-/* molecule, Copyright (c) 2001-2006 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2016 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:
+ https://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
*/
#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" \
- "*noLabelThreshold: 30 \n" \
+ "*atomFont: -*-helvetica-medium-r-normal-*-*-240-*-*-*-*-*-*\n" \
+ "*titleFont: -*-helvetica-medium-r-normal-*-*-180-*-*-*-*-*-*\n" \
+ "*noLabelThreshold: 150 \n" \
"*wireframeThreshold: 150 \n" \
+ "*suppressRotationAnimation: True\n" \
# define refresh_molecule 0
# define release_molecule 0
#include "colors.h"
#include "sphere.h"
#include "tube.h"
-#include "glxfonts.h"
+#include "texfont.h"
#include "rotator.h"
#include "gltrackball.h"
#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__
ISO C89 compilers are required to support" when includng
the following data file... */
# endif
-const char * const builtin_pdb_data[] = {
+static const char * const builtin_pdb_data[] = {
# include "molecules.h"
};
+#ifndef HAVE_MOBILE
+# define LOAD_FILES
+#endif
+
+
typedef struct {
const char *name;
GLfloat size, size2;
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, }},
int mode; /* 0 = normal, 1 = out, 2 = in */
int mode_tick;
+ int next; /* 0 = random, -1 = back, 1 = forward */
GLuint molecule_dlist;
GLuint shell_dlist;
- XFontStruct *xfont1, *xfont2;
- GLuint font1_dlist, font2_dlist;
+ texture_font_data *atom_font, *title_font;
+
int polygon_count;
time_t draw_time;
int draw_tick;
- int scale_down;
+ GLfloat overall_scale;
+ int low_rez_p;
} molecule_configuration;
{&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},
sphere (molecule_configuration *mc,
GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
{
- int stacks = (mc->scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
- int slices = (mc->scale_down ? SPHERE_SLICES_2 : SPHERE_SLICES);
+ int stacks = (mc->low_rez_p ? SPHERE_STACKS_2 : SPHERE_STACKS);
+ int slices = (mc->low_rez_p ? SPHERE_SLICES_2 : SPHERE_SLICES);
glPushMatrix ();
glTranslatef (x, y, z);
load_fonts (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- load_font (mi->dpy, "atomFont", &mc->xfont1, &mc->font1_dlist);
- load_font (mi->dpy, "titleFont", &mc->xfont2, &mc->font2_dlist);
+ mc->atom_font = load_texture_font (mi->dpy, "atomFont");
+ mc->title_font = load_texture_font (mi->dpy, "titleFont");
}
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]);
glBegin(GL_LINES);
- if (x1 > 0) x1 = 0; if (x2 < 0) x2 = 0;
- if (y1 > 0) y1 = 0; if (y2 < 0) y2 = 0;
- if (z1 > 0) z1 = 0; if (z2 < 0) z2 = 0;
+ if (x1 > 0) x1 = 0;
+ if (x2 < 0) x2 = 0;
+ if (y1 > 0) y1 = 0;
+ if (y2 < 0) y2 = 0;
+ if (z1 > 0) z1 = 0;
+ if (z2 < 0) z2 = 0;
glVertex3f(x1, 0, 0); glVertex3f(x2, 0, 0);
glVertex3f(0 , y1, 0); glVertex3f(0, y2, 0);
glVertex3f(0, 0, z1); glVertex3f(0, 0, z2);
glEnd();
- glPopAttrib();
+ if (!wire)
+ glEnable (GL_LIGHTING);
}
mc->molecule_size = size;
- mc->scale_down = 0;
+ mc->low_rez_p = 0;
+ mc->overall_scale = 1;
if (size > max_size)
{
- GLfloat scale = max_size / size;
- glScalef (scale, scale, scale);
+ mc->overall_scale = max_size / size;
+ glScalef (mc->overall_scale, mc->overall_scale, mc->overall_scale);
- mc->scale_down = scale < 0.3;
+ mc->low_rez_p = mc->overall_scale < 0.3;
}
glTranslatef (-(x1 + w/2),
}
else
{
- int faces = (mc->scale_down ? TUBE_FACES_2 : TUBE_FACES);
+ int faces = (mc->low_rez_p ? TUBE_FACES_2 : TUBE_FACES);
# ifdef SMOOTH_TUBE
int smooth = True;
# else
int smooth = False;
# endif
- GLfloat thickness = 0.07 * b->strength;
- GLfloat cap_size = 0.03;
+ Bool cap_p = (!do_atoms || do_shells);
+ GLfloat base = 0.07;
+ GLfloat thickness = base * b->strength;
+ GLfloat cap_size = (cap_p ? base / 2 : 0);
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, cap_p, 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)
}
+#ifdef LOAD_FILES
static int
parse_pdb_file (molecule *m, const char *name)
{
return 0;
}
+#endif /* LOAD_FILES */
typedef struct { char *atom; int count; } atom_and_count;
load_molecules (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- int wire = MI_IS_WIREFRAME(mi);
int i;
mc->nmolecules = 0;
+# ifdef LOAD_FILES
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.
