6.09HEADmaster

1 files changed, 0 insertions, 1720 deletions

diff --git a/hacks/glx/molecule.c b/hacks/glx/molecule.c
deleted file mode 100644
index c173c6b..0000000
--- a/hacks/glx/molecule.c
+++ /dev/null
@@ -1,1720 +0,0 @@
-/* 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 for any purpose is hereby granted without fee, provided that
- * the above copyright notice appear in all copies and that both that
- * copyright notice and this permission notice appear in supporting
- * documentation.  No representations are made about the suitability of this
- * software for any purpose.  It is provided "as is" without express or 
- * implied warranty.
- */
-
-
-/* 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:     sans-serif 24\n" \
-			"*titleFont:    sans-serif 18\n" \
-			"*noLabelThreshold:    150    \n" \
-			"*wireframeThreshold:  150    \n" \
-			"*suppressRotationAnimation: True\n" \
-
-# define release_molecule 0
-
-#include "xlockmore.h"
-#include "colors.h"
-#include "sphere.h"
-#include "tube.h"
-#include "texfont.h"
-#include "rotator.h"
-#include "gltrackball.h"
-
-#ifdef USE_GL /* whole file */
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <dirent.h>
-#include <ctype.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_ESHELLS     "True"
-#define DEF_BBOX        "False"
-#define DEF_SHELL_ALPHA "0.3"
-#define DEF_MOLECULE    "(default)"
-#define DEF_VERBOSE     "False"
-
-#define SPHERE_SLICES 48  /* how densely to render spheres */
-#define SPHERE_STACKS 24
-
-#define SMOOTH_TUBE       /* whether to have smooth or faceted tubes */
-
-#ifdef SMOOTH_TUBE
-# define TUBE_FACES  12   /* how densely to render tubes */
-#else
-# define TUBE_FACES  8
-#endif
-
-#define SPHERE_SLICES_2  14
-#define SPHERE_STACKS_2  8
-#define TUBE_FACES_2     6
-
-
-# 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
-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;
-  const char *color;
-  const char *text_color;
-  GLfloat gl_color[8];
-} atom_data;
-
-
-/* These are the traditional colors used to render these atoms,
-   and their approximate size in angstroms.
- */
-static const atom_data all_atom_data[] = {
-  { "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", "#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, }},
-  { "bond", 0,     0,    "#B3B3B3", "#FFFF00", { 0, }},
-  { "*",    1.40,  0.47, "#008B00", "#90EE90", { 0, }}
-};
-
-
-typedef struct {
-  int id;		/* sequence number in the PDB file */
-  char *label;		/* The atom name */
-  GLfloat x, y, z;	/* position in 3-space (angstroms) */
-  const atom_data *data; /* computed: which style of atom this is */
-} molecule_atom;
-
-typedef struct {
-  int from, to;		/* atom sequence numbers */
-  int strength;		/* how many bonds are between these two atoms */
-} molecule_bond;
-
-
-typedef struct {
-  char *label;		/* description of this compound */
-  int natoms, atoms_size;
-  int nbonds, bonds_size;
-  molecule_atom *atoms;
-  molecule_bond *bonds;
-} molecule;
-
-
-typedef struct {
-  GLXContext *glx_context;
-  rotator *rot;
-  trackball_state *trackball;
-  Bool button_down_p;
-
-  GLfloat molecule_size;	   /* max dimension of molecule bounding box */
-
-  GLfloat no_label_threshold;	   /* Things happen when molecules are huge */
-  GLfloat wireframe_threshold;
-
-  int which;			   /* which of the molecules is being shown */
-  int nmolecules;
-  molecule *molecules;
-
-  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;
-
-  texture_font_data *atom_font, *title_font;
-
-  int polygon_count;
-
-  time_t draw_time;
-  int draw_tick;
-
-  GLfloat overall_scale;
-  int low_rez_p;
-
-} molecule_configuration;
-
-
-static molecule_configuration *mcs = NULL;
-
-static int timeout;
-static char *molecule_str;
-static char *do_spin;
-static Bool do_wander;
-static Bool do_titles;
-static Bool do_labels;
-static Bool do_atoms;
-static Bool do_bonds;
-static Bool do_shells;
-static Bool do_bbox;
-static Bool verbose_p;
-static GLfloat shell_alpha;
-
-/* saved to reset */
-static Bool orig_do_labels, orig_do_atoms, orig_do_bonds, orig_do_shells,
-    orig_wire;
-
-
-static XrmOptionDescRec opts[] = {
-  { "-molecule",	".molecule",	XrmoptionSepArg, 0 },
