X-Git-Url: http://git.hungrycats.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=hacks%2Fglx%2Fmolecule.c;h=992ff7ca1417f4bdf198ef6fa0fb77e53729d84b;hb=9c9d475ff889ed8be02e8ce8c17da28b93278fca;hp=75010b8ee0b8c17cd798be8a3b10b12fe13ab1f1;hpb=13dbc569cdc6e29019722c0ef9b932a925efbcad;p=xscreensaver diff --git a/hacks/glx/molecule.c b/hacks/glx/molecule.c index 75010b8e..992ff7ca 100644 --- a/hacks/glx/molecule.c +++ b/hacks/glx/molecule.c @@ -1,4 +1,4 @@ -/* molecule, Copyright (c) 2001 Jamie Zawinski +/* molecule, Copyright (c) 2001-2004 Jamie Zawinski * Draws molecules, based on coordinates from PDB (Protein Data Base) files. * * Permission to use, copy, modify, distribute, and sell this software and its @@ -16,57 +16,12 @@ 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 +#include +#include +#include #include #define PROGCLASS "Molecule" @@ -139,6 +94,11 @@ static int scale_down; #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" }; @@ -159,6 +119,7 @@ typedef struct { 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, }}, @@ -248,15 +209,15 @@ static XrmOptionDescRec opts[] = { }; 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}; @@ -349,7 +310,7 @@ get_atom_data (const char *atom_name) 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; } @@ -691,21 +652,6 @@ build_molecule (ModeInfo *mi) 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); @@ -739,7 +685,7 @@ build_molecule (ModeInfo *mi) tube (from->x, from->y, from->z, to->x, to->y, to->z, thickness, cap_size, - faces, smooth, wire); + faces, smooth, False, wire); } } @@ -752,50 +698,6 @@ build_molecule (ModeInfo *mi) 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); @@ -947,6 +849,12 @@ parse_pdb_data (molecule *m, const char *data, const char *filename, int line) 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", @@ -1013,7 +921,7 @@ parse_pdb_data (molecule *m, const char *data, const char *filename, int line) } -static void +static int parse_pdb_file (molecule *m, const char *name) { FILE *in; @@ -1027,7 +935,7 @@ parse_pdb_file (molecule *m, const char *name) 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); @@ -1047,7 +955,7 @@ parse_pdb_file (molecule *m, const char *name) { fprintf (stderr, "%s: file %s contains no atomic coordinates!\n", progname, name); - exit (1); + return -1; } if (!m->nbonds && do_bonds) @@ -1056,6 +964,8 @@ parse_pdb_file (molecule *m, const char *name) progname, name); do_bonds = 0; } + + return 0; } @@ -1175,41 +1085,137 @@ load_molecules (ModeInfo *mi) { 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, "", 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; - } } } @@ -1355,7 +1361,7 @@ init_molecule (ModeInfo *mi) spinz ? spin_speed : 0, 1.0, do_wander ? wander_speed : 0, - True); + (spinx && spiny && spinz)); mc->trackball = gltrackball_init (); } @@ -1374,6 +1380,94 @@ init_molecule (ModeInfo *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) { @@ -1450,6 +1544,8 @@ 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);