diff options
Diffstat (limited to 'hacks/glx/molecule.c')
| -rw-r--r-- | hacks/glx/molecule.c | 1720 |
1 files changed, 0 insertions, 1720 deletions
diff --git a/hacks/glx/molecule.c b/hacks/glx/molecule.c deleted file mode 100644 index c173c6b..0000000 --- a/hacks/glx/molecule.c +++ /dev/null @@ -1,1720 +0,0 @@ -/* molecule, Copyright (c) 2001-2016 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 for any purpose is hereby granted without fee, provided that - * the above copyright notice appear in all copies and that both that - * copyright notice and this permission notice appear in supporting - * documentation. No representations are made about the suitability of this - * software for any purpose. It is provided "as is" without express or - * implied warranty. - */ - - -/* Documentation on the PDB file format: - https://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 - */ - -#define DEFAULTS "*delay: 10000 \n" \ - "*showFPS: False \n" \ - "*wireframe: False \n" \ - "*atomFont: sans-serif 24\n" \ - "*titleFont: sans-serif 18\n" \ - "*noLabelThreshold: 150 \n" \ - "*wireframeThreshold: 150 \n" \ - "*suppressRotationAnimation: True\n" \ - -# define release_molecule 0 - -#include "xlockmore.h" -#include "colors.h" -#include "sphere.h" -#include "tube.h" -#include "texfont.h" -#include "rotator.h" -#include "gltrackball.h" - -#ifdef USE_GL /* whole file */ - -#include <sys/types.h> -#include <sys/stat.h> -#include <dirent.h> -#include <ctype.h> - -#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 */ - -#ifdef SMOOTH_TUBE -# define TUBE_FACES 12 /* how densely to render tubes */ -#else -# define TUBE_FACES 8 -#endif - -#define SPHERE_SLICES_2 14 -#define SPHERE_STACKS_2 8 -#define TUBE_FACES_2 6 - - -# 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 -static const char * const builtin_pdb_data[] = { -# include "molecules.h" -}; - - -#ifndef HAVE_MOBILE -# define LOAD_FILES -#endif - - -typedef struct { - const char *name; - GLfloat size, size2; - const char *color; - const char *text_color; - GLfloat gl_color[8]; -} atom_data; - - -/* These are the traditional colors used to render these atoms, - and their approximate size in angstroms. - */ -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, }} -}; - - -typedef struct { - int id; /* sequence number in the PDB file */ - char *label; /* The atom name */ - GLfloat x, y, z; /* position in 3-space (angstroms) */ - const atom_data *data; /* computed: which style of atom this is */ -} molecule_atom; - -typedef struct { - int from, to; /* atom sequence numbers */ - int strength; /* how many bonds are between these two atoms */ -} molecule_bond; - - -typedef struct { - char *label; /* description of this compound */ - int natoms, atoms_size; - int nbonds, bonds_size; - molecule_atom *atoms; - molecule_bond *bonds; -} molecule; - - -typedef struct { - GLXContext *glx_context; - rotator *rot; - trackball_state *trackball; - Bool button_down_p; - - GLfloat molecule_size; /* max dimension of molecule bounding box */ - - GLfloat no_label_threshold; /* Things happen when molecules are huge */ - GLfloat wireframe_threshold; - - int which; /* which of the molecules is being shown */ - int nmolecules; - molecule *molecules; - - int mode; /* 0 = normal, 1 = out, 2 = in */ - int mode_tick; - int next; /* 0 = random, -1 = back, 1 = forward */ - - GLuint molecule_dlist; - GLuint