-  { "-timeout",		".timeout",	XrmoptionSepArg, 0 },
-  { "-spin",		".spin",	XrmoptionSepArg, 0 },
-  { "+spin",		".spin",	XrmoptionNoArg, "" },
-  { "-wander",		".wander",	XrmoptionNoArg, "True" },
-  { "+wander",		".wander",	XrmoptionNoArg, "False" },
-  { "-labels",		".labels",	XrmoptionNoArg, "True" },
-  { "+labels",		".labels",	XrmoptionNoArg, "False" },
-  { "-titles",		".titles",	XrmoptionNoArg, "True" },
-  { "+titles",		".titles",	XrmoptionNoArg, "False" },
-  { "-atoms",		".atoms",	XrmoptionNoArg, "True" },
-  { "+atoms",		".atoms",	XrmoptionNoArg, "False" },
-  { "-bonds",		".bonds",	XrmoptionNoArg, "True" },
-  { "+bonds",		".bonds",	XrmoptionNoArg, "False" },
-  { "-shells",		".eshells",	XrmoptionNoArg, "True" },
-  { "+shells",		".eshells",	XrmoptionNoArg, "False" },
-  { "-shell-alpha",	".shellAlpha",	XrmoptionSepArg, 0 },
-  { "-bbox",		".bbox",	XrmoptionNoArg, "True" },
-  { "+bbox",		".bbox",	XrmoptionNoArg, "False" },
-  { "-verbose",		".verbose",	XrmoptionNoArg, "True" },
-};
-
-static argtype vars[] = {
-  {&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_atoms,	  "atoms",	"Atoms",	DEF_ATOMS,    t_Bool},
-  {&do_bonds,	  "bonds",	"Bonds",	DEF_BONDS,    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},
-  {&shell_alpha,  "shellAlpha",	"ShellAlpha",	DEF_SHELL_ALPHA, t_Float},
-  {&verbose_p,	  "verbose",	"Verbose",	DEF_VERBOSE,  t_Bool},
-};
-
-ENTRYPOINT ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
-
-
-
-
-/* shapes */
-
-static int
-sphere (molecule_configuration *mc,
-        GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
-{
-  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);
-  glScalef (diameter, diameter, diameter);
-  unit_sphere (stacks, slices, wire);
-  glPopMatrix ();
-
-  return stacks * slices;
-}
-
-
-static void
-load_fonts (ModeInfo *mi)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-  mc->atom_font = load_texture_font (mi->dpy, "atomFont");
-  mc->title_font = load_texture_font (mi->dpy, "titleFont");
-}
-
-
-static const atom_data *
-get_atom_data (const char *atom_name)
-{
-  int i;
-  const atom_data *d = 0;
-  char *n = strdup (atom_name);
-  char *n2 = n;
-  int L;
-
-  while (!isalpha(*n)) n++;
-  L = strlen(n);
-  while (L > 0 && !isalpha(n[L-1]))
-    n[--L] = 0;
-
-  for (i = 0; i < countof(all_atom_data); i++)
-    {
-      d = &all_atom_data[i];
-      if (!strcasecmp (n, all_atom_data[i].name))
-        break;
-    }
-
-  free (n2);
-  return d;
-}
-
-
-static void
-set_atom_color (ModeInfo *mi, const molecule_atom *a, 
-                Bool font_p, GLfloat alpha)
-{
-  const atom_data *d;
-  GLfloat gl_color[4];
-
-  if (a)
-    d = a->data;
-  else
-    d = get_atom_data ("bond");
-
-  if (font_p)
-    {
-      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];
-    }
-
-  if (gl_color[3] == 0)
-    {
-      const char *string = !font_p ? d->color : d->text_color;
-      XColor xcolor;
-      if (!XParseColor (mi->dpy, mi->xgwa.colormap, string, &xcolor))
-        {
-          fprintf (stderr, "%s: unparsable color in %s: %s\n", progname,
-                   (a ? a->label : d->name), string);
-          exit (1);
-        }
-
-      gl_color[0] = xcolor.red   / 65536.0;
-      gl_color[1] = xcolor.green / 65536.0;
-      gl_color[2] = xcolor.blue  / 65536.0;
-    }
-  
-  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
-    glMaterialfv (GL_FRONT, GL_AMBIENT_AND_DIFFUSE, gl_color);
-}
-
-
-static GLfloat
-atom_size (const molecule_atom *a)
-{
-  if (do_bonds)
-    return a->data->size2;
-  else
-    return a->data->size;
-}
-
-
-static molecule_atom *
-get_atom (molecule_atom *atoms, int natoms, int id)
-{
-  int i;
-
-  /* quick short-circuit */
-  if (id < natoms)
-    {
-      if (atoms[id].id == id)
-        return &atoms[id];
-      if (id > 0 && atoms[id-1].id == id)
-        return &atoms[id-1];
-      if (id < natoms-1 && atoms[id+1].id == id)
-        return &atoms[id+1];
-    }
-
-  for (i = 0; i < natoms; i++)
-    if (id == atoms[i].id)
-      return &atoms[i];
-
-  fprintf (stderr, "%s: no atom %d\n", progname, id);
-  abort();
-}
-
-
-static void
-molecule_bounding_box (ModeInfo *mi,
-                       GLfloat *x1, GLfloat *y1, GLfloat *z1,
