-/* molecule, Copyright (c) 2001 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2004 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
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 <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
+#include <dirent.h>
#include <X11/Intrinsic.h>
#define PROGCLASS "Molecule"
#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"
#define DEF_BONDS "True"
#define DEF_BBOX "False"
#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" \
#include "xlockmore.h"
#include "colors.h"
+#include "sphere.h"
+#include "tube.h"
+#include "glxfonts.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 SPHERE_STACKS 10
-
+#define SPHERE_SLICES 24 /* how densely to render spheres */
+#define SPHERE_STACKS 12
#define SMOOTH_TUBE /* whether to have smooth or faceted tubes */
#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"
};
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, }},
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 */
int nmolecules;
molecule *molecules;
+ int mode; /* 0 = normal, 1 = out, 2 = in */
+ int mode_tick;
+
GLuint molecule_dlist;
XFontStruct *xfont1, *xfont2;
static Bool do_atoms;
static Bool do_bonds;
static Bool do_bbox;
+static Bool verbose_p;
static Bool orig_do_labels, orig_do_bonds, orig_wire; /* saved to reset */
{ "+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" },
+ { "-bbox", ".bbox", XrmoptionNoArg, "True" },
+ { "+bbox", ".bbox", XrmoptionNoArg, "False" },
+ { "-verbose",".verbose",XrmoptionNoArg, "True" },
};
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},
+ {&verbose_p, "verbose","Verbose",DEF_VERBOSE,t_Bool},
};
ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
/* shapes */
static void
-unit_tube (Bool wire)
-{
- int i;
- int faces = (scale_down ? TUBE_FACES_2 : TUBE_FACES);
- GLfloat step = M_PI * 2 / faces;
- GLfloat th;
- int z = 0;
-
- /* side walls
- */
- glFrontFace(GL_CCW);
-
-# ifdef SMOOTH_TUBE
- glBegin(wire ? GL_LINES : GL_QUAD_STRIP);
-# else
- glBegin(wire ? GL_LINES : GL_QUADS);
-# endif
-
- for (i = 0, th = 0; i <= faces; i++)
- {
- GLfloat x = cos (th);
- GLfloat y = sin (th);
- glNormal3f(x, 0, y);
- glVertex3f(x, 0.0, y);
- glVertex3f(x, 1.0, y);
- th += step;
-
-# ifndef SMOOTH_TUBE
- x = cos (th);
- y = sin (th);
- glVertex3f(x, 1.0, y);
- glVertex3f(x, 0.0, y);
-# endif
- }
- glEnd();
-
- /* End caps
- */
- for (z = 0; z <= 1; z++)
- {
- glFrontFace(z == 0 ? GL_CCW : GL_CW);
- glNormal3f(0, (z == 0 ? -1 : 1), 0);
- glBegin(wire ? GL_LINE_LOOP : GL_TRIANGLE_FAN);
- if (! wire) glVertex3f(0, z, 0);
- for (i = 0, th = 0; i <= faces; i++)
- {
- GLfloat x = cos (th);
- GLfloat y = sin (th);
- glVertex3f(x, z, y);
- th += step;
- }
- glEnd();
- }
-}
-
-
-static void
-tube (GLfloat x1, GLfloat y1, GLfloat z1,
- GLfloat x2, GLfloat y2, GLfloat z2,
- GLfloat diameter, GLfloat cap_size,
- Bool wire)
-{
- GLfloat length, angle, a, b, c;
-
- if (diameter <= 0) abort();
-
- a = (x2 - x1);
- b = (y2 - y1);
- c = (z2 - z1);
-
- length = sqrt (a*a + b*b + c*c);
- angle = acos (a / length);
-
- glPushMatrix();
- glTranslatef(x1, y1, z1);
- glScalef (length, length, length);
-
- if (c == 0 && b == 0)
- glRotatef (angle / (M_PI / 180), 0, 1, 0);
- else
- glRotatef (angle / (M_PI / 180), 0, -c, b);
-
- glRotatef (-90, 0, 0, 1);
- glScalef (diameter/length, 1, diameter/length);
-
- /* extend the endpoints of the tube by the cap size in both directions */
- if (cap_size != 0)
- {
- GLfloat c = cap_size/length;
- glTranslatef (0, -c, 0);
- glScalef (1, 1+c+c, 1);
- }
-
- unit_tube (wire);
- glPopMatrix();
-}
-
-
-/* lifted from glplanet */
-/* Function for determining points on the surface of the sphere */
-static void