*/
+ int wire = MI_IS_WIREFRAME(mi);
struct stat st;
int nfiles = 0;
int list_size = 0;
files = 0;
mc->nmolecules = molecule_ctr;
}
+# endif /* LOAD_FILES */
if (mc->nmolecules == 0) /* do the builtins if no files */
{
0.0, 0.0, 0.0,
0.0, 1.0, 0.0);
+# ifdef HAVE_MOBILE /* Keep it the same relative size when rotated. */
+ {
+ int o = (int) current_device_rotation();
+ if (o != 0 && o != 180 && o != -180)
+ glScalef (1/h, 1/h, 1/h);
+ }
+# endif
+
glClear(GL_COLOR_BUFFER_BIT);
}
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
const char *s = "Constructing molecules...";
- print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
- mi->xgwa.width, mi->xgwa.height,
- 10, mi->xgwa.height - 10,
- s);
+ print_texture_label (mi->dpy, mc->title_font,
+ mi->xgwa.width, mi->xgwa.height,
+ 0, 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)
- {
- mc->button_down_p = True;
- gltrackball_start (mc->trackball,
- event->xbutton.x, event->xbutton.y,
- MI_WIDTH (mi), MI_HEIGHT (mi));
- return True;
- }
- else if (event->xany.type == ButtonRelease &&
- 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)
+ if (gltrackball_event_handler (event, mc->trackball,
+ MI_WIDTH (mi), MI_HEIGHT (mi),
+ &mc->button_down_p))
+ return True;
+ else
{
- KeySym keysym;
- char c = 0;
- XLookupString (&event->xkey, &c, 1, &keysym, 0);
+ if (event->xany.type == KeyPress)
+ {
+ KeySym keysym;
+ char c = 0;
+ XLookupString (&event->xkey, &c, 1, &keysym, 0);
+ if (c == '<' || c == ',' || c == '-' || c == '_' ||
+ keysym == XK_Left || keysym == XK_Up || keysym == XK_Prior)
+ {
+ mc->next = -1;
+ goto SWITCH;
+ }
+ else if (c == '>' || c == '.' || c == '=' || c == '+' ||
+ keysym == XK_Right || keysym == XK_Down ||
+ keysym == XK_Next)
+ {
+ mc->next = 1;
+ goto SWITCH;
+ }
+ }
- if (c == ' ' || c == '\t' || c == '\r' || c == '\n')
+ if (screenhack_event_helper (MI_DISPLAY(mi), MI_WINDOW(mi), event))
{
- GLfloat speed = 4.0;
+ SWITCH:
mc->mode = 1;
- mc->mode_tick = 10 * speed;
+ mc->mode_tick = 4;
return True;
}
}
- else if (event->xany.type == MotionNotify &&
- mc->button_down_p)
- {
- gltrackball_track (mc->trackball,
- event->xmotion.x, event->xmotion.y,
- MI_WIDTH (mi), MI_HEIGHT (mi));
- return True;
- }
return False;
}
molecule_configuration *mc;
int wire;
- if (!mcs) {
- mcs = (molecule_configuration *)
- calloc (MI_NUM_SCREENS(mi), sizeof (molecule_configuration));
- if (!mcs) {
- fprintf(stderr, "%s: out of memory\n", progname);
- exit(1);
- }
- }
+ MI_INIT (mi, mcs, NULL);
mc = &mcs[MI_SCREEN(mi)];
spin_accel,
do_wander ? wander_speed : 0,
(spinx && spiny && spinz));
- mc->trackball = gltrackball_init ();
+ mc->trackball = gltrackball_init (True);
}
orig_do_labels = do_labels;
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
molecule *m = &mc->molecules[mc->which];
- int i, j;
+ int i;
if (!do_labels)
return;
- if (!wire)
- glDisable (GL_LIGHTING); /* don't light fonts */
-
for (i = 0; i < m->natoms; i++)
{
molecule_atom *a = &m->atoms[i];
/* First, we translate the origin to the center of the atom.