-                       GLfloat *x2, GLfloat *y2, GLfloat *z2)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-  molecule *m = &mc->molecules[mc->which];
-  int i;
-
-  if (m->natoms == 0)
-    {
-      *x1 = *y1 = *z1 = *x2 = *y2 = *z2 = 0;
-    }
-  else
-    {
-      *x1 = *x2 = m->atoms[0].x;
-      *y1 = *y2 = m->atoms[0].y;
-      *z1 = *z2 = m->atoms[0].z;
-    }
-
-  for (i = 1; i < m->natoms; i++)
-    {
-      if (m->atoms[i].x < *x1) *x1 = m->atoms[i].x;
-      if (m->atoms[i].y < *y1) *y1 = m->atoms[i].y;
-      if (m->atoms[i].z < *z1) *z1 = m->atoms[i].z;
-
-      if (m->atoms[i].x > *x2) *x2 = m->atoms[i].x;
-      if (m->atoms[i].y > *y2) *y2 = m->atoms[i].y;
-      if (m->atoms[i].z > *z2) *z2 = m->atoms[i].z;
-    }
-
-  *x1 -= 1.5;
-  *y1 -= 1.5;
-  *z1 -= 1.5;
-  *x2 += 1.5;
-  *y2 += 1.5;
-  *z2 += 1.5;
-}
-
-
-static void
-draw_bounding_box (ModeInfo *mi)
-{
-  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);
-
-  glMaterialfv (GL_FRONT, GL_AMBIENT_AND_DIFFUSE, c1);
-  glFrontFace(GL_CCW);
-
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(0, 1, 0);
-  glVertex3f(x1, y1, z1); glVertex3f(x1, y1, z2);
-  glVertex3f(x2, y1, z2); glVertex3f(x2, y1, z1);
-  glEnd();
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(0, -1, 0);
-  glVertex3f(x2, y2, z1); glVertex3f(x2, y2, z2);
-  glVertex3f(x1, y2, z2); glVertex3f(x1, y2, z1);
-  glEnd();
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(0, 0, 1);
-  glVertex3f(x1, y1, z1); glVertex3f(x2, y1, z1);
-  glVertex3f(x2, y2, z1); glVertex3f(x1, y2, z1);
-  glEnd();
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(0, 0, -1);
-  glVertex3f(x1, y2, z2); glVertex3f(x2, y2, z2);
-  glVertex3f(x2, y1, z2); glVertex3f(x1, y1, z2);
-  glEnd();
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(1, 0, 0);
-  glVertex3f(x1, y2, z1); glVertex3f(x1, y2, z2);
-  glVertex3f(x1, y1, z2); glVertex3f(x1, y1, z1);
-  glEnd();
-  glBegin(wire ? GL_LINE_LOOP : GL_QUADS);
-  glNormal3f(-1, 0, 0);
-  glVertex3f(x2, y1, z1); glVertex3f(x2, y1, z2);
-  glVertex3f(x2, y2, z2); glVertex3f(x2, y2, z1);
-  glEnd();
-
-  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;
-  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();
-
-  if (!wire)
-    glEnable (GL_LIGHTING);
-}
-
-
-/* Since PDB files don't always have the molecule centered around the
-   origin, and since some molecules are pretty large, scale and/or
-   translate so that the whole molecule is visible in the window.
- */
-static void
-ensure_bounding_box_visible (ModeInfo *mi)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-
-  GLfloat x1, y1, z1, x2, y2, z2;
-  GLfloat w, h, d;
-  GLfloat size;
-  GLfloat max_size = 10;  /* don't bother scaling down if the molecule
-                             is already smaller than this */
-
-  molecule_bounding_box (mi, &x1, &y1, &z1, &x2, &y2, &z2);
-  w = x2-x1;
-  h = y2-y1;
-  d = z2-z1;
-
-  size = (w > h ? w : h);
-  size = (size > d ? size : d);
-
-  mc->molecule_size = size;
-
-  mc->low_rez_p = 0;
-  mc->overall_scale = 1;
-
-  if (size > max_size)
-    {
-      mc->overall_scale = max_size / size;
-      glScalef (mc->overall_scale, mc->overall_scale, mc->overall_scale);
-
-      mc->low_rez_p = mc->overall_scale < 0.3;
-    }
-
-  glTranslatef (-(x1 + w/2),
-                -(y1 + h/2),
-                -(z1 + d/2));
-}
-
-
-
-/* Constructs the GL shapes of the current molecule
- */
-static void
-build_molecule (ModeInfo *mi, Bool transparent_p)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-  int wire = MI_IS_WIREFRAME(mi);
-  int i;
-  GLfloat alpha = transparent_p ? shell_alpha : 1.0;
-  int polys = 0;
-
-  molecule *m = &mc->molecules[mc->which];
-
-  if (wire)
-    {
-      glDisable(GL_CULL_FACE);
-      glDisable(GL_LIGHTING);
-      glDisable(GL_LIGHT0);
-      glDisable(GL_DEPTH_TEST);
-      glDisable(GL_NORMALIZE);
-      glDisable(GL_CULL_FACE);
-    }
-  else
-    {
-      glEnable(GL_CULL_FACE);
-      glEnable(GL_LIGHTING);
-      glEnable(GL_LIGHT0);
-      glEnable(GL_DEPTH_TEST);
-      glEnable(GL_NORMALIZE);
-      glEnable(GL_CULL_FACE);
-    }
-
-  if (!wire)
-    set_atom_color (mi, 0, False, alpha);
-
-  if (do_bonds)
-    for (i = 0; i < m->nbonds; i++)
