-/* molecule, Copyright (c) 2001-2005 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2006 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://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
+ http://www.wwpdb.org/docs.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
*/
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <unistd.h>
-#include <dirent.h>
-#include <X11/Intrinsic.h>
-
-#define PROGCLASS "Molecule"
-#define HACK_INIT init_molecule
-#define HACK_DRAW draw_molecule
-#define HACK_RESHAPE reshape_molecule
-#define HACK_HANDLE_EVENT molecule_handle_event
-#define EVENT_MASK PointerMotionMask
-#define molecule_opts xlockmore_opts
-
-#define DEF_TIMEOUT "20"
-#define DEF_SPIN "XYZ"
-#define DEF_WANDER "False"
-#define DEF_LABELS "True"
-#define DEF_TITLES "True"
-#define DEF_ATOMS "True"
-#define DEF_BONDS "True"
-#define DEF_SHELLS "False"
-#define DEF_BBOX "False"
-#define DEF_SHELL_ALPHA "0.3"
-#define DEF_MOLECULE "(default)"
-#define DEF_VERBOSE "False"
-
#define DEFAULTS "*delay: 10000 \n" \
"*showFPS: False \n" \
"*wireframe: False \n" \
"*noLabelThreshold: 30 \n" \
"*wireframeThreshold: 150 \n" \
-
+# define refresh_molecule 0
+# define release_molecule 0
#undef countof
#define countof(x) (sizeof((x))/sizeof((*x)))
#ifdef USE_GL /* whole file */
-#include <stdlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <dirent.h>
#include <ctype.h>
-#include <time.h>
-#include <sys/time.h>
-#include <GL/glu.h>
+
+#define DEF_TIMEOUT "20"
+#define DEF_SPIN "XYZ"
+#define DEF_WANDER "False"
+#define DEF_LABELS "True"
+#define DEF_TITLES "True"
+#define DEF_ATOMS "True"
+#define DEF_BONDS "True"
+#define DEF_SHELLS "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 TUBE_FACES 8
#endif
-static int scale_down;
#define SPHERE_SLICES_2 7
#define SPHERE_STACKS_2 4
#define TUBE_FACES_2 3
/* These are the traditional colors used to render these atoms,
and their approximate size in angstroms.
*/
-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, }},
- { "S", 1.80, 0, "Yellow4", "Yellow1", { 0, }},
- { "bond", 0, 0, "Grey70", "Yellow1", { 0, }},
- { "*", 1.40, 0, "Green4", "LightGreen", { 0, }}
+static const atom_data all_atom_data[] = {
+ { "H", 1.17, 0.40, "#FFFFFF", "#B3B3B3", { 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, }},
+ { "O", 1.40, 0.47, "#FF0000", "#FFB6C1", { 0, }},
+ { "P", 1.28, 0.43, "#9370DB", "#DB7093", { 0, }},
+ { "S", 1.80, 0.60, "#8B8B00", "#FFFF00", { 0, }},
+ { "bond", 0, 0, "#B3B3B3", "#FFFF00", { 0, }},
+ { "*", 1.40, 0.47, "#008B00", "#90EE90", { 0, }}
};
int id; /* sequence number in the PDB file */
const char *label; /* The atom name */
GLfloat x, y, z; /* position in 3-space (angstroms) */
- atom_data *data; /* computed: which style of atom this is */
+ const atom_data *data; /* computed: which style of atom this is */
} molecule_atom;
typedef struct {
GLuint font1_dlist, font2_dlist;
int polygon_count;
+ time_t draw_time;
+ int draw_tick;
+
+ int scale_down;
+
} molecule_configuration;
{&verbose_p, "verbose", "Verbose", DEF_VERBOSE, t_Bool},
};
-ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
+ENTRYPOINT ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
/* shapes */
static int
-sphere (GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
+sphere (molecule_configuration *mc,
+ GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
{
- int stacks = (scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
- int slices = (scale_down ? SPHERE_SLICES_2 : SPHERE_SLICES);
+ int stacks = (mc->scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
+ int slices = (mc->scale_down ? SPHERE_SLICES_2 : SPHERE_SLICES);
glPushMatrix ();
glTranslatef (x, y, z);
}
-static atom_data *
+static const atom_data *
get_atom_data (const char *atom_name)
{
int i;
- atom_data *d = 0;
+ const atom_data *d = 0;
char *n = strdup (atom_name);
char *n2 = n;
int L;
static void
-set_atom_color (ModeInfo *mi, molecule_atom *a, Bool font_p, GLfloat alpha)
+set_atom_color (ModeInfo *mi, const molecule_atom *a,
+ Bool font_p, GLfloat alpha)
{
- atom_data *d;
- GLfloat *gl_color;
+ const atom_data *d;
+ GLfloat gl_color[4];
if (a)
d = a->data;
else
+ d = get_atom_data ("bond");
+
+ if (font_p)
{
- static atom_data *def_data = 0;
- if (!def_data) def_data = get_atom_data ("bond");
- d = def_data;
+ gl_color[0] = d->gl_color[4];
+ gl_color[1] = d->gl_color[5];
+ gl_color[2] = d->gl_color[6];
+ gl_color[3] = d->gl_color[7];
+ }
+ else
+ {
+ gl_color[0] = d->gl_color[0];
+ gl_color[1] = d->gl_color[1];
+ gl_color[2] = d->gl_color[2];
+ gl_color[3] = d->gl_color[3];
}
-
- gl_color = (!font_p ? d->gl_color : (d->gl_color + 4));
if (gl_color[3] == 0)
{
static GLfloat
-atom_size (molecule_atom *a)
+atom_size (const molecule_atom *a)
{
if (do_bonds)
- {
- if (a->data->size2 == 0)
- {
- /* let the molecules have the same relative sizes, but scale
- them to a smaller range, so that the bond-tubes are
- actually visible...