-parametric_sphere (float theta, float rho, GLfloat *vector)
-{
- vector[0] = -sin(theta) * sin(rho);
- vector[1] = cos(theta) * sin(rho);
- vector[2] = cos(rho);
-}
-
-/* lifted from glplanet */
-static void
-unit_sphere (Bool wire)
+sphere (GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
{
int stacks = (scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
int slices = (scale_down ? SPHERE_SLICES_2 : SPHERE_SLICES);
- int i, j;
- float drho, dtheta;
- float rho, theta;
- GLfloat vector[3];
- GLfloat ds, dt, t, s;
-
- if (!do_bonds && !scale_down) /* if balls are bigger, be smoother... */
- slices *= 2, stacks *= 2;
-
- if (!wire)
- glShadeModel(GL_SMOOTH);
-
- /* Generate a sphere with quadrilaterals.
- * Quad vertices are determined using a parametric sphere function.
- * For fun, you could generate practically any parameteric surface and
- * map an image onto it.
- */
- drho = M_PI / stacks;
- dtheta = 2.0 * M_PI / slices;
- ds = 1.0 / slices;
- dt = 1.0 / stacks;
-
- glFrontFace(GL_CCW);
- glBegin( wire ? GL_LINE_LOOP : GL_QUADS );
-
- t = 0.0;
- for (i=0; i < stacks; i++) {
- rho = i * drho;
- s = 0.0;
- for (j=0; j < slices; j++) {
- theta = j * dtheta;
-
- glTexCoord2f (s,t);
- parametric_sphere (theta, rho, vector);
- glNormal3fv (vector);
- parametric_sphere (theta, rho, vector);
- glVertex3f (vector[0], vector[1], vector[2]);
-
- glTexCoord2f (s,t+dt);
- parametric_sphere (theta, rho+drho, vector);
- glNormal3fv (vector);
- parametric_sphere (theta, rho+drho, vector);
- glVertex3f (vector[0], vector[1], vector[2]);
-
- glTexCoord2f (s+ds,t+dt);
- parametric_sphere (theta + dtheta, rho+drho, vector);
- glNormal3fv (vector);
- parametric_sphere (theta + dtheta, rho+drho, vector);
- glVertex3f (vector[0], vector[1], vector[2]);
-
- glTexCoord2f (s+ds, t);
- parametric_sphere (theta + dtheta, rho, vector);
- glNormal3fv (vector);
- parametric_sphere (theta + dtheta, rho, vector);
- glVertex3f (vector[0], vector[1], vector[2]);
-
- s = s + ds;
- }
- t = t + dt;
- }
- glEnd();
-}
-
-
-static void
-sphere (GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
-{
glPushMatrix ();
glTranslatef (x, y, z);
glScalef (diameter, diameter, diameter);
- unit_sphere (wire);
+ unit_sphere (stacks, slices, wire);
glPopMatrix ();
}
-static void
-load_font (ModeInfo *mi, char *res, XFontStruct **fontP, GLuint *dlistP)
-{
- const char *font = get_string_resource (res, "Font");
- XFontStruct *f;
- Font id;
- int first, last;
-
- if (!font) font = "-*-times-bold-r-normal-*-180-*";
-
- f = XLoadQueryFont(mi->dpy, font);
- if (!f) f = XLoadQueryFont(mi->dpy, "fixed");
-
- id = f->fid;
- first = f->min_char_or_byte2;
- last = f->max_char_or_byte2;
-
- clear_gl_error ();
- *dlistP = glGenLists ((GLuint) last+1);
- check_gl_error ("glGenLists");
- glXUseXFont(id, first, last-first+1, *dlistP + first);
- check_gl_error ("glXUseXFont");
-
- *fontP = f;
-}
-
-
static void
load_fonts (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
- load_font (mi, "atomFont", &mc->xfont1, &mc->font1_dlist);
- load_font (mi, "titleFont", &mc->xfont2, &mc->font2_dlist);
-}
-
-
-static int
-string_width (XFontStruct *f, const char *c)
-{
- int w = 0;
- while (*c)
- {
- int cc = *((unsigned char *) c);
- w += (f->per_char
- ? f->per_char[cc-f->min_char_or_byte2].rbearing
- : f->min_bounds.rbearing);
- c++;
- }
- return w;
+ load_font (mi->dpy, "atomFont", &mc->xfont1, &mc->font1_dlist);
+ load_font (mi->dpy, "titleFont", &mc->xfont2, &mc->font2_dlist);
}
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;
}
}
-static void
-print_title_string (ModeInfo *mi, const char *string,
- GLfloat x, GLfloat y, GLfloat line_height)
-{
- molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