-      {
-        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)
-          {
-            glBegin(GL_LINES);
-            glVertex3f(from->x, from->y, from->z);
-            glVertex3f(to->x,   to->y,   to->z);
-            glEnd();
-            polys++;
-          }
-        else
-          {
-            int faces = (mc->low_rez_p ? TUBE_FACES_2 : TUBE_FACES);
-# ifdef SMOOTH_TUBE
-            int smooth = True;
-# else
-            int smooth = False;
-# endif
-            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;
-
-            polys += tube (from->x, from->y, from->z,
-                           to->x,   to->y,   to->z,
-                           thickness, cap_size,
-                           faces, smooth, cap_p, wire);
-          }
-      }
-
-  if (!wire && do_atoms)
-    for (i = 0; i < m->natoms; i++)
-      {
-        const molecule_atom *a = &m->atoms[i];
-        GLfloat size = atom_size (a);
-        set_atom_color (mi, a, False, alpha);
-        polys += sphere (mc, a->x, a->y, a->z, size, wire);
-      }
-
-  if (do_bbox && !transparent_p)
-    {
-      draw_bounding_box (mi);
-      polys += 4;
-    }
-
-  mc->polygon_count += polys;
-}
-
-
-
-/* loading */
-
-static void
-push_atom (molecule *m,
-           int id, char *label,
-           GLfloat x, GLfloat y, GLfloat z)
-{
-  m->natoms++;
-  if (m->atoms_size < m->natoms)
-    {
-      m->atoms_size += 20;
-      m->atoms = (molecule_atom *) realloc (m->atoms,
-                                            m->atoms_size * sizeof(*m->atoms));
-    }
-  m->atoms[m->natoms-1].id = id;
-  m->atoms[m->natoms-1].label = label;
-  m->atoms[m->natoms-1].x = x;
-  m->atoms[m->natoms-1].y = y;
-  m->atoms[m->natoms-1].z = z;
-  m->atoms[m->natoms-1].data = get_atom_data (label);
-}
-
-
-static void
-push_bond (molecule *m, int from, int to)
-{
-  int i;
-
-  for (i = 0; i < m->nbonds; i++)
-    if ((m->bonds[i].from == from && m->bonds[i].to   == to) ||
-        (m->bonds[i].to   == from && m->bonds[i].from == to))
-      {
-        m->bonds[i].strength++;
-        return;
-      }
-
-  m->nbonds++;
-  if (m->bonds_size < m->nbonds)
-    {
-      m->bonds_size += 20;
-      m->bonds = (molecule_bond *) realloc (m->bonds,
-                                            m->bonds_size * sizeof(*m->bonds));
-    }
-  m->bonds[m->nbonds-1].from = from;
-  m->bonds[m->nbonds-1].to = to;
-  m->bonds[m->nbonds-1].strength = 1;
-}
-
-
-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.
- */
-static void
-parse_pdb_data (molecule *m, const char *data, const char *filename, int line)
-{
-  const char *s = data;
-  char *ss;
-  while (*s)
-    {
-      if ((!m->label || !*m->label) &&
-          (!strncmp (s, "HEADER", 6) || !strncmp (s, "COMPND", 6)))
-        {
-          char *name = calloc (1, 100);
-          char *n2 = name;
-          sprintf (n2, "%.99s", s);
-          n2 += 7;
-          while (isspace(*n2)) n2++;
-
-          ss = strchr (n2, '\n');
-          if (ss) *ss = 0;
-          ss = strchr (n2, '\r');
-          if (ss) *ss = 0;
-
-          ss = n2+strlen(n2)-1;
-          while (isspace(*ss) && ss > n2)
-            *ss-- = 0;
-
-          if (strlen (n2) > 4 &&
-              !strcmp (n2 + strlen(n2) - 4, ".pdb"))
-            n2[strlen(n2)-4] = 0;
-
-          if (m->label) free (m->label);
-          m->label = strdup (n2);
-          free (name);
-        }
-      else if (!strncmp (s, "TITLE ", 6) ||
-               !strncmp (s, "HEADER", 6) ||
-               !strncmp (s, "COMPND", 6) ||
-               !strncmp (s, "AUTHOR", 6) ||
-               !strncmp (s, "REVDAT", 6) ||
-               !strncmp (s, "SOURCE", 6) ||
-               !strncmp (s, "EXPDTA", 6) ||
-               !strncmp (s, "JRNL  ", 6) ||
-               !strncmp (s, "REMARK", 6) ||
-               !strncmp (s, "SEQRES", 6) ||
-               !strncmp (s, "HET   ", 6) ||
-               !strncmp (s, "FORMUL", 6) ||
-               !strncmp (s, "CRYST1", 6) ||
-               !strncmp (s, "ORIGX1", 6) ||
-               !strncmp (s, "ORIGX2", 6) ||
-               !strncmp (s, "ORIGX3", 6) ||
-               !strncmp (s, "SCALE1", 6) ||
-               !strncmp (s, "SCALE2", 6) ||
