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.
*/
#include <X11/Intrinsic.h>
#define HACK_INIT init_molecule
#define HACK_DRAW draw_molecule
#define HACK_RESHAPE reshape_molecule
+#define HACK_HANDLE_EVENT molecule_handle_event
+#define EVENT_MASK PointerMotionMask
#define molecule_opts xlockmore_opts
#define DEF_TIMEOUT "20"
#include "colors.h"
#include "sphere.h"
#include "tube.h"
+#include "rotator.h"
+#include "gltrackball.h"
#ifdef USE_GL /* whole file */
+#include <stdlib.h>
#include <ctype.h>
+#include <time.h>
+#include <sys/time.h>
#include <GL/glu.h>
#define SPHERE_SLICES 16 /* how densely to render spheres */
#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"
};
typedef struct {
GLXContext *glx_context;
-
- GLfloat rotx, roty, rotz; /* current object rotation */
- GLfloat dx, dy, dz; /* current rotational velocity */
- GLfloat ddx, ddy, ddz; /* current rotational acceleration */
- GLfloat d_max; /* max velocity */
-
- Bool spin_x, spin_y, spin_z;
+ rotator *rot;
+ trackball_state *trackball;
+ Bool button_down_p;
GLfloat molecule_size; /* max dimension of molecule bounding box */
static void
print_title_string (ModeInfo *mi, const char *string,
- GLfloat x, GLfloat y, GLfloat line_height)
+ GLfloat x, GLfloat y, XFontStruct *font)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-
+ GLfloat line_height = font->ascent + font->descent;
+ GLfloat sub_shift = (line_height * 0.3);
+
y -= line_height;
- glPushAttrib (GL_LIGHTING | GL_DEPTH_TEST);
+ glPushAttrib (GL_TRANSFORM_BIT | /* for matrix contents */
+ GL_ENABLE_BIT); /* for various glDisable calls */
glDisable (GL_LIGHTING);
glDisable (GL_DEPTH_TEST);
{
glPushMatrix();
{
int i;
+ int x2 = x;
+ Bool sub_p = False;
glLoadIdentity();
gluOrtho2D (0, mi->xgwa.width, 0, mi->xgwa.height);
{
char c = string[i];
if (c == '\n')
- glRasterPos2f (x, (y -= line_height));
+ {
+ glRasterPos2f (x, (y -= line_height));
+ x2 = x;
+ }
+ else if (c == '(' && (isdigit (string[i+1])))
+ {
+ sub_p = True;
+ glRasterPos2f (x2, (y -= sub_shift));
+ }
+ else if (c == ')' && sub_p)
+ {
+ sub_p = False;
+ glRasterPos2f (x2, (y += sub_shift));
+ }
else
- glCallList (mc->font2_dlist + (int)(c));
+ {
+ glCallList (mc->font2_dlist + (int)(c));
+ x2 += (font->per_char
+ ? font->per_char[c - font->min_char_or_byte2].width
+ : font->min_bounds.width);
+ }
}
}
glPopMatrix();
tube (from->x, from->y, from->z,
to->x, to->y, to->z,
thickness, cap_size,
- faces, smooth, wire);
+ faces, smooth, False, wire);
}
}
- for (i = 0; i < m->natoms; i++)
- {
- molecule_atom *a = &m->atoms[i];
- int i;
-
- if (!wire && do_atoms)
- {
- GLfloat size = atom_size (a);
- set_atom_color (mi, a, False);
- sphere (a->x, a->y, a->z, size, wire);
- }
-
- if (do_labels)
- {
- glPushAttrib (GL_LIGHTING | GL_DEPTH_TEST);
- glDisable (GL_LIGHTING);
- glDisable (GL_DEPTH_TEST);
-
- if (!wire)
- set_atom_color (mi, a, True);
-
- glRasterPos3f (a->x, a->y, a->z);
-
- {
- GLdouble mm[17], pm[17];
- GLint vp[5];
- GLdouble wx=-1, wy=-1, wz=-1;
- glGetDoublev (GL_MODELVIEW_MATRIX, mm);
- glGetDoublev (GL_PROJECTION_MATRIX, pm);
- glGetIntegerv (GL_VIEWPORT, vp);
-
- /* Convert 3D coordinates to window coordinates */
- gluProject (a->x, a->y, a->z, mm, pm, vp, &wx, &wy, &wz);
-
- /* Fudge the window coordinates to center the string */
- wx -= string_width (mc->xfont1, a->label) / 2;
- wy -= mc->xfont1->descent;
-
- /* Convert new window coordinates back to 3D coordinates */
- gluUnProject (wx, wy, wz, mm, pm, vp, &wx, &wy, &wz);
- glRasterPos3f (wx, wy, wz);
- }
-
