-/* molecule, Copyright (c) 2001-2004 Jamie Zawinski <jwz@jwz.org>
+/* molecule, Copyright (c) 2001-2006 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
/* Documentation on the PDB file format:
- http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
+ http://en.wikipedia.org/wiki/Protein_Data_Bank_%28file_format%29
+ http://www.wwpdb.org/docs.html
+ http://www.wwpdb.org/documentation/format32/v3.2.html
+ http://www.wwpdb.org/documentation/format32/sect9.html
+ http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
Good source of PDB files:
http://www.sci.ouc.bc.ca/chem/molecule/molecule.html
+ http://www.umass.edu/microbio/rasmol/whereget.htm
+ http://www.wwpdb.org/docs.html
*/
-#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_SPIN "XYZ"
-#define DEF_WANDER "False"
-#define DEF_LABELS "True"
-#define DEF_TITLES "True"
-#define DEF_ATOMS "True"
-#define DEF_BONDS "True"
-#define DEF_BBOX "False"
-#define DEF_MOLECULE "(default)"
-
#define DEFAULTS "*delay: 10000 \n" \
- "*timeout: " DEF_TIMEOUT "\n" \
"*showFPS: False \n" \
"*wireframe: False \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" \
+ "*atomFont: -*-helvetica-medium-r-normal-*-180-*\n" \
+ "*atomFont2: -*-helvetica-bold-r-normal-*-80-*\n" \
+ "*titleFont: -*-helvetica-medium-r-normal-*-180-*\n" \
"*noLabelThreshold: 30 \n" \
"*wireframeThreshold: 150 \n" \
-
+# define refresh_molecule 0
+# define release_molecule 0
#undef countof
#define countof(x) (sizeof((x))/sizeof((*x)))
#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 <sys/types.h>
+#include <sys/stat.h>
+#include <dirent.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 DEF_TIMEOUT "20"
+#define DEF_SPIN "XYZ"
+#define DEF_WANDER "False"
+#define DEF_LABELS "True"
+#define DEF_TITLES "True"
+#define DEF_ATOMS "True"
+#define DEF_BONDS "True"
+#define DEF_ESHELLS "True"
+#define DEF_BBOX "False"
+#define DEF_SHELL_ALPHA "0.3"
+#define DEF_MOLECULE "(default)"
+#define DEF_VERBOSE "False"
+
+#define SPHERE_SLICES 48 /* how densely to render spheres */
+#define SPHERE_STACKS 24
#define SMOOTH_TUBE /* whether to have smooth or faceted tubes */
# define TUBE_FACES 8
#endif
-static int scale_down;
-#define SPHERE_SLICES_2 7
-#define SPHERE_STACKS_2 4
-#define TUBE_FACES_2 3
+#define SPHERE_SLICES_2 14
+#define SPHERE_STACKS_2 8
+#define TUBE_FACES_2 6
# ifdef __GNUC__
/* These are the traditional colors used to render these atoms,
and their approximate size in angstroms.