-               !strncmp (s, "SCALE3", 6) ||
-               !strncmp (s, "MASTER", 6) ||
-               !strncmp (s, "KEYWDS", 6) ||
-               !strncmp (s, "DBREF ", 6) ||
-               !strncmp (s, "HETNAM", 6) ||
-               !strncmp (s, "HETSYN", 6) ||
-               !strncmp (s, "HELIX ", 6) ||
-               !strncmp (s, "LINK  ", 6) ||
-               !strncmp (s, "MTRIX1", 6) ||
-               !strncmp (s, "MTRIX2", 6) ||
-               !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) ||
-               !strncmp (s, "TER\n", 4) ||
-               !strncmp (s, "END\n", 4) ||
-               !strncmp (s, "\n", 1))
-        /* ignored. */
-        ;
-      else if (!strncmp (s, "ATOM   ", 7))
-        {
-          int id;
-          const char *end = strchr (s, '\n');
-          int L = end - s;
-          char *oname = (char *) calloc (1, 4);
-          char *name = oname;
-          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)
-            *ss-- = 0;
-	  ss = name + 1;
-	  while(*ss)
-          {
-	    *ss = tolower(*ss);
-            ss++;
-          }
-          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,
-                   id, name, x, y, z);
-*/
-          push_atom (m, id, strdup(name), x, y, z);
-          free (oname);
-        }
-      else if (!strncmp (s, "HETATM ", 7))
-        {
-          int id;
-          char *oname = (char *) calloc (1, 4);
-          char *name = oname;
-          GLfloat x = -999, y = -999, z = -999;
-
-          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;
-          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,
-                   id, name, x, y, z);
-*/
-          push_atom (m, id, strdup(name), x, y, z);
-          free (oname);
-        }
-      else if (!strncmp (s, "CONECT ", 7))
-        {
-          int atoms[11];
-          int i = sscanf (s + 8, " %d %d %d %d %d %d %d %d %d %d %d %d ",
-                          &atoms[0], &atoms[1], &atoms[2], &atoms[3], 
-                          &atoms[4], &atoms[5], &atoms[6], &atoms[7], 
-                          &atoms[8], &atoms[9], &atoms[10], &atoms[11]);
-          int j;
-          for (j = 1; j < i; j++)
-            if (atoms[j] > 0)
-              {
-/*
-                fprintf (stderr, "%s: %s: %d: bond: %d %d\n",
-                         progname, filename, line, atoms[0], atoms[j]);
-*/
-                push_bond (m, atoms[0], atoms[j]);
-              }
-        }
-      else
-        {
-          char *s1 = strdup (s);
-          for (ss = s1; *ss && *ss != '\n'; ss++)
-            ;
-          *ss = 0;
-          fprintf (stderr, "%s: %s: %d: unrecognised line: %s\n",
-                   progname, filename, line, s1);
-        }
-
-      while (*s && *s != '\n')
-        s++;
-      if (*s == '\n')
-        s++;
-      line++;
-    }
-}
-
-
-#ifdef LOAD_FILES
-static int
-parse_pdb_file (molecule *m, const char *name)
-{
-  FILE *in;
-  int buf_size = 40960;
-  char *buf;
-  int line = 1;
-
-  in = fopen(name, "r");
-  if (!in)
-    {
-      char *buf = (char *) malloc(1024 + strlen(name));
-      sprintf(buf, "%s: error reading \"%s\"", progname, name);
-      perror(buf);
-      free(buf);
-      return -1;
-    }
-
-  buf = (char *) malloc (buf_size);
-
-  while (fgets (buf, buf_size-1, in))
-    {
-      char *s;
-      for (s = buf; *s; s++)
-        if (*s == '\r') *s = '\n';
-      parse_pdb_data (m, buf, name, line++);
-    }
-
-  free (buf);
-  fclose (in);
-
-  if (!m->natoms)
-    {
-      fprintf (stderr, "%s: file %s contains no atomic coordinates!\n",
-               progname, name);
-      return -1;
-    }
-
-  if (!m->nbonds && do_bonds)
-    {
-      fprintf (stderr, "%s: warning: file %s contains no atomic bond info.\n",
-               progname, name);
-      do_bonds = 0;
-    }
-
-  return 0;
-}
-#endif /* LOAD_FILES */
-
-
-typedef struct { char *atom; int count; } atom_and_count;
-
-/* When listing the components of a molecule, the convention is to put the
-   carbon atoms first, the hydrogen atoms second, and the other atom types
-   sorted alphabetically after that (although for some molecules, the usual
-   order is different: we special-case a few of those.)