- Then we retrieve the prevailing modelview matrix (which
+ Then we retrieve the prevailing modelview matrix, which
includes any rotation, wandering, and user-trackball-rolling
of the scene.
glTranslatef (0, 0, (size * 1.1)); /* move toward camera */
- glRasterPos3f (0, 0, 0); /* draw text here */
+ glRotatef (current_device_rotation(), 0, 0, 1); /* right side up */
- /* 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,
- NULL);
-
- for (j = 0; j < strlen(a->label); j++)
-
- glCallList (mc->font1_dlist + (int)(a->label[j]));
+ {
+ XCharStruct e;
+ int w, h;
+ GLfloat s;
+
+ texture_string_metrics (mc->atom_font, a->label, &e, 0, 0);
+ w = e.width;
+ h = e.ascent + e.descent;
+
+ s = 1.0 / h; /* Scale to unit */
+ s *= mc->overall_scale; /* Scale to size of atom */
+ s *= 0.8; /* Shrink a bit */
+ glScalef (s, s, 1);
+ glTranslatef (-w/2, -h/2, 0);
+ print_texture_string (mc->atom_font, a->label);
+ }
glPopMatrix();
}
-
- /* More efficient to always call glEnable() with correct values
- than to call glPushAttrib()/glPopAttrib(), since reading
- attributes from GL does a round-trip and stalls the pipeline.
- */
- if (!wire)
- glEnable (GL_LIGHTING);
}
{
mc->which = random() % mc->nmolecules;
}
+ else if (mc->next < 0)
+ {
+ mc->which--;
+ if (mc->which < 0) mc->which = mc->nmolecules-1;
+ mc->next = 0;
+ }
+ else if (mc->next > 0)
+ {
+ mc->which++;
+ if (mc->which >= mc->nmolecules) mc->which = 0;
+ mc->next = 0;
+ }
else
{
int n = mc->which;
{
/* randomize molecules every -timeout seconds */
mc->mode = 1; /* go out */
- mc->mode_tick = 10 * speed;
+ mc->mode_tick = 80 / speed;
mc->draw_time = now;
}
}
{
if (--mc->mode_tick <= 0)
{
- mc->mode_tick = 10 * speed;
+ mc->mode_tick = 80 / speed;
mc->mode = 2; /* go in */
pick_new_molecule (mi, mc->draw_time);
- mc->draw_time = now;
}
}
else if (mc->mode == 2) /* in */
if (mc->mode != 0)
{
GLfloat s = (mc->mode == 1
- ? mc->mode_tick / (10 * speed)
- : ((10 * speed) - mc->mode_tick + 1) / (10 * speed));
+ ? mc->mode_tick / (80 / speed)
+ : ((80 / speed) - mc->mode_tick + 1) / (80 / speed));
glScalef (s, s, s);
}
if (do_titles && m->label && *m->label)
{
set_atom_color (mi, 0, True, 1);
- print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
- mi->xgwa.width, mi->xgwa.height,
- 10, mi->xgwa.height - 10,
- m->label);
+ print_texture_label (mi->dpy, mc->title_font,
+ mi->xgwa.width, mi->xgwa.height,
+ 1, m->label);
}
}
glPopMatrix();
projects / xscreensaver / blobdiff