-/* 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
Good source of PDB files:
http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
-
- TO DO:
-
- - I'm not sure the text labels are being done in the best way;
- they are sometimes, but not always, occluded by spheres that
- pass in front of them.
-
- GENERAL OPENGL NAIVETY:
-
- I don't understand the *right* way to place text in front of the
- atoms. What I'm doing now is close, but has glitches. I think I
- understand glPolygonOffset(), but I think it doesn't help me.
-
- Here's how I'd phrase the problem I'm trying to solve:
-
- - I have a bunch of spherical objects of various sizes
- - I want a piece of text in the scene, between each object
- and the observer
- - the position of this text should be apparently tangential
- to the surface of the sphere, so that:
- - it is never inside the sphere;
- - but can be occluded by other objects in the scene.
-
- So I was trying to use glPolygonOffset() to say "pretend all
- polygons are N units deeper than they actually are" where N was
- somewhere around the maximal radius of the objects. Which wasn't a
- perfect solution, but was close. But it turns out that can't work,
- because the second arg to glPolygonOffset() is multiplied by some
- minimal depth quantum which is not revealed, so I can't pass it an
- offset in scene units -- only in multiples of the quantum. So I
- don't know how many quanta in radius my spheres are.
-
- I think I need to position and render the text with glRasterPos3f()
- so that the text is influenced by the depth buffer. If I used 2f,
- or an explicit constant Z value, then the text would always be in
- front of each sphere, and text would be visible for spheres that
- were fully occluded, which isn't what I want.
-
- So my only guess at this point is that I need to position the text
- exactly where I want it, tangential to the spheres -- but that
- means I need to be able to compute that XYZ position, which is
- dependent on the position of the observer! Which means two things:
- first, while generating my scene, I need to take into account the
- position of the observer, and I don't have a clue how to do that;
- and second, it means I can't put my whole molecule in a display
- list, because the XYZ position of the text in the scene changes at
- every frame, as the molecule rotates.
-
- This just *can't* be as hard as it seems!
*/
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <dirent.h>
#include <X11/Intrinsic.h>
#define PROGCLASS "Molecule"
#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, }},
};
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;
}
glEnable(GL_CULL_FACE);
}
-#if 0
- if (do_labels && !wire)
- {
- /* This is so all polygons are drawn slightly farther back in the depth
- buffer, so that when we render text directly on top of the spheres,
- it still shows up. */
- glEnable (GL_POLYGON_OFFSET_FILL);
- glPolygonOffset (1.0, (do_bonds ? 10.0 : 35.0));
- }
- else
- {
- glDisable (GL_POLYGON_OFFSET_FILL);
- }
-#endif
-
if (!wire)
set_atom_color (mi, 0, False);
tube (from->x, from->y, from->z,
to->x, to->y, to->z,
thickness, cap_size,
- faces, smooth, wire);
+ faces, smooth, False, wire);
}
}
sphere (a->x, a->y, a->z, size, wire);
}
- /* Second pass to draw labels, after all atoms and bonds are in place
- */
- if (do_labels)
- for (i = 0; i < m->natoms; i++)
- {
- molecule_atom *a = &m->atoms[i];
- int j;
-
- if (!wire)
- {
- glDisable (GL_LIGHTING);
-#if 1
- glDisable (GL_DEPTH_TEST);
-#endif
- }
-
- if (!wire)
- set_atom_color (mi, a, True);
-
- glRasterPos3f (a->x, a->y, a->z);
-
- /* 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]));
-
- /* 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);
-#if 1
- glEnable(GL_DEPTH_TEST);
-#endif
- }
- }
-
if (do_bbox)
draw_bounding_box (mi);
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;
}
{
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 */
+ 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;
- }
}
}
spinz ? spin_speed : 0,
1.0,
do_wander ? wander_speed : 0,
- True);
+ (spinx && spiny && spinz));
mc->trackball = gltrackball_init ();
}
}
+/* Put the labels on the atoms.
+ This can't be a part of the display list because of the games
+ we play with the translation matrix.
+ */
+void
+draw_labels (ModeInfo *mi)
+{
+ molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
+ int wire = MI_IS_WIREFRAME(mi);
+ molecule *m = &mc->molecules[mc->which];
+ int i, j;
+
+ 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];
+ GLfloat size = atom_size (a);
+ GLfloat m[4][4];
+
+ glPushMatrix();
+
+ if (!wire)
+ set_atom_color (mi, a, True);
+
+ /* First, we translate the origin to the center of the atom.
+
+ Then we retrieve the prevailing modelview matrix (which
+ includes any rotation, wandering, and user-trackball-rolling
+ of the scene.
+
+ We set the top 3x3 cells of that matrix to be the identity
+ matrix. This removes all rotation from the matrix, while
+ leaving the translation alone. This has the effect of
+ leaving the prevailing coordinate system perpendicular to
+ the camera view: were we to draw a square face, it would
+ be in the plane of the screen.
+
+ Now we translate by `size' toward the viewer -- so that the
+ origin is *just in front* of the ball.
+
+ Then we draw the label text, allowing the depth buffer to
+ do its work: that way, labels on atoms will be occluded
+ properly when other atoms move in front of them.
+
+ This technique (of neutralizing rotation relative to the
+ observer, after both rotations and translations have been
+ applied) is known as "billboarding".
+ */
+
+ glTranslatef(a->x, a->y, a->z); /* get matrix */
+ glGetFloatv (GL_MODELVIEW_MATRIX, &m[0][0]); /* load rot. identity */
+ m[0][0] = 1; m[1][0] = 0; m[2][0] = 0;
+ m[0][1] = 0; m[1][1] = 1; m[2][1] = 0;
+ m[0][2] = 0; m[1][2] = 0; m[2][2] = 1;
+ glLoadIdentity(); /* reset modelview */
+ glMultMatrixf (&m[0][0]); /* replace with ours */
+
+ glTranslatef (0, 0, (size * 1.1)); /* move toward camera */
+
+ 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,
+ NULL);
+
+ for (j = 0; j < strlen(a->label); j++)
+ glCallList (mc->font1_dlist + (int)(a->label[j]));
+
+ 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);
+}
+
+
void
draw_molecule (ModeInfo *mi)
{
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
glCallList (mc->molecule_dlist);
+ draw_labels (mi);
+
glPopMatrix ();
if (mi->fps_p) do_fps (mi);
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