-/* molecule, Copyright (c) 2001-2004 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2005 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
#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" \
- "*timeout: " DEF_TIMEOUT "\n" \
"*showFPS: False \n" \
"*wireframe: False \n" \
- "*verbose: " DEF_VERBOSE "\n" \
- "*molecule: " DEF_MOLECULE "\n" \
- "*spin: " DEF_SPIN "\n" \
- "*wander: " DEF_WANDER "\n" \
- "*labels: " DEF_LABELS "\n" \
- "*atoms: " DEF_ATOMS "\n" \
- "*bonds: " DEF_BONDS "\n" \
- "*bbox: " DEF_BBOX "\n" \
"*atomFont: -*-times-bold-r-normal-*-240-*\n" \
"*titleFont: -*-times-bold-r-normal-*-180-*\n" \
"*noLabelThreshold: 30 \n" \
int mode_tick;
GLuint molecule_dlist;
+ GLuint shell_dlist;
XFontStruct *xfont1, *xfont2;
GLuint font1_dlist, font2_dlist;
+ int polygon_count;
} molecule_configuration;
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;
-static Bool orig_do_labels, orig_do_bonds, orig_wire; /* saved to reset */
+/* 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" },
- { "-bbox", ".bbox", XrmoptionNoArg, "True" },
- { "+bbox", ".bbox", XrmoptionNoArg, "False" },
- { "-verbose",".verbose",XrmoptionNoArg, "True" },
+ { "-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_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},
- {&verbose_p, "verbose","Verbose",DEF_VERBOSE,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_atoms, "atoms", "Atoms", DEF_ATOMS, t_Bool},
+ {&do_bonds, "bonds", "Bonds", DEF_BONDS, t_Bool},
+ {&do_shells, "eshells", "EShells", DEF_SHELLS, 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},
};
ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
\f
/* shapes */
-static void
+static int
sphere (GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
{
int stacks = (scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
glScalef (diameter, diameter, diameter);
unit_sphere (stacks, slices, wire);
glPopMatrix ();
+
+ return stacks * slices;
}
static void
-set_atom_color (ModeInfo *mi, molecule_atom *a, Bool font_p)
+set_atom_color (ModeInfo *mi, molecule_atom *a, Bool font_p, GLfloat alpha)
{
atom_data *d;
GLfloat *gl_color;
gl_color[0] = xcolor.red / 65536.0;
gl_color[1] = xcolor.green / 65536.0;
gl_color[2] = xcolor.blue / 65536.0;
- gl_color[3] = 1.0;
}
+ gl_color[3] = alpha;
+
if (font_p)
- glColor3f (gl_color[0], gl_color[1], gl_color[2]);
+ glColor4f (gl_color[0], gl_color[1], gl_color[2], gl_color[3]);
else
glMaterialfv (GL_FRONT, GL_AMBIENT_AND_DIFFUSE, gl_color);
}
if (m->atoms[i].z > *z2) *z2 = m->atoms[i].z;
}
- *x1 -= 1;
- *y1 -= 1;
- *z1 -= 1;
- *x2 += 1;
- *y2 += 1;
- *z2 += 1;
+ *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 GLfloat c1[4] = { 0.2, 0.2, 0.6, 1.0 };
+ static GLfloat c1[4] = { 0.2, 0.2, 0.4, 1.0 };
static GLfloat c2[4] = { 1.0, 0.0, 0.0, 1.0 };
int wire = MI_IS_WIREFRAME(mi);
GLfloat x1, y1, z1, x2, y2, z2;
/* Constructs the GL shapes of the current molecule
*/
static void
-build_molecule (ModeInfo *mi)
+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)
- set_atom_color (mi, 0, False);
+ set_atom_color (mi, 0, False, alpha);
if (do_bonds)
for (i = 0; i < m->nbonds; i++)
glVertex3f(from->x, from->y, from->z);
glVertex3f(to->x, to->y, to->z);
glEnd();
+ polys++;
}
else
{
tube (from->x, from->y, from->z,
to->x, to->y, to->z,
thickness, cap_size,
- faces, smooth, False, wire);
+ faces, smooth, (!do_atoms || do_shells), wire);
+ polys += faces;
}
}
{
molecule_atom *a = &m->atoms[i];
GLfloat size = atom_size (a);
- set_atom_color (mi, a, False);
- sphere (a->x, a->y, a->z, size, wire);
+ set_atom_color (mi, a, False, alpha);
+ polys += sphere (a->x, a->y, a->z, size, wire);
}
- if (do_bbox)
- draw_bounding_box (mi);
-
- if (do_titles && m->label && *m->label)
+ if (do_bbox && !transparent_p)
{
- set_atom_color (mi, 0, True);
- print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
- mi->xgwa.width, mi->xgwa.height,
- 10, mi->xgwa.height - 10,
- m->label);
+ draw_bounding_box (mi);
+ polys += 4;
}
+
+ mc->polygon_count += polys;
}
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)");
+ 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)");
+ 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]");
}
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
- gluPerspective (30.0, 1/h, 20.0, 40.0);
+ gluPerspective (30.0, 1/h, 20.0, 100.0);
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
glLightfv(GL_LIGHT0, GL_AMBIENT, amb);
glLightfv(GL_LIGHT0, GL_DIFFUSE, dif);
glLightfv(GL_LIGHT0, GL_SPECULAR, spc);
-
- orig_do_labels = do_labels;
- orig_do_bonds = do_bonds;
- orig_wire = MI_IS_WIREFRAME(mi);
}
mc->trackball = gltrackball_init ();
}
+ 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;
glPushMatrix();
if (!wire)
- set_atom_color (mi, a, True);
+ set_atom_color (mi, a, True, 1);
/* First, we translate the origin to the center of the atom.
free (name);
}
+ mc->polygon_count = 0;
+
glNewList (mc->molecule_dlist, GL_COMPILE);
ensure_bounding_box_visible (mi);
do_labels = orig_do_labels;
- do_bonds = orig_do_bonds;
+ 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)
MI_IS_WIREFRAME(mi) = 1;
if (MI_IS_WIREFRAME(mi))
- do_bonds = 1;
+ do_bonds = 1, do_shells = 0;
+
+ if (!do_bonds)
+ do_shells = 0;
- build_molecule (mi);
+ 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;
+ }
}
glScalef (s, s, s);
}
+ glPushMatrix();
glCallList (mc->molecule_dlist);
if (mc->mode == 0)
- draw_labels (mi);
+ {
+ 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);
+ print_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ m->label);
+ }
+ }
+ 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();
projects / xscreensaver / blobdiff