- */
-static int
-cmp_atoms (const void *aa, const void *bb)
-{
-  const atom_and_count *a = (atom_and_count *) aa;
-  const atom_and_count *b = (atom_and_count *) bb;
-  if (!a->atom) return  1;
-  if (!b->atom) return -1;
-  if (!strcmp(a->atom, "C")) return -1;
-  if (!strcmp(b->atom, "C")) return  1;
-  if (!strcmp(a->atom, "H")) return -1;
-  if (!strcmp(b->atom, "H")) return  1;
-  return strcmp (a->atom, b->atom);
-}
-
-static void special_case_formula (char *f);
-
-static void
-generate_molecule_formula (molecule *m)
-{
-  char *buf = (char *) malloc (m->natoms * 10);
-  char *s = buf;
-  int i;
-  atom_and_count counts[200];
-  memset (counts, 0, sizeof(counts));
-  *s = 0;
-  for (i = 0; i < m->natoms; i++)
-    {
-      int j = 0;
-      char *a = (char *) m->atoms[i].label;
-      char *e;
-      while (!isalpha(*a)) a++;
-      a = strdup (a);
-      for (e = a; isalpha(*e); e++);
-      *e = 0;
-      while (counts[j].atom && !!strcmp(a, counts[j].atom))
-        j++;
-      if (counts[j].atom)
-        free (a);
-      else
-        counts[j].atom = a;
-      counts[j].count++;
-    }
-
-  i = 0;
-  while (counts[i].atom) i++;
-  qsort (counts, i, sizeof(*counts), cmp_atoms);
-
-  i = 0;
-  while (counts[i].atom)
-    {
-      strcat (s, counts[i].atom);
-      free (counts[i].atom);
-      s += strlen (s);
-      if (counts[i].count > 1)
-        sprintf (s, "[%d]", counts[i].count);  /* use [] to get subscripts */
-      s += strlen (s);
-      i++;
-    }
-
-  special_case_formula (buf);
-
-  if (!m->label) m->label = strdup("");
-  s = (char *) malloc (strlen (m->label) + strlen (buf) + 2);
-  strcpy (s, m->label);
-  strcat (s, "\n");
-  strcat (s, buf);
-  free (m->label);
-  free (buf);
-  m->label = s;
-}
-
-/* thanks to Rene Uittenbogaard <ruittenb@wish.nl> */
-static void
-special_case_formula (char *f)
-{
-  if      (!strcmp(f, "H[2]Be"))   strcpy(f, "BeH[2]");
-  else if (!strcmp(f, "H[3]B"))    strcpy(f, "BH[3]");
-  else if (!strcmp(f, "H[3]N"))    strcpy(f, "NH[3]");
-  else if (!strcmp(f, "CHN"))      strcpy(f, "HCN");
-  else if (!strcmp(f, "CKN"))      strcpy(f, "KCN");
-  else if (!strcmp(f, "H[4]N[2]")) strcpy(f, "N[2]H[4]");
-  else if (!strcmp(f, "Cl[3]P"))   strcpy(f, "PCl[3]");
-  else if (!strcmp(f, "Cl[5]P"))   strcpy(f, "PCl[5]");
-}
-
-
-static void
-insert_vertical_whitespace (char *string)
-{
-  while (*string)
-    {
-      if ((string[0] == ',' ||
-           string[0] == ';' ||
-           string[0] == ':') &&
-          string[1] == ' ')
-        string[0] = ' ', string[1] = '\n';
-      string++;
-    }
-}
-
-
-/* Construct the molecule data from either: the builtins; or from
-   the (one) .pdb file specified with -molecule.
- */
-static void
-load_molecules (ModeInfo *mi)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(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;
-      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;
-    }
-# endif /* LOAD_FILES */
-
-  if (mc->nmolecules == 0)	/* do the builtins if no files */
-    {
-      mc->nmolecules = countof(builtin_pdb_data);
-      if (mc->molecules) free (mc->molecules);
-      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);
-        }
-    }
-
-  for (i = 0; i < mc->nmolecules; i++)
-    {
-      generate_molecule_formula (&mc->molecules[i]);
-      insert_vertical_whitespace ((char *) mc->molecules[i].label);
-    }
-}
-
-
-
-/* Window management, etc
- */
-ENTRYPOINT void
-reshape_molecule (ModeInfo *mi, int width, int height)
-{
-  GLfloat h = (GLfloat) height / (GLfloat) width;
-  int y = 0;
-
-  if (width > height * 5) {   /* tiny window: show middle */
-    height = width * 9/16;
-    y = -height/2;
-    h = height / (GLfloat) width;
-  }
-
-  glViewport (0, y, (GLint) width, (GLint) height);
-
-  glMatrixMode(GL_PROJECTION);
-  glLoadIdentity();
-  gluPerspective (30.0, 1/h, 20.0, 100.0);
-
-  glMatrixMode(GL_MODELVIEW);
-  glLoadIdentity();
-  gluLookAt( 0.0, 0.0, 30.0,
-             0.0, 0.0, 0.0,
-             0.0, 1.0, 0.0);
-
-  {
-    GLfloat s = (MI_WIDTH(mi) < MI_HEIGHT(mi)
-                 ? (MI_WIDTH(mi) / (GLfloat) MI_HEIGHT(mi))
-                 : 1);
-    glScalef (s, s, s);
-  }
-
-  glClear(GL_COLOR_BUFFER_BIT);
-}
-
-
-static void
-gl_init (ModeInfo *mi)
-{
-  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);
-  glLightfv(GL_LIGHT0, GL_SPECULAR, spc);
-}
-
-
-static void
-startup_blurb (ModeInfo *mi)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-  const char *s = "Constructing molecules...";