- */
- GLfloat bot = 0.4;
- GLfloat top = 0.6;
- GLfloat min = 1.17;
- GLfloat max = 1.80;
- GLfloat ratio = (a->data->size - min) / (max - min);
- a->data->size2 = bot + (ratio * (top - bot));
- }
- return a->data->size2;
- }
+ return a->data->size2;
else
return a->data->size;
}
static void
draw_bounding_box (ModeInfo *mi)
{
- static GLfloat c1[4] = { 0.2, 0.2, 0.4, 1.0 };
- static GLfloat c2[4] = { 1.0, 0.0, 0.0, 1.0 };
+ static const GLfloat c1[4] = { 0.2, 0.2, 0.4, 1.0 };
+ static const GLfloat c2[4] = { 1.0, 0.0, 0.0, 1.0 };
int wire = MI_IS_WIREFRAME(mi);
GLfloat x1, y1, z1, x2, y2, z2;
molecule_bounding_box (mi, &x1, &y1, &z1, &x2, &y2, &z2);
mc->molecule_size = size;
- scale_down = 0;
+ mc->scale_down = 0;
if (size > max_size)
{
GLfloat scale = max_size / size;
glScalef (scale, scale, scale);
- scale_down = scale < 0.3;
+ mc->scale_down = scale < 0.3;
}
glTranslatef (-(x1 + w/2),
if (do_bonds)
for (i = 0; i < m->nbonds; i++)
{
- molecule_bond *b = &m->bonds[i];
- molecule_atom *from = get_atom (m->atoms, m->natoms, b->from);
- molecule_atom *to = get_atom (m->atoms, m->natoms, b->to);
+ const molecule_bond *b = &m->bonds[i];
+ const molecule_atom *from = get_atom (m->atoms, m->natoms, b->from);
+ const molecule_atom *to = get_atom (m->atoms, m->natoms, b->to);
if (wire)
{
}
else
{
- int faces = (scale_down ? TUBE_FACES_2 : TUBE_FACES);
+ int faces = (mc->scale_down ? TUBE_FACES_2 : TUBE_FACES);
# ifdef SMOOTH_TUBE
int smooth = True;
# else
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);
}
}
if (!wire && do_atoms)
for (i = 0; i < m->natoms; i++)
{
- molecule_atom *a = &m->atoms[i];
+ const molecule_atom *a = &m->atoms[i];
GLfloat size = atom_size (a);
set_atom_color (mi, a, False, alpha);
- polys += sphere (a->x, a->y, a->z, size, wire);
+ polys += sphere (mc, a->x, a->y, a->z, size, wire);
}
if (do_bbox && !transparent_p)
}
+static void
+parse_error (const char *file, int lineno, const char *line)
+{
+ fprintf (stderr, "%s: %s: parse error, line %d: %s\n",
+ progname, file, lineno, line);
+ exit (1);
+}
+
/* This function is crap.