- for (i = 0; i < strlen(a->label); i++)
- glCallList (mc->font1_dlist + (int)(a->label[i]));
-
- glPopAttrib();
- }
- }
+ if (!wire && do_atoms)
+ for (i = 0; i < m->natoms; i++)
+ {
+ 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);
+ }
if (do_bbox)
draw_bounding_box (mi);
if (do_titles && m->label && *m->label)
print_title_string (mi, m->label,
10, mi->xgwa.height - 10,
- mc->xfont2->ascent + mc->xfont2->descent);
+ mc->xfont2);
}
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 ",
+ 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]);
}
+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;
- struct { char *atom; int count; } counts[200];
+ atom_and_count counts[200];
memset (counts, 0, sizeof(counts));
*s = 0;
for (i = 0; i < m->natoms; i++)
counts[j].count++;
}
+ i = 0;
+ while (counts[i].atom) i++;
+ qsort (counts, i, sizeof(*counts), cmp_atoms);
+
i = 0;
while (counts[i].atom)
{
i++;
}
+ special_case_formula (buf);
+
if (!m->label) m->label = strdup("");
s = (char *) malloc (strlen (m->label) + strlen (buf) + 2);
strcpy (s, m->label);
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)
{
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
+ gluPerspective (30.0, 1/h, 20.0, 40.0);
- gluPerspective( 30.0, 1/h, 1.0, 100.0 );
- gluLookAt( 0.0, 0.0, 15.0,
- 0.0, 0.0, 0.0,
- 0.0, 1.0, 0.0);
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
- glTranslatef(0.0, 0.0, -15.0);
+ gluLookAt( 0.0, 0.0, 30.0,
+ 0.0, 0.0, 0.0,
+ 0.0, 1.0, 0.0);
glClear(GL_COLOR_BUFFER_BIT);
}
static void
gl_init (ModeInfo *mi)
{
- static GLfloat pos[4] = {5.0, 5.0, 10.0, 1.0};
+ static GLfloat pos[4] = {1.0, 0.4, 0.9, 0.0};
+ static GLfloat amb[4] = {0.0, 0.0, 0.0, 1.0};
+ static GLfloat dif[4] = {0.8, 0.8, 0.8, 1.0};
+ static 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);
orig_do_labels = do_labels;
orig_do_bonds = do_bonds;
}
-/* lifted from lament.c */
-#define RAND(n) ((long) ((random() & 0x7fffffff) % ((long) (n))))
-#define RANDSIGN() ((random() & 1) ? 1 : -1)
-
static void
-rotate(GLfloat *pos, GLfloat *v, GLfloat *dv, GLfloat max_v)
+startup_blurb (ModeInfo *mi)
{
- double ppos = *pos;
-
- /* tick position */
- if (ppos < 0)
- ppos = -(ppos + *v);
- else
- ppos += *v;
-
- if (ppos > 1.0)
- ppos -= 1.0;
- else if (ppos < 0)
- ppos += 1.0;
-
- if (ppos < 0) abort();
- if (ppos > 1.0) abort();
- *pos = (*pos > 0 ? ppos : -ppos);
+ molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
+ const char *s = "Constructing molecules...";
+ print_title_string (mi, s,
+ mi->xgwa.width - (string_width (mc->xfont2, s) + 40),
+ 10 + mc->xfont2->ascent + mc->xfont2->descent,
+ mc->xfont2);
+ glFinish();
+ glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
+}
- /* accelerate */
- *v += *dv;
+Bool
+molecule_handle_event (ModeInfo *mi, XEvent *event)
+{
+ molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- /* clamp velocity */
- if (*v > max_v || *v < -max_v)
+ if (event->xany.type == ButtonPress &&
+ event->xbutton.button & Button1)
{
- *dv = -*dv;
+ mc->button_down_p = True;
+ gltrackball_start (mc->trackball,
+ event->xbutton.x, event->xbutton.y,
+ MI_WIDTH (mi), MI_HEIGHT (mi));
+ return True;
}
- /* If it stops, start it going in the other direction. */
- else if (*v < 0)
+ else if (event->xany.type == ButtonRelease &&
+ event->xbutton.button & Button1)
{
- if (random() % 4)
- {
- *v = 0;
-
- /* keep going in the same direction */
- if (random() % 2)
- *dv = 0;
- else if (*dv < 0)
- *dv = -*dv;
- }
- else
- {
- /* reverse gears */
- *v = -*v;
- *dv = -*dv;
- *pos = -*pos;
- }