-
- y -= line_height;
-
- glPushAttrib (GL_LIGHTING | GL_DEPTH_TEST);
- glDisable (GL_LIGHTING);
- glDisable (GL_DEPTH_TEST);
- {
- glMatrixMode(GL_PROJECTION);
- glPushMatrix();
- {
- glLoadIdentity();
-
- glMatrixMode(GL_MODELVIEW);
- glPushMatrix();
- {
- int i;
- glLoadIdentity();
-
- gluOrtho2D (0, mi->xgwa.width, 0, mi->xgwa.height);
-
- set_atom_color (mi, 0, True);
-
- glRasterPos2f (x, y);
- for (i = 0; i < strlen(string); i++)
- {
- char c = string[i];
- if (c == '\n')
- glRasterPos2f (x, (y -= line_height));
- else
- glCallList (mc->font2_dlist + (int)(c));
- }
- }
- glPopMatrix();
- }
- glMatrixMode(GL_PROJECTION);
- glPopMatrix();
- }
- glPopAttrib();
-
- glMatrixMode(GL_MODELVIEW);
-}
-
/* Constructs the GL shapes of the current molecule
*/
}
else
{
+ int faces = (scale_down ? TUBE_FACES_2 : TUBE_FACES);
+# ifdef SMOOTH_TUBE
+ int smooth = True;
+# else
+ int smooth = False;
+# endif
GLfloat thickness = 0.07 * b->strength;
GLfloat cap_size = 0.03;
if (thickness > 0.3)
thickness = 0.3;
+
tube (from->x, from->y, from->z,
to->x, to->y, to->z,
- thickness, cap_size, wire);
+ thickness, cap_size,
+ 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);
+ {
+ 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);
+ }
}
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",
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]);
}
-static void
+static int
parse_pdb_file (molecule *m, const char *name)
{
FILE *in;
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);
{
fprintf (stderr, "%s: file %s contains no atomic coordinates!\n",
progname, name);
- exit (1);
+ return -1;
}
if (!m->nbonds && do_bonds)
progname, name);
do_bonds = 0;
}
+
+ return 0;
}
+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)
{
free (counts[i].atom);
s += strlen (s);
if (counts[i].count > 1)
- sprintf (s, "(%d)", counts[i].count);
+ 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);
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)
{
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
+ int i;
+
+ 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);
+ }
- if (!molecule_str || !*molecule_str ||
- !strcmp(molecule_str, "(default)")) /* do the builtins */
+ 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, "<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);
- 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;
- }
}
}
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_gl_string (mi->dpy, mc->xfont2, mc->font2_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ s);
+ 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 == ButtonPress &&
+ (event->xbutton.button == Button4 ||
+ event->xbutton.button == Button5))
{
- if (*dv == 0)
- *dv = 0.00001;
- else if (random() & 1)
- *dv *= 1.2;
- else
- *dv *= 0.8;
+ gltrackball_mousewheel (mc->trackball, event->xbutton.button, 10,
+ !!event->xbutton.state);
+ return True;
}
-}
+ else if (event->xany.type == KeyPress)
+ {
+ KeySym keysym;
+ char c = 0;
+ XLookupString (&event->xkey, &c, 1, &keysym, 0);
+ if (c == ' ' || c == '\t' || c == '\r' || c == '\n')
+ {
+ GLfloat speed = 4.0;
+ mc->mode = 1;
+ mc->mode_tick = 10 * speed;
+ return True;
+ }
+ }
+ else if (event->xany.type == MotionNotify &&
+ mc->button_down_p)
+ {
+ 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 = 0.5;
+ double spin_accel = 0.3;
+ double wander_speed = 0.01;
+
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,
+ spin_accel,
+ do_wander ? wander_speed : 0,
+ (spinx && spiny && spinz));
+ mc->trackball = gltrackball_init ();
}
mc->molecule_dlist = glGenLists(1);
"NoLabelThreshold");
mc->wireframe_threshold = get_float_resource ("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.