*/
!strncmp (s, "MTRIX3", 6) ||
!strncmp (s, "SHEET ", 6) ||
!strncmp (s, "CISPEP", 6) ||
+/*
+ !strncmp (s, "SEQADV", 6) ||
+ !strncmp (s, "SITE ", 5) ||
+ !strncmp (s, "FTNOTE", 6) ||
+ !strncmp (s, "MODEL ", 5) ||
+ !strncmp (s, "ENDMDL", 6) ||
+ !strncmp (s, "SPRSDE", 6) ||
+ !strncmp (s, "MODRES", 6) ||
+ */
!strncmp (s, "GENERATED BY", 12) ||
!strncmp (s, "TER ", 4) ||
!strncmp (s, "END ", 4) ||
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
- sscanf (s+7, " %d ", &id);
+ if (1 != sscanf (s+7, " %d ", &id))
+ parse_error (filename, line, s);
strncpy (name, s+12, 3);
while (isspace(*name)) name++;
*ss = tolower(*ss);
ss++;
}
- sscanf (s + 32, " %f %f %f ", &x, &y, &z);
+ if (3 != sscanf (s + 32, " %f %f %f ", &x, &y, &z))
+ parse_error (filename, line, s);
+
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
- sscanf (s+7, " %d ", &id);
+ if (1 != sscanf (s+7, " %d ", &id))
+ parse_error (filename, line, s);
strncpy (name, s+12, 3);
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss-- = 0;
- sscanf (s + 30, " %f %f %f ", &x, &y, &z);
+ if (3 != sscanf (s + 30, " %f %f %f ", &x, &y, &z))
+ parse_error (filename, line, s);
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
\f
/* Window management, etc
*/
-void
+ENTRYPOINT void
reshape_molecule (ModeInfo *mi, int width, int height)
{
GLfloat h = (GLfloat) height / (GLfloat) width;
static void
gl_init (ModeInfo *mi)
{
- static GLfloat pos[4] = {1.0, 0.4, 0.9, 0.0};
- static GLfloat amb[4] = {0.0, 0.0, 0.0, 1.0};
- static GLfloat dif[4] = {0.8, 0.8, 0.8, 1.0};
- static GLfloat spc[4] = {1.0, 1.0, 1.0, 1.0};
+ static const GLfloat pos[4] = {1.0, 0.4, 0.9, 0.0};
+ static const GLfloat amb[4] = {0.0, 0.0, 0.0, 1.0};
+ static const GLfloat dif[4] = {0.8, 0.8, 0.8, 1.0};
+ static const GLfloat spc[4] = {1.0, 1.0, 1.0, 1.0};
glLightfv(GL_LIGHT0, GL_POSITION, pos);
glLightfv(GL_LIGHT0, GL_AMBIENT, amb);
glLightfv(GL_LIGHT0, GL_DIFFUSE, dif);
glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
}
-Bool
+ENTRYPOINT Bool
molecule_handle_event (ModeInfo *mi, XEvent *event)
{
molecule_configuration *mc = &mcs[MI_SCREEN(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);
}
-void
+ENTRYPOINT void
init_molecule (ModeInfo *mi)
{
molecule_configuration *mc;
if (*s == 'x' || *s == 'X') spinx = True;
else if (*s == 'y' || *s == 'Y') spiny = True;
else if (*s == 'z' || *s == 'Z') spinz = True;
+ else if (*s == '0') ;
else
{
fprintf (stderr,
load_molecules (mi);
mc->which = random() % mc->nmolecules;
- mc->no_label_threshold = get_float_resource ("noLabelThreshold",
+ mc->no_label_threshold = get_float_resource (mi->dpy, "noLabelThreshold",
"NoLabelThreshold");
- mc->wireframe_threshold = get_float_resource ("wireframeThreshold",
+ mc->wireframe_threshold = get_float_resource (mi->dpy, "wireframeThreshold",
"WireframeThreshold");
mc->mode = 0;
This can't be a part of the display list because of the games
we play with the translation matrix.
*/
-void
+static void
draw_labels (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
NULL);
for (j = 0; j < strlen(a->label); j++)
+
glCallList (mc->font1_dlist + (int)(a->label[j]));
glPopMatrix();
}
-void
+ENTRYPOINT 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 */
if (!mc->glx_context)
return;
- if (last == 0)
+ glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *(mc->glx_context));
+
+ if (mc->draw_time == 0)
{
- pick_new_molecule (mi, last);
- last = now;
+ pick_new_molecule (mi, mc->draw_time);
+ mc->draw_time = now;
}
else if (mc->mode == 0)
{
- static int tick = 0;
- if (tick++ > 10)
+ if (mc->draw_tick++ > 10)
{
time_t now = time((time_t *) 0);
- if (last == 0) last = now;
- tick = 0;
+ if (mc->draw_time == 0) mc->draw_time = now;
+ mc->draw_tick = 0;
if (!mc->button_down_p &&
mc->nmolecules > 1 &&
- last + timeout <= now)
+ mc->draw_time + timeout <= now)
{
/* randomize molecules every -timeout seconds */
mc->mode = 1; /* go out */
mc->mode_tick = 10 * speed;
- last = now;
+ mc->draw_time = now;
}
}
}
{
mc->mode_tick = 10 * speed;
mc->mode = 2; /* go in */
- pick_new_molecule (mi, last);
- last = now;
+ pick_new_molecule (mi, mc->draw_time);
+ mc->draw_time = now;
}
}
else if (mc->mode == 2) /* in */
glXSwapBuffers(dpy, window);
}
+XSCREENSAVER_MODULE ("Molecule", molecule)
+
#endif /* USE_GL */
projects / xscreensaver / blobdiff