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 <X11/Intrinsic.h>
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);
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);
}
+/* 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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