+ */
+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);
+}
+
+
+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
+ {
+ 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);
+ }
+
+ glNewList (mc->molecule_dlist, GL_COMPILE);
+ ensure_bounding_box_visible (mi);
+
+ do_labels = orig_do_labels;
+ do_bonds = orig_do_bonds;
+ 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;
+
+ build_molecule (mi);
+ glEndList();
+}
+
+
void
draw_molecule (ModeInfo *mi)
{
static time_t last = 0;
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);
if (!mc->glx_context)
return;
- if (last + timeout <= now) /* randomize molecules every -timeout seconds */
+ if (last == 0)
{
- if (mc->nmolecules == 1)
- {
- if (last != 0) goto SKIP;
- mc->which = 0;
- }
- else if (last == 0)
+ pick_new_molecule (mi, last);
+ last = now;
+ }
+ else if (mc->mode == 0)
+ {
+ static int tick = 0;
+ if (tick++ > 10)
{
- mc->which = random() % mc->nmolecules;
+ time_t now = time((time_t *) 0);
+ if (last == 0) last = now;
+ tick = 0;
+
+ if (!mc->button_down_p &&
+ mc->nmolecules > 1 &&
+ last + timeout <= now)
+ {
+ /* randomize molecules every -timeout seconds */
+ mc->mode = 1; /* go out */
+ mc->mode_tick = 10 * speed;
+ last = now;
+ }
}
- else
+ }
+ else if (mc->mode == 1) /* out */
+ {
+ if (--mc->mode_tick <= 0)
{
- int n = mc->which;
- while (n == mc->which)
- n = random() % mc->nmolecules;
- mc->which = n;
+ mc->mode_tick = 10 * speed;
+ mc->mode = 2; /* go in */
+ pick_new_molecule (mi, last);
+ last = now;
}
-
- last = now;
-
-
- glNewList (mc->molecule_dlist, GL_COMPILE);
- ensure_bounding_box_visible (mi);
-
- do_labels = orig_do_labels;
- do_bonds = orig_do_bonds;
- 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;
-
- build_molecule (mi);
- glEndList();
}
- SKIP:
+ 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);
{
- GLfloat x, y, z;
+ 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);
+ }
- if (do_wander)
- {
- static int frame = 0;
+ glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
-# define SINOID(SCALE,SIZE) \
- ((((1 + sin((frame * (SCALE)) / 2 * M_PI)) / 2.0) * (SIZE)) - (SIZE)/2)
+ if (mc->mode != 0)
+ {
+ GLfloat s = (mc->mode == 1
+ ? mc->mode_tick / (10 * speed)
+ : ((10 * speed) - mc->mode_tick + 1) / (10 * speed));
+ glScalef (s, s, s);
+ }
- x = SINOID(0.031, 9.0);
- y = SINOID(0.023, 9.0);
- z = SINOID(0.017, 9.0);
- frame++;
- glTranslatef(x, y, z);
- }
+ glCallList (mc->molecule_dlist);
- 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);
- }
- }
+ if (mc->mode == 0)
+ draw_labels (mi);
- glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
- glCallList (mc->molecule_dlist);
glPopMatrix ();
if (mi->fps_p) do_fps (mi);
projects / xscreensaver / blobdiff