shell_dlist; - - texture_font_data *atom_font, *title_font; - - int polygon_count; - - time_t draw_time; - int draw_tick; - - GLfloat overall_scale; - int low_rez_p; - -} molecule_configuration; - - -static molecule_configuration *mcs = NULL; - -static int timeout; -static char *molecule_str; -static char *do_spin; -static Bool do_wander; -static Bool do_titles; -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; - -/* 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" }, - { "-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_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}, -}; - -ENTRYPOINT ModeSpecOpt molecule_opts = {countof(opts), opts, countof(vars), vars, NULL}; - - - - -/* shapes */ - -static int -sphere (molecule_configuration *mc, - GLfloat x, GLfloat y, GLfloat z, GLfloat diameter, Bool wire) -{ - int stacks = (mc->low_rez_p ? SPHERE_STACKS_2 : SPHERE_STACKS); - int slices = (mc->low_rez_p ? SPHERE_SLICES_2 : SPHERE_SLICES); - - glPushMatrix (); - glTranslatef (x, y, z); - glScalef (diameter, diameter, diameter); - unit_sphere (stacks, slices, wire); - glPopMatrix (); - - return stacks * slices; -} - - -static void -load_fonts (ModeInfo *mi) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - mc->atom_font = load_texture_font (mi->dpy, "atomFont"); - mc->title_font = load_texture_font (mi->dpy, "titleFont"); -} - - -static const atom_data * -get_atom_data (const char *atom_name) -{ - int i; - const atom_data *d = 0; - char *n = strdup (atom_name); - char *n2 = n; - int L; - - while (!isalpha(*n)) n++; - L = strlen(n); - while (L > 0 && !isalpha(n[L-1])) - n[--L] = 0; - - for (i = 0; i < countof(all_atom_data); i++) - { - d = &all_atom_data[i]; - if (!strcasecmp (n, all_atom_data[i].name)) - break; - } - - free (n2); - return d; -} - - -static void -set_atom_color (ModeInfo *mi, const molecule_atom *a, - Bool font_p, GLfloat alpha) -{ - const atom_data *d; - GLfloat gl_color[4]; - - if (a) - d = a->data; - else - d = get_atom_data ("bond"); - - if (font_p) - { - 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]; - } - - if (gl_color[3] == 0) - { - const char *string = !font_p ? d->color : d->text_color; - XColor xcolor; - if (!XParseColor (mi->dpy, mi->xgwa.colormap, string, &xcolor)) - { - fprintf (stderr, "%s: unparsable color in %s: %s\n", progname, - (a ? a->label : d->name), string); - exit (1); - } - - gl_color[0] = xcolor.red / 65536.0; - gl_color[1] = xcolor.green / 65536.0; - gl_color[2] = xcolor.blue / 65536.0; - } - - 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) - 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 (const molecule_atom *a) -{ - if (do_bonds) - return a->data->size2; - else - return a->data->size; -} - - -static molecule_atom * -get_atom (molecule_atom *atoms, int natoms, int id) -{ - int i; - - /* quick short-circuit */ - if (id < natoms) - { - if (atoms[id].id == id) - return &atoms[id]; - if (id > 0 && atoms[id-1].id == id) - return &atoms[id-1]; - if (id < natoms-1 && atoms[id+1].id == id) - return &atoms[id+1]; - } - - for (i = 0; i < natoms; i++) - if (id == atoms[i].id) - return &atoms[i]; - - fprintf (stderr, "%s: no atom %d\n", progname, id); - abort(); -} - - -static void -molecule_bounding_box (ModeInfo *mi, - GLfloat *x1, GLfloat *y1, GLfloat *z1, - GLfloat *x2, GLfloat *y2, GLfloat *z2) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - molecule *m = &mc->molecules[mc->which]; - int i; - - if (m->natoms == 0) - { - *x1 = *y1 = *z1 = *x2 = *y2 = *z2 = 0; - } - else - { - *x1 = *x2 = m->atoms[0].x; - *y1 = *y2 = m->atoms[0].y; - *z1 = *z2 = m->atoms[0].z; - } - - for (i = 1; i < m->natoms; i++) - { - if (m->atoms[i].x < *x1) *x1 = m->atoms[i].x; - if (m->atoms[i].y < *y1) *y1 = m->atoms[i].y; - if (m->atoms[i].z < *z1) *z1 = m->atoms[i].z; - - if (m->atoms[i].x > *x2) *x2 = m->atoms[i].x; - if (m->atoms[i].y > *y2) *y2 = m->atoms[i].y; - if (m->atoms[i].z > *z2) *z2 = m->atoms[i].z; - } - - *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 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); - - glMaterialfv (GL_FRONT, GL_AMBIENT_AND_DIFFUSE, c1); - glFrontFace(GL_CCW); - - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(0, 1, 0); - glVertex3f(x1, y1, z1); glVertex3f(x1, y1, z2); - glVertex3f(x2, y1, z2); glVertex3f(x2, y1, z1); - glEnd(); - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(0, -1, 0); - glVertex3f(x2, y2, z1); glVertex3f(x2, y2, z2); - glVertex3f(x1, y2, z2); glVertex3f(x1, y2, z1); - glEnd(); - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(0, 0, 1); - glVertex3f(x1, y1, z1); glVertex3f(x2, y1, z1); - glVertex3f(x2, y2, z1); glVertex3f(x1, y2, z1); - glEnd(); - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(0, 0, -1); - glVertex3f(x1, y2, z2); glVertex3f(x2, y2, z2); - glVertex3f(x2, y1, z2); glVertex3f(x1, y1, z2); - glEnd(); - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(1, 0, 0); - glVertex3f(x1, y2, z1); glVertex3f(x1, y2, z2); - glVertex3f(x1, y1, z2); glVertex3f(x1, y1, z1); - glEnd(); - glBegin(wire ? GL_LINE_LOOP : GL_QUADS); - glNormal3f(-1, 0, 0); - glVertex3f(x2, y1, z1); glVertex3f(x2, y1, z2); - glVertex3f(x2, y2, z2); glVertex3f(x2, y2, z1); - glEnd(); - - glDisable (GL_LIGHTING); - - glColor3f (c2[0], c2[1], c2[2]); - glBegin(GL_LINES); - if (x1 > 0) x1 = 0; - if (x2 < 0) x2 = 0; - if (y1 > 0) y1 = 0; - if (y2 < 0) y2 = 0; - if (z1 > 0) z1 = 0; - if (z2 < 0) z2 = 0; - glVertex3f(x1, 0, 0); glVertex3f(x2, 0, 0); - glVertex3f(0 , y1, 0); glVertex3f(0, y2, 0); - glVertex3f(0, 0, z1); glVertex3f(0, 0, z2); - glEnd(); - - if (!wire) - glEnable (GL_LIGHTING); -} - - -/* Since PDB files don't always have the molecule centered around the - origin, and since some molecules are pretty large, scale and/or - translate so that the whole molecule is visible in the window. - */ -static void -ensure_bounding_box_visible (ModeInfo *mi) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - - GLfloat x1, y1, z1, x2, y2, z2; - GLfloat w, h, d; - GLfloat size; - GLfloat max_size = 10; /* don't bother scaling down if the molecule - is already smaller than this */ - - molecule_bounding_box (mi, &x1, &y1, &z1, &x2, &y2, &z2); - w = x2-x1; - h = y2-y1; - d = z2-z1; - - size = (w > h ? w : h); - size = (size > d ? size : d); - - mc->molecule_size = size; - - mc->low_rez_p = 0; - mc->overall_scale = 1; - - if (size > max_size) - { - mc->overall_scale = max_size / size; - glScalef (mc->overall_scale, mc->overall_scale, mc->overall_scale); - - mc->low_rez_p = mc->overall_scale < 0.3; - } - - glTranslatef (-(x1 + w/2), - -(y1 + h/2), - -(z1 + d/2)); -} - - - -/* Constructs the GL shapes of the current molecule - */ -static void -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) - { - glDisable(GL_CULL_FACE); - glDisable(GL_LIGHTING); - glDisable(GL_LIGHT0); - glDisable(GL_DEPTH_TEST); - glDisable(GL_NORMALIZE); - glDisable(GL_CULL_FACE); - } - else - { - glEnable(GL_CULL_FACE); - glEnable(GL_LIGHTING); - glEnable(GL_LIGHT0); - glEnable(GL_DEPTH_TEST); - glEnable(GL_NORMALIZE); - glEnable(GL_CULL_FACE); - } - - if (!wire) - set_atom_color (mi, 0, False, alpha); - - if (do_bonds) - for (i = 0; i < m->nbonds; i++) - { - 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) - { - glBegin(GL_LINES); - glVertex3f(from->x, from->y, from->z); - glVertex3f(to->x, to->y, to->z); - glEnd(); - polys++; - } - else - { - int faces = (mc->low_rez_p ? TUBE_FACES_2 : TUBE_FACES); -# ifdef SMOOTH_TUBE - int smooth = True; -# else - int smooth = False; -# endif - Bool cap_p = (!do_atoms || do_shells); - GLfloat base = 0.07; - GLfloat thickness = base * b->strength; - GLfloat cap_size = (cap_p ? base / 2 : 0); - if (thickness > 0.3) - thickness = 0.3; - - polys += tube (from->x, from->y, from->z, - to->x, to->y, to->z, - thickness, cap_size, - faces, smooth, cap_p, wire); - } - } - - if (!wire && do_atoms) - for (i = 0; i < m->natoms; i++) - { - const molecule_atom *a = &m->atoms[i]; - GLfloat size = atom_size (a); - set_atom_color (mi, a, False, alpha); - polys += sphere (mc, a->x, a->y, a->z, size, wire); - } - - if (do_bbox && !transparent_p) - { - draw_bounding_box (mi); - polys += 4; - } - - mc->polygon_count += polys; -} - - - -/* loading */ - -static void -push_atom (molecule *m, - int id, char *label, - GLfloat x, GLfloat y, GLfloat z) -{ - m->natoms++; - if (m->atoms_size < m->natoms) - { - m->atoms_size += 20; - m->atoms = (molecule_atom *) realloc (m->atoms, - m->atoms_size * sizeof(*m->atoms)); - } - m->atoms[m->natoms-1].id = id; - m->atoms[m->natoms-1].label = label; - m->atoms[m->natoms-1].x = x; - m->atoms[m->natoms-1].y = y; - m->atoms[m->natoms-1].z = z; - m->atoms[m->natoms-1].data = get_atom_data (label); -} - - -static void -push_bond (molecule *m, int from, int to) -{ - int i; - - for (i = 0; i < m->nbonds; i++) - if ((m->bonds[i].from == from && m->bonds[i].to == to) || - (m->bonds[i].to == from && m->bonds[i].from == to)) - { - m->bonds[i].strength++; - return; - } - - m->nbonds++; - if (m->bonds_size < m->nbonds) - { - m->bonds_size += 20; - m->bonds = (molecule_bond *) realloc (m->bonds, - m->bonds_size * sizeof(*m->bonds)); - } - m->bonds[m->nbonds-1].from = from; - m->bonds[m->nbonds-1].to = to; - m->bonds[m->nbonds-1].strength = 1; -} - - -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. - */ -static void -parse_pdb_data (molecule *m, const char *data, const char *filename, int line) -{ - const char *s = data; - char *ss; - while (*s) - { - if ((!m->label || !*m->label) && - (!strncmp (s, "HEADER", 6) || !strncmp (s, "COMPND", 6))) - { - char *name = calloc (1, 100); - char *n2 = name; - sprintf (n2, "%.99s", s); - n2 += 7; - while (isspace(*n2)) n2++; - - ss = strchr (n2, '\n'); - if (ss) *ss = 0; - ss = strchr (n2, '\r'); - if (ss) *ss = 0; - - ss = n2+strlen(n2)-1; - while (isspace(*ss) && ss > n2) - *ss-- = 0; - - if (strlen (n2) > 4 && - !strcmp (n2 + strlen(n2) - 4, ".pdb")) - n2[strlen(n2)-4] = 0; - - if (m->label) free (m->label); - m->label = strdup (n2); - free (name); - } - else if (!strncmp (s, "TITLE ", 6) || - !strncmp (s, "HEADER", 6) || - !strncmp (s, "COMPND", 6) || - !strncmp (s, "AUTHOR", 6) || - !strncmp (s, "REVDAT", 6) || - !strncmp (s, "SOURCE", 6) || - !strncmp (s, "EXPDTA", 6) || - !strncmp (s, "JRNL ", 6) || - !strncmp (s, "REMARK", 6) || - !strncmp (s, "SEQRES", 6) || - !strncmp (s, "HET ", 6) || - !strncmp (s, "FORMUL", 6) || - !strncmp (s, "CRYST1", 6) || - !strncmp (s, "ORIGX1", 6) || - !strncmp (s, "ORIGX2", 6) || - !strncmp (s, "ORIGX3", 6) || - !strncmp (s, "SCALE1", 6) || - !strncmp (s, "SCALE2", 6) || - !strncmp (s, "SCALE3", 6) || - !strncmp (s, "MASTER", 6) || - !strncmp (s, "KEYWDS", 6) || - !strncmp (s, "DBREF ", 6) || - !strncmp (s, "HETNAM", 6) || - !strncmp (s, "HETSYN", 6) || - !strncmp (s, "HELIX ", 6) || - !strncmp (s, "LINK ", 6) || - !strncmp (s, "MTRIX1", 6) || - !strncmp (s, "MTRIX2", 6) || - !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) || - !strncmp (s, "TER\n", 4) || - !strncmp (s, "END\n", 4) || - !strncmp (s, "\n", 1)) - /* ignored. */ - ; - else if (!strncmp (s, "ATOM ", 7)) - { - int id; - const char *end = strchr (s, '\n'); - int L = end - s; - char *oname = (char *) calloc (1, 4); - char *name = oname; - GLfloat x = -999, y = -999, z = -999; - - 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-- = 0; - ss = name + 1; - while(*ss) - { - *ss = tolower(*ss); - ss++; - } - 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, - id, name, x, y, z); -*/ - push_atom (m, id, strdup(name), x, y, z); - free (oname); - } - else if (!strncmp (s, "HETATM ", 7)) - { - int id; - char *oname = (char *) calloc (1, 4); - char *name = oname; - GLfloat x = -999, y = -999, z = -999; - - 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; - 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, - id, name, x, y, z); -*/ - push_atom (m, id, strdup(name), x, y, z); - free (oname); - } - 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 %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]); - int j; - for (j = 1; j < i; j++) - if (atoms[j] > 0) - { -/* - fprintf (stderr, "%s: %s: %d: bond: %d %d\n", - progname, filename, line, atoms[0], atoms[j]); -*/ - push_bond (m, atoms[0], atoms[j]); - } - } - else - { - char *s1 = strdup (s); - for (ss = s1; *ss && *ss != '\n'; ss++) - ; - *ss = 0; - fprintf (stderr, "%s: %s: %d: unrecognised line: %s\n", - progname, filename, line, s1); - } - - while (*s && *s != '\n') - s++; - if (*s == '\n') - s++; - line++; - } -} - - -#ifdef LOAD_FILES -static int -parse_pdb_file (molecule *m, const char *name) -{ - FILE *in; - int buf_size = 40960; - char *buf; - int line = 1; - - in = fopen(name, "r"); - if (!in) - { - char *buf = (char *) malloc(1024 + strlen(name)); - sprintf(buf, "%s: error reading \"%s\"", progname, name); - perror(buf); - free(buf); - return -1; - } - - buf = (char *) malloc (buf_size); - - while (fgets (buf, buf_size-1, in)) - { - char *s; - for (s = buf; *s; s++) - if (*s == '\r') *s = '\n'; - parse_pdb_data (m, buf, name, line++); - } - - free (buf); - fclose (in); - - if (!m->natoms) - { - fprintf (stderr, "%s: file %s contains no atomic coordinates!\n", - progname, name); - return -1; - } - - if (!m->nbonds && do_bonds) - { - fprintf (stderr, "%s: warning: file %s contains no atomic bond info.