*/
-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, }},
- { "S", 1.80, 0, "Yellow4", "Yellow1", { 0, }},
- { "bond", 0, 0, "Grey70", "Yellow1", { 0, }},
- { "*", 1.40, 0, "Green4", "LightGreen", { 0, }}
+static const atom_data all_atom_data[] = {
+ { "H", 1.17, 0.40, "#FFFFFF", "#000000", { 0, }},
+ { "C", 1.75, 0.58, "#999999", "#FFFFFF", { 0, }},
+ { "CA", 1.80, 0.60, "#0000FF", "#ADD8E6", { 0, }},
+ { "N", 1.55, 0.52, "#A2B5CD", "#EE99FF", { 0, }},
+ { "O", 1.40, 0.47, "#FF0000", "#FFB6C1", { 0, }},
+ { "P", 1.28, 0.43, "#9370DB", "#DB7093", { 0, }},
+ { "S", 1.80, 0.60, "#8B8B00", "#FFFF00", { 0, }},
+ { "bond", 0, 0, "#B3B3B3", "#FFFF00", { 0, }},
+ { "*", 1.40, 0.47, "#008B00", "#90EE90", { 0, }}
};
int id; /* sequence number in the PDB file */
const char *label; /* The atom name */
GLfloat x, y, z; /* position in 3-space (angstroms) */
- atom_data *data; /* computed: which style of atom this is */
+ const atom_data *data; /* computed: which style of atom this is */
} molecule_atom;
typedef struct {
int nmolecules;
molecule *molecules;
+ int mode; /* 0 = normal, 1 = out, 2 = in */
+ int mode_tick;
+
GLuint molecule_dlist;
+ GLuint shell_dlist;
- XFontStruct *xfont1, *xfont2;
- GLuint font1_dlist, font2_dlist;
+ XFontStruct *xfont1, *xfont2, *xfont3;
+ GLuint font1_dlist, font2_dlist, font3_dlist;
+ int polygon_count;
+
+ time_t draw_time;
+ int draw_tick;
+
+ int scale_down;
} 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" },
+ { "-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},
+ {&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_ESHELLS, 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};
+ENTRYPOINT ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL};
\f
/* shapes */
-static void
-sphere (GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire)
+static int
+sphere (molecule_configuration *mc,
+ 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 stacks = (mc->scale_down ? SPHERE_STACKS_2 : SPHERE_STACKS);
+ int slices = (mc->scale_down ? SPHERE_SLICES_2 : SPHERE_SLICES);
glPushMatrix ();
glTranslatef (x, y, z);
glScalef (diameter, diameter, diameter);
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;
+ return stacks * slices;
}
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);
+ load_font (mi->dpy, "atomFont", &mc->xfont1, &mc->font1_dlist);
+ load_font (mi->dpy, "atomFont2", &mc->xfont2, &mc->font2_dlist);
+ load_font (mi->dpy, "titleFont", &mc->xfont3, &mc->font3_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;
-}
-
-
-static atom_data *
+static const atom_data *
get_atom_data (const char *atom_name)
{
int i;
- atom_data *d = 0;
+ const atom_data *d = 0;
char *n = strdup (atom_name);
char *n2 = n;
int L;
static void
-set_atom_color (ModeInfo *mi, molecule_atom *a, Bool font_p)
+set_atom_color (ModeInfo *mi, const molecule_atom *a,
+ Bool font_p, GLfloat alpha)
{
- atom_data *d;
- GLfloat *gl_color;
+ const atom_data *d;
+ GLfloat gl_color[4];
if (a)
d = a->data;
else
+ d = get_atom_data ("bond");
+
+ if (font_p)
{
- static atom_data *def_data = 0;
- if (!def_data) def_data = get_atom_data ("bond");
- d = def_data;
+ gl_color[0] = d->gl_color[4];
+ gl_color[1] = d->gl_color[5];
+ gl_color[2] = d->gl_color[6];
+ gl_color[3] = d->gl_color[7];
+ }
+ else
+ {
+ gl_color[0] = d->gl_color[0];
+ gl_color[1] = d->gl_color[1];
+ gl_color[2] = d->gl_color[2];
+ gl_color[3] = d->gl_color[3];
}
-
- gl_color = (!font_p ? d->gl_color : (d->gl_color + 4));
if (gl_color[3] == 0)
{
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 we're not drawing atoms, and the color is black, use white instead.
+ This is a kludge so that H can have black text over its white ball,
+ but the text still shows up if balls are off.
+ */
+ if (font_p && !do_atoms &&
+ gl_color[0] == 0 && gl_color[1] == 0 && gl_color[2] == 0)
+ {
+ gl_color[0] = gl_color[1] = gl_color[2] = 1;
+ }
+
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);
}
static GLfloat
-atom_size (molecule_atom *a)
+atom_size (const molecule_atom *a)
{
if (do_bonds)
- {
- if (a->data->size2 == 0)
- {
- /* let the molecules have the same relative sizes, but scale
- them to a smaller range, so that the bond-tubes are
- actually visible...