+ mc->button_down_p = False;
+ return True;
}
-
- /* Alter direction of rotational acceleration randomly. */
- if (! (random() % 120))
- *dv = -*dv;
-
- /* Change acceleration very occasionally. */
- if (! (random() % 200))
+ else if (event->xany.type == MotionNotify &&
+ mc->button_down_p)
{
- if (*dv == 0)
- *dv = 0.00001;
- else if (random() & 1)
- *dv *= 1.2;
- else
- *dv *= 0.8;
+ gltrackball_track (mc->trackball,
+ event->xmotion.x, event->xmotion.y,
+ MI_WIDTH (mi), MI_HEIGHT (mi));
+ return True;
}
-}
-
-static void
-startup_blurb (ModeInfo *mi)
-{
- molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- const char *s = "Constructing molecules...";
- print_title_string (mi, s,
- mi->xgwa.width - (string_width (mc->xfont2, s) + 40),
- 10 + mc->xfont2->ascent + mc->xfont2->descent,
- mc->xfont2->ascent + mc->xfont2->descent);
- glFinish();
- glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
+ return False;
}
+
void
init_molecule (ModeInfo *mi)
{
wire = MI_IS_WIREFRAME(mi);
- mc->rotx = frand(1.0) * RANDSIGN();
- mc->roty = frand(1.0) * RANDSIGN();
- mc->rotz = frand(1.0) * RANDSIGN();
-
- /* bell curve from 0-6 degrees, avg 3 */
- mc->dx = (frand(1) + frand(1) + frand(1)) / (360/2);
- mc->dy = (frand(1) + frand(1) + frand(1)) / (360/2);
- mc->dz = (frand(1) + frand(1) + frand(1)) / (360/2);
-
- mc->d_max = mc->dx * 2;
-
- mc->ddx = 0.00006 + frand(0.00003);
- mc->ddy = 0.00006 + frand(0.00003);
- mc->ddz = 0.00006 + frand(0.00003);
-
{
+ Bool spinx=False, spiny=False, spinz=False;
+ double spin_speed = 2.0;
+ double wander_speed = 0.03;
+
char *s = do_spin;
while (*s)
{
- if (*s == 'x' || *s == 'X') mc->spin_x = 1;
- else if (*s == 'y' || *s == 'Y') mc->spin_y = 1;
- else if (*s == 'z' || *s == 'Z') mc->spin_z = 1;
+ if (*s == 'x' || *s == 'X') spinx = True;
+ else if (*s == 'y' || *s == 'Y') spiny = True;
+ else if (*s == 'z' || *s == 'Z') spinz = True;
else
{
fprintf (stderr,
}
s++;
}
+
+ mc->rot = make_rotator (spinx ? spin_speed : 0,
+ spiny ? spin_speed : 0,
+ spinz ? spin_speed : 0,
+ 1.0,
+ do_wander ? wander_speed : 0,
+ (spinx && spiny && spinz));
+ mc->trackball = gltrackball_init ();
}
mc->molecule_dlist = glGenLists(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.
+ */
+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)
{
if (!mc->glx_context)
return;
- if (last + timeout <= now) /* randomize molecules every -timeout seconds */
+ if (last + timeout <= now && /* randomize molecules every -timeout seconds */
+ !mc->button_down_p)
{
if (mc->nmolecules == 1)
{
glScalef(1.1, 1.1, 1.1);
{
- GLfloat x, y, z;
-
- if (do_wander)
- {
- static int frame = 0;
-
-# define SINOID(SCALE,SIZE) \
- ((((1 + sin((frame * (SCALE)) / 2 * M_PI)) / 2.0) * (SIZE)) - (SIZE)/2)
-
- x = SINOID(0.031, 9.0);
- y = SINOID(0.023, 9.0);
- z = SINOID(0.017, 9.0);
- frame++;
- glTranslatef(x, y, z);
- }
-
- if (mc->spin_x || mc->spin_y || mc->spin_z)
- {
- x = mc->rotx;
- y = mc->roty;
- z = mc->rotz;
- if (x < 0) x = 1 - (x + 1);
- if (y < 0) y = 1 - (y + 1);
- if (z < 0) z = 1 - (z + 1);
-
- if (mc->spin_x) glRotatef(x * 360, 1.0, 0.0, 0.0);
- if (mc->spin_y) glRotatef(y * 360, 0.0, 1.0, 0.0);
- if (mc->spin_z) glRotatef(z * 360, 0.0, 0.0, 1.0);
-
- rotate(&mc->rotx, &mc->dx, &mc->ddx, mc->d_max);
- rotate(&mc->roty, &mc->dy, &mc->ddy, mc->d_max);
- rotate(&mc->rotz, &mc->dz, &mc->ddz, mc->d_max);
- }
+ 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);
glCallList (mc->molecule_dlist);
+ draw_labels (mi);
+
glPopMatrix ();
if (mi->fps_p) do_fps (mi);
projects / xscreensaver / blobdiff