-#ifndef HAVE_ANDROID   /* Doesn't work -- causes whole scene to be black */
-  print_texture_label (mi->dpy, mc->title_font,
-                       mi->xgwa.width, mi->xgwa.height,
-                       0, s);
-#endif
-  glFinish();
-  glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
-}
-
-ENTRYPOINT Bool
-molecule_handle_event (ModeInfo *mi, XEvent *event)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-
-  if (gltrackball_event_handler (event, mc->trackball,
-                                 MI_WIDTH (mi), MI_HEIGHT (mi),
-                                 &mc->button_down_p))
-    return True;
-  else
-    {
-      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 (screenhack_event_helper (MI_DISPLAY(mi), MI_WINDOW(mi), event))
-        {
-        SWITCH:
-          mc->mode = 1;
-          mc->mode_tick = 4;
-          return True;
-        }
-    }
-
-  return False;
-}
-
-
-ENTRYPOINT void 
-init_molecule (ModeInfo *mi)
-{
-  molecule_configuration *mc;
-  int wire;
-
-  MI_INIT (mi, mcs);
-
-  mc = &mcs[MI_SCREEN(mi)];
-
-  if ((mc->glx_context = init_GL(mi)) != NULL) {
-    gl_init(mi);
-    reshape_molecule (mi, MI_WIDTH(mi), MI_HEIGHT(mi));
-  }
-
-  load_fonts (mi);
-  startup_blurb (mi);
-
-  wire = MI_IS_WIREFRAME(mi);
-
-  {
-    Bool spinx=False, spiny=False, spinz=False;
-    double spin_speed   = 0.5;
-    double spin_accel   = 0.3;
-    double wander_speed = 0.01;
-
-    char *s = do_spin;
-    while (*s)
-      {
-        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,
-         "%s: spin must contain only the characters X, Y, or Z (not \"%s\")\n",
-                     progname, do_spin);
-            exit (1);
-          }
-        s++;
-      }
-
-    mc->rot = make_rotator (spinx ? spin_speed : 0,
-                            spiny ? spin_speed : 0,
-                            spinz ? spin_speed : 0,
-                            spin_accel,
-                            do_wander ? wander_speed : 0,
-                            (spinx && spiny && spinz));
-    mc->trackball = gltrackball_init (True);
-  }
-
-#ifdef HAVE_ANDROID   /* Doesn't work -- not transparent */
-  do_shells = False;
-#endif
-
-  orig_do_labels = do_labels;
-  orig_do_atoms  = do_atoms;
-  orig_do_bonds  = do_bonds;
-  orig_do_shells = do_shells;
-  orig_wire = MI_IS_WIREFRAME(mi);
-
-  mc->molecule_dlist = glGenLists(1);
-  if (do_shells)
-    mc->shell_dlist = glGenLists(1);
-
-  load_molecules (mi);
-  mc->which = random() % mc->nmolecules;
-
-  mc->no_label_threshold = get_float_resource (mi->dpy, "noLabelThreshold",
-                                               "NoLabelThreshold");
-  mc->wireframe_threshold = get_float_resource (mi->dpy, "wireframeThreshold",
-                                                "WireframeThreshold");
-  mc->mode = 0;
-
-  if (wire)
-    do_bonds = 1;
-}
-
-
-/* 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.
- */
-static 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;
-
-  if (!do_labels)
-    return;
-
-  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, 1);
-
-      /* 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 */
-
-      glRotatef (current_device_rotation(), 0, 0, 1);  /* right side up */
-
-      {
-        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);
-#ifndef HAVE_ANDROID   /* Doesn't work -- causes whole scene to be black */
-        print_texture_string (mc->atom_font, a->label);
-#endif
-      }
-
-      glPopMatrix();
-    }
-}
-
-
-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 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;
-      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);
-    }
-
-  mc->polygon_count = 0;
-
-  glNewList (mc->molecule_dlist, GL_COMPILE);
-  ensure_bounding_box_visible (mi);
-
-  do_labels = orig_do_labels;
-  do_atoms  = orig_do_atoms;
-  do_bonds  = orig_do_bonds;
-  do_shells = orig_do_shells;
-  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, do_shells = 0;
-
-  if (!do_bonds)
-    do_shells = 0;
-
-  if (! (do_bonds || do_atoms || do_labels))
-    {
-      /* Make sure *something* shows up! */
-      MI_IS_WIREFRAME(mi) = 1;
-      do_bonds = 1;
-    }
-
-  build_molecule (mi, False);
-  glEndList();
-
-  if (do_shells)
-    {
-      glNewList (mc->shell_dlist, GL_COMPILE);
-      ensure_bounding_box_visible (mi);
-
-      do_labels = 0;
-      do_atoms  = 1;
-      do_bonds  = 0;