- */
- GLfloat bot = 0.4;
- GLfloat top = 0.6;
- GLfloat min = 1.17;
- GLfloat max = 1.80;
- GLfloat ratio = (a->data->size - min) / (max - min);
- a->data->size2 = bot + (ratio * (top - bot));
- }
- return a->data->size2;
- }
+ return a->data->size2;
else
return a->data->size;
}
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 c2[4] = { 1.0, 0.0, 0.0, 1.0 };
+ static const GLfloat c1[4] = { 0.2, 0.2, 0.4, 1.0 };
+ static const GLfloat c2[4] = { 1.0, 0.0, 0.0, 1.0 };
int wire = MI_IS_WIREFRAME(mi);
GLfloat x1, y1, z1, x2, y2, z2;
molecule_bounding_box (mi, &x1, &y1, &z1, &x2, &y2, &z2);
mc->molecule_size = size;
- scale_down = 0;
+ mc->scale_down = 0;
if (size > max_size)
{
GLfloat scale = max_size / size;
glScalef (scale, scale, scale);
- scale_down = scale < 0.3;
+ mc->scale_down = scale < 0.3;
}
glTranslatef (-(x1 + w/2),
}
-static void
-print_title_string (ModeInfo *mi, const char *string,
- 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_TRANSFORM_BIT | /* for matrix contents */
- GL_ENABLE_BIT); /* for various glDisable calls */
- glDisable (GL_LIGHTING);
- glDisable (GL_DEPTH_TEST);
- {
- glMatrixMode(GL_PROJECTION);
- glPushMatrix();
- {
- glLoadIdentity();
-
- glMatrixMode(GL_MODELVIEW);
- glPushMatrix();
- {
- int i;
- int x2 = x;
- Bool sub_p = False;
- 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));
- 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));
- x2 += (font->per_char
- ? font->per_char[c - font->min_char_or_byte2].width
- : font->min_bounds.width);
- }
- }
- }
- glPopMatrix();
- }
- glMatrixMode(GL_PROJECTION);
- glPopMatrix();
- }
- glPopAttrib();
-
- glMatrixMode(GL_MODELVIEW);
-}
-
/* 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++)
{
- molecule_bond *b = &m->bonds[i];
- molecule_atom *from = get_atom (m->atoms, m->natoms, b->from);
- molecule_atom *to = get_atom (m->atoms, m->natoms, b->to);
+ const molecule_bond *b = &m->bonds[i];
+ const molecule_atom *from = get_atom (m->atoms, m->natoms, b->from);
+ const molecule_atom *to = get_atom (m->atoms, m->natoms, b->to);
if (wire)
{
glVertex3f(from->x, from->y, from->z);
glVertex3f(to->x, to->y, to->z);
glEnd();
+ polys++;
}
else
{
- int faces = (scale_down ? TUBE_FACES_2 : TUBE_FACES);
+ int faces = (mc->scale_down ? TUBE_FACES_2 : TUBE_FACES);
# ifdef SMOOTH_TUBE
int smooth = True;
# else
if (thickness > 0.3)
thickness = 0.3;
- tube (from->x, from->y, from->z,
- to->x, to->y, to->z,
- thickness, cap_size,
- faces, smooth, False, wire);
+ polys += tube (from->x, from->y, from->z,
+ to->x, to->y, to->z,
+ thickness, cap_size,
+ faces, smooth, (!do_atoms || do_shells), wire);
}
}
if (!wire && do_atoms)
for (i = 0; i < m->natoms; i++)
{
- molecule_atom *a = &m->atoms[i];
+ const 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 (mc, a->x, a->y, a->z, size, wire);
}
- if (do_bbox)
- draw_bounding_box (mi);
+ if (do_bbox && !transparent_p)
+ {
+ draw_bounding_box (mi);
+ polys += 4;
+ }
- if (do_titles && m->label && *m->label)
- print_title_string (mi, m->label,
- 10, mi->xgwa.height - 10,
- mc->xfont2);
+ mc->polygon_count += polys;
}
}
+static void
+parse_error (const char *file, int lineno, const char *line)
+{
+ fprintf (stderr, "%s: %s: parse error, line %d: %s\n",
+ progname, file, lineno, line);
+ exit (1);
+}
+
/* This function is crap.
