+ int i;
if (!do_labels)
return;
glTranslatef (0, 0, (size * 1.1)); /* move toward camera */
+# ifdef HAVE_GLBITMAP
glRasterPos3f (0, 0, 0); /* draw text here */
/* Before drawing the string, shift the origin to center
the text over the origin of the sphere. */
glBitmap (0, 0, 0, 0,
- -string_width (mc->xfont1, a->label) / 2,
- -mc->xfont1->descent,
+ -string_width (xfont, a->label, 0) / 2,
+ -xfont->descent,
NULL);
-
- for (j = 0; j < strlen(a->label); j++)
-
- glCallList (mc->font1_dlist + (int)(a->label[j]));
+ {
+ int j;
+ for (j = 0; j < strlen(a->label); j++)
+ glCallList (font_dlist + (int)(a->label[j]));
+ }
+# else
+ {
+ int h;
+ int w = texture_string_width (font_data, a->label, &h);
+ GLfloat s = 1.0 / h;
+ GLfloat max = 18; /* max point size to avoid pixellated text */
+ if (h > max) s *= max/h;
+ glScalef (s, s, 1);
+ glTranslatef (-w/2, h*2/3, 0);
+ print_gl_string (mi->dpy,
+# ifdef HAVE_GLBITMAP
+ xfont, font_dlist,
+# else
+ font_data,
+# endif
+ 0, 0, 0, 0,
+ a->label, False);
+ }
+# endif
glPopMatrix();
}
if (do_titles && m->label && *m->label)
{
set_atom_color (mi, 0, True, 1);
- print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ print_gl_string (mi->dpy,
+# ifdef HAVE_GLBITMAP
+ mc->xfont3, mc->font3_dlist,
+# else
+ mc->font3_data,
+# endif
mi->xgwa.width, mi->xgwa.height,
10, mi->xgwa.height - 10,
- m->label);
+ m->label, False);
}
}
glPopMatrix();
projects / xscreensaver / blobdiff