-
-      build_molecule (mi, True);
-
-      glEndList();
-      do_bonds  = orig_do_bonds;
-      do_atoms  = orig_do_atoms;
-      do_labels = orig_do_labels;
-    }
-}
-
-
-ENTRYPOINT void
-draw_molecule (ModeInfo *mi)
-{
-  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);
-  Window window = MI_WINDOW(mi);
-
-  if (!mc->glx_context)
-    return;
-
-  glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *mc->glx_context);
-
-  if (mc->draw_time == 0)
-    {
-      pick_new_molecule (mi, mc->draw_time);
-      mc->draw_time = now;
-    }
-  else if (mc->mode == 0)
-    {
-      if (mc->draw_tick++ > 10)
-        {
-          time_t now = time((time_t *) 0);
-          if (mc->draw_time == 0) mc->draw_time = now;
-          mc->draw_tick = 0;
-
-          if (!mc->button_down_p &&
-              mc->nmolecules > 1 &&
-              mc->draw_time + timeout <= now)
-            {
-              /* randomize molecules every -timeout seconds */
-              mc->mode = 1;    /* go out */
-              mc->mode_tick = 80 / speed;
-              mc->draw_time = now;
-            }
-        }
-    }
-  else if (mc->mode == 1)   /* out */
-    {
-      if (--mc->mode_tick <= 0)
-        {
-          mc->mode_tick = 80 / speed;
-          mc->mode = 2;  /* go in */
-          pick_new_molecule (mi, mc->draw_time);
-        }
-    }
-  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);
-
-  {
-    double x, y, z;
-    get_position (mc->rot, &x, &y, &z, !mc->button_down_p);
-    glTranslatef((x - 0.5) * 9,
-                 (y - 0.5) * 9,
-                 (z - 0.5) * 9);
-
-    gltrackball_rotate (mc->trackball);
-
-    get_rotation (mc->rot, &x, &y, &z, !mc->button_down_p);
-    glRotatef (x * 360, 1.0, 0.0, 0.0);
-    glRotatef (y * 360, 0.0, 1.0, 0.0);
-    glRotatef (z * 360, 0.0, 0.0, 1.0);
-  }
-
-  glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
-
-  if (mc->mode != 0)
-    {
-      GLfloat s = (mc->mode == 1
-                   ? mc->mode_tick / (80 / speed)
-                   : ((80 / speed) - mc->mode_tick + 1) / (80 / speed));
-      glScalef (s, s, s);
-    }
-
-  glPushMatrix();
-  glCallList (mc->molecule_dlist);
-
-  if (mc->mode == 0)
-    {
-      molecule *m = &mc->molecules[mc->which];
-
-      draw_labels (mi);
-
-      /* This can't go in the display list, or the characters are spaced
-         wrongly when the window is resized. */
-      if (do_titles && m->label && *m->label)
-        {
-          set_atom_color (mi, 0, True, 1);
-#ifndef HAVE_ANDROID   /* Doesn't work -- causes whole scene to be black */
-          print_texture_label (mi->dpy, mc->title_font,
-                               mi->xgwa.width, mi->xgwa.height,
-                               1, m->label);
-#endif
-        }
-    }
-  glPopMatrix();
-
-  if (do_shells)
-    {
-      glColorMask (GL_FALSE, GL_FALSE, GL_FALSE, GL_FALSE);
-      glPushMatrix();
-      glCallList (mc->shell_dlist);
-      glPopMatrix();
-      glColorMask (GL_TRUE, GL_TRUE, GL_TRUE, GL_TRUE);
-
-      glDepthFunc (GL_EQUAL);
-      glEnable (GL_BLEND);
-      glBlendFunc (GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-      glPushMatrix();
-      glCallList (mc->shell_dlist);
-      glPopMatrix();
-      glDepthFunc (GL_LESS);
-      glDisable (GL_BLEND);
-    }
-
-  glPopMatrix ();
-
-  mi->polygon_count = mc->polygon_count;
-
-  if (mi->fps_p) do_fps (mi);
-  glFinish();
-
-  glXSwapBuffers(dpy, window);
-}
-
-
-ENTRYPOINT void
-free_molecule (ModeInfo *mi)
-{
-  molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-  int i, j;
-
-  if (!mc->glx_context) return;
-  glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *mc->glx_context);
-
-  for (i = 0; i < mc->nmolecules; i++) {
-    molecule *m = &mc->molecules[i];
-    for (j = 0; j < m->natoms; j++)
-      free (m->atoms[j].label);
-    free (m->atoms);
-    free (m->bonds);
-    free (m->label);
-  }
-  if (mc->molecules) free (mc->molecules);
-  if (mc->trackball) gltrackball_free (mc->trackball);
-  if (mc->rot) free_rotator (mc->rot);
-  if (mc->atom_font) free_texture_font (mc->atom_font);
-  if (mc->title_font) free_texture_font (mc->title_font);
-
-  if (glIsList(mc->molecule_dlist)) glDeleteLists(mc->molecule_dlist, 1);
-  if (glIsList(mc->shell_dlist)) glDeleteLists(mc->shell_dlist, 1);
-  if (glIsList(mc->molecule_dlist)) glDeleteLists(mc->molecule_dlist, 1);
-}
-
-XSCREENSAVER_MODULE ("Molecule", molecule)
-
-#endif /* USE_GL */