*/
!strncmp (s, "MTRIX3", 6) ||
!strncmp (s, "SHEET ", 6) ||
!strncmp (s, "CISPEP", 6) ||
+/*
+ !strncmp (s, "SEQADV", 6) ||
+ !strncmp (s, "SITE ", 5) ||
+ !strncmp (s, "FTNOTE", 6) ||
+ !strncmp (s, "MODEL ", 5) ||
+ !strncmp (s, "ENDMDL", 6) ||
+ !strncmp (s, "SPRSDE", 6) ||
+ !strncmp (s, "MODRES", 6) ||
+ */
!strncmp (s, "GENERATED BY", 12) ||
!strncmp (s, "TER ", 4) ||
!strncmp (s, "END ", 4) ||
else if (!strncmp (s, "ATOM ", 7))
{
int id;
+ const char *end = strchr (s, '\n');
+ int L = end - s;
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
- sscanf (s+7, " %d ", &id);
+ if (1 != sscanf (s+7, " %d ", &id))
+ parse_error (filename, line, s);
+ /* Use the "atom name" field if that is all that is available. */
strncpy (name, s+12, 3);
+
+ /* But prefer the "element" field. */
+ if (L > 77 && !isspace(s[77])) {
+ /* fprintf(stderr, " \"%s\" -> ", name); */
+ name[0] = s[76];
+ name[1] = s[77];
+ name[2] = 0;
+ /* fprintf(stderr, "\"%s\"\n", name); */
+ }
+
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss = tolower(*ss);
ss++;
}
- sscanf (s + 32, " %f %f %f ", &x, &y, &z);
+ if (3 != sscanf (s + 32, " %f %f %f ", &x, &y, &z))
+ parse_error (filename, line, s);
+
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
char *name = (char *) calloc (1, 4);
GLfloat x = -999, y = -999, z = -999;
- sscanf (s+7, " %d ", &id);
+ if (1 != sscanf (s+7, " %d ", &id))
+ parse_error (filename, line, s);
strncpy (name, s+12, 3);
while (isspace(*name)) name++;
ss = name + strlen(name)-1;
while (isspace(*ss) && ss > name)
*ss-- = 0;
- sscanf (s + 30, " %f %f %f ", &x, &y, &z);
+ if (3 != sscanf (s + 30, " %f %f %f ", &x, &y, &z))
+ parse_error (filename, line, s);
/*
fprintf (stderr, "%s: %s: %d: atom: %d \"%s\" %9.4f %9.4f %9.4f\n",
progname, filename, line,
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++;
}
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]");
}
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
- Bool verbose_p = False;
int i;
mc->nmolecules = 0;
\f
/* Window management, etc
*/
-void
+ENTRYPOINT void
reshape_molecule (ModeInfo *mi, int width, int height)
{
GLfloat h = (GLfloat) height / (GLfloat) width;
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();
static void
gl_init (ModeInfo *mi)
{
- 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};
+ static const GLfloat pos[4] = {1.0, 0.4, 0.9, 0.0};
+ static const GLfloat amb[4] = {0.0, 0.0, 0.0, 1.0};
+ static const GLfloat dif[4] = {0.8, 0.8, 0.8, 1.0};
+ static const 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;
- orig_wire = MI_IS_WIREFRAME(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);
+ print_gl_string (mi->dpy, mc->xfont3, mc->font3_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ s, False);
glFinish();
glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi));
}
-Bool
+ENTRYPOINT Bool
molecule_handle_event (ModeInfo *mi, XEvent *event)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
if (event->xany.type == ButtonPress &&
- event->xbutton.button & Button1)
+ event->xbutton.button == Button1)
{
mc->button_down_p = True;
gltrackball_start (mc->trackball,
return True;
}
else if (event->xany.type == ButtonRelease &&
- event->xbutton.button & Button1)
+ event->xbutton.button == Button1)
{
mc->button_down_p = False;
return True;
}
+ else if (event->xany.type == ButtonPress &&
+ (event->xbutton.button == Button4 ||
+ event->xbutton.button == Button5 ||
+ event->xbutton.button == Button6 ||
+ event->xbutton.button == Button7))
+ {
+ 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)
{
}
-void
+ENTRYPOINT void
init_molecule (ModeInfo *mi)
{
molecule_configuration *mc;
{
Bool spinx=False, spiny=False, spinz=False;
- double spin_speed = 2.0;
- double wander_speed = 0.03;
+ 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') spinx = True;
else if (*s == 'y' || *s == 'Y') spiny = True;
else if (*s == 'z' || *s == 'Z') spinz = True;
+ else if (*s == '0') ;
else
{
fprintf (stderr,
mc->rot = make_rotator (spinx ? spin_speed : 0,
spiny ? spin_speed : 0,
spinz ? spin_speed : 0,
- 1.0,
+ spin_accel,
do_wander ? wander_speed : 0,
(spinx && spiny && spinz));
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;
- mc->no_label_threshold = get_float_resource ("noLabelThreshold",
+ mc->no_label_threshold = get_float_resource (mi->dpy, "noLabelThreshold",
"NoLabelThreshold");
- mc->wireframe_threshold = get_float_resource ("wireframeThreshold",
+ mc->wireframe_threshold = get_float_resource (mi->dpy, "wireframeThreshold",
"WireframeThreshold");
+ mc->mode = 0;
if (wire)
do_bonds = 1;
This can't be a part of the display list because of the games
we play with the translation matrix.
*/
-void
+static void
draw_labels (ModeInfo *mi)
{
molecule_configuration *mc = &mcs[MI_SCREEN(mi)];
int wire = MI_IS_WIREFRAME(mi);
molecule *m = &mc->molecules[mc->which];
+ XFontStruct *xfont = (mc->scale_down ? mc->xfont2 : mc->xfont1);
+ GLuint font_dlist = (mc->scale_down ? mc->font2_dlist : mc->font1_dlist);
int i, j;
if (!do_labels)
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.
/* 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,
+ -string_width (xfont, a->label, 0) / 2,
+ -xfont->descent,
NULL);
for (j = 0; j < strlen(a->label); j++)
- glCallList (mc->font1_dlist + (int)(a->label[j]));
+
+ glCallList (font_dlist + (int)(a->label[j]));
glPopMatrix();
}
}
-void
+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);
+ }
+
+ mc->polygon_count = 0;
+
+ glNewList (mc->molecule_dlist, GL_COMPILE);
+ ensure_bounding_box_visible (mi);
+
+ do_labels = orig_do_labels;
+ 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)
+ do_labels = 0;
+ if (mc->molecule_size > mc->wireframe_threshold)
+ MI_IS_WIREFRAME(mi) = 1;
+
+ if (MI_IS_WIREFRAME(mi))
+ do_bonds = 1, do_shells = 0;
+
+ if (!do_bonds)
+ do_shells = 0;
+
+ 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;
+ }
+}
+
+
+ENTRYPOINT 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 */
- !mc->button_down_p)
+ glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *(mc->glx_context));
+
+ if (mc->draw_time == 0)
{
- if (mc->nmolecules == 1)
- {
- if (last != 0) goto SKIP;
- mc->which = 0;
- }
- else if (last == 0)
+ pick_new_molecule (mi, mc->draw_time);
+ mc->draw_time = now;
+ }
+ else if (mc->mode == 0)
+ {
+ if (mc->draw_tick++ > 10)
{
- mc->which = random() % mc->nmolecules;
+ time_t now = time((time_t *) 0);
+ if (mc->draw_time == 0) mc->draw_time = now;
+ mc->draw_tick = 0;
+
+ if (!mc->button_down_p &&
+ mc->nmolecules > 1 &&
+ mc->draw_time + timeout <= now)
+ {
+ /* randomize molecules every -timeout seconds */
+ mc->mode = 1; /* go out */
+ mc->mode_tick = 10 * speed;
+ mc->draw_time = 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, mc->draw_time);
+ mc->draw_time = 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);
}
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
+
+ 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);
+ }
+
+ glPushMatrix();
glCallList (mc->molecule_dlist);
- draw_labels (mi);
+
+ if (mc->mode == 0)
+ {
+ 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->xfont3, mc->font3_dlist,
+ mi->xgwa.width, mi->xgwa.height,
+ 10, mi->xgwa.height - 10,
+ m->label, False);
+ }
+ }
+ 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();
glXSwapBuffers(dpy, window);
}
+XSCREENSAVER_MODULE ("Molecule", molecule)
+
#endif /* USE_GL */