\n", - progname, name); - do_bonds = 0; - } - - return 0; -} -#endif /* LOAD_FILES */ - - -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; - atom_and_count counts[200]; - memset (counts, 0, sizeof(counts)); - *s = 0; - for (i = 0; i < m->natoms; i++) - { - int j = 0; - char *a = (char *) m->atoms[i].label; - char *e; - while (!isalpha(*a)) a++; - a = strdup (a); - for (e = a; isalpha(*e); e++); - *e = 0; - while (counts[j].atom && !!strcmp(a, counts[j].atom)) - j++; - if (counts[j].atom) - free (a); - else - counts[j].atom = a; - counts[j].count++; - } - - i = 0; - while (counts[i].atom) i++; - qsort (counts, i, sizeof(*counts), cmp_atoms); - - i = 0; - while (counts[i].atom) - { - strcat (s, counts[i].atom); - free (counts[i].atom); - s += strlen (s); - if (counts[i].count > 1) - 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); - strcat (s, "\n"); - strcat (s, buf); - free (m->label); - free (buf); - 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) -{ - while (*string) - { - if ((string[0] == ',' || - string[0] == ';' || - string[0] == ':') && - string[1] == ' ') - string[0] = ' ', string[1] = '\n'; - string++; - } -} - - -/* Construct the molecule data from either: the builtins; or from - the (one) .pdb file specified with -molecule. - */ -static void -load_molecules (ModeInfo *mi) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - int i; - - mc->nmolecules = 0; -# ifdef LOAD_FILES - 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. - */ - int wire = MI_IS_WIREFRAME(mi); - 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; - } -# endif /* LOAD_FILES */ - - if (mc->nmolecules == 0) /* do the builtins if no files */ - { - mc->nmolecules = countof(builtin_pdb_data); - if (mc->molecules) free (mc->molecules); - 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); - } - } - - for (i = 0; i < mc->nmolecules; i++) - { - generate_molecule_formula (&mc->molecules[i]); - insert_vertical_whitespace ((char *) mc->molecules[i].label); - } -} - - - -/* Window management, etc - */ -ENTRYPOINT void -reshape_molecule (ModeInfo *mi, int width, int height) -{ - GLfloat h = (GLfloat) height / (GLfloat) width; - int y = 0; - - if (width > height * 5) { /* tiny window: show middle */ - height = width * 9/16; - y = -height/2; - h = height / (GLfloat) width; - } - - glViewport (0, y, (GLint) width, (GLint) height); - - glMatrixMode(GL_PROJECTION); - glLoadIdentity(); - gluPerspective (30.0, 1/h, 20.0, 100.0); - - glMatrixMode(GL_MODELVIEW); - glLoadIdentity(); - gluLookAt( 0.0, 0.0, 30.0, - 0.0, 0.0, 0.0, - 0.0, 1.0, 0.0); - - { - GLfloat s = (MI_WIDTH(mi) < MI_HEIGHT(mi) - ? (MI_WIDTH(mi) / (GLfloat) MI_HEIGHT(mi)) - : 1); - glScalef (s, s, s); - } - - glClear(GL_COLOR_BUFFER_BIT); -} - - -static void -gl_init (ModeInfo *mi) -{ - 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); -} - - -static void -startup_blurb (ModeInfo *mi) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - const char *s = "Constructing molecules..."; -#ifndef HAVE_ANDROID /* Doesn't work -- causes whole scene to be black */ - print_texture_label (mi->dpy, mc->title_font, - mi->xgwa.width, mi->xgwa.height, - 0, s); -#endif - glFinish(); - glXSwapBuffers(MI_DISPLAY(mi), MI_WINDOW(mi)); -} - -ENTRYPOINT Bool -molecule_handle_event (ModeInfo *mi, XEvent *event) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - - if (gltrackball_event_handler (event, mc->trackball, - MI_WIDTH (mi), MI_HEIGHT (mi), - &mc->button_down_p)) - return True; - else - { - if (event->xany.type == KeyPress) - { - KeySym keysym; - char c = 0; - XLookupString (&event->xkey, &c, 1, &keysym, 0); - if (c == '<' || c == ',' || c == '-' || c == '_' || - keysym == XK_Left || keysym == XK_Up || keysym == XK_Prior) - { - mc->next = -1; - goto SWITCH; - } - else if (c == '>' || c == '.' || c == '=' || c == '+' || - keysym == XK_Right || keysym == XK_Down || - keysym == XK_Next) - { - mc->next = 1; - goto SWITCH; - } - } - - if (screenhack_event_helper (MI_DISPLAY(mi), MI_WINDOW(mi), event)) - { - SWITCH: - mc->mode = 1; - mc->mode_tick = 4; - return True; - } - } - - return False; -} - - -ENTRYPOINT void -init_molecule (ModeInfo *mi) -{ - molecule_configuration *mc; - int wire; - - MI_INIT (mi, mcs); - - mc = &mcs[MI_SCREEN(mi)]; - - if ((mc->glx_context = init_GL(mi)) != NULL) { - gl_init(mi); - reshape_molecule (mi, MI_WIDTH(mi), MI_HEIGHT(mi)); - } - - load_fonts (mi); - startup_blurb (mi); - - wire = MI_IS_WIREFRAME(mi); - - { - 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') 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, - "%s: spin must contain only the characters X, Y, or Z (not \"%s\")\n", - progname, do_spin); - exit (1); - } - 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 (True); - } - -#ifdef HAVE_ANDROID /* Doesn't work -- not transparent */ - do_shells = False; -#endif - - 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 (mi->dpy, "noLabelThreshold", - "NoLabelThreshold"); - mc->wireframe_threshold = get_float_resource (mi->dpy, "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. - */ -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]; - int i; - - if (!do_labels) - return; - - 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, 1); - - /* 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 */ - - glRotatef (current_device_rotation(), 0, 0, 1); /* right side up */ - - { - XCharStruct e; - int w, h; - GLfloat s; - - texture_string_metrics (mc->atom_font, a->label, &e, 0, 0); - w = e.width; - h = e.ascent + e.descent; - - s = 1.0 / h; /* Scale to unit */ - s *= mc->overall_scale; /* Scale to size of atom */ - s *= 0.8; /* Shrink a bit */ - glScalef (s, s, 1); - glTranslatef (-w/2, -h/2, 0); -#ifndef HAVE_ANDROID /* Doesn't work -- causes whole scene to be black */ - print_texture_string (mc->atom_font, a->label); -#endif - } - - glPopMatrix(); - } -} - - -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 if (mc->next < 0) - { - mc->which--; - if (mc->which < 0) mc->which = mc->nmolecules-1; - mc->next = 0; - } - else if (mc->next > 0) - { - mc->which++; - if (mc->which >= mc->nmolecules) mc->which = 0; - mc->next = 0; - } - 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) -{ - 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); - Window window = MI_WINDOW(mi); - - if (!mc->glx_context) - return; - - glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *mc->glx_context); - - if (mc->draw_time == 0) - { - pick_new_molecule (mi, mc->draw_time); - mc->draw_time = now; - } - else if (mc->mode == 0) - { - if (mc->draw_tick++ > 10) - { - 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 = 80 / speed; - mc->draw_time = now; - } - } - } - else if (mc->mode == 1) /* out */ - { - if (--mc->mode_tick <= 0) - { - mc->mode_tick = 80 / speed; - mc->mode = 2; /* go in */ - pick_new_molecule (mi, mc->draw_time); - } - } - 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); - - { - 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); - - if (mc->mode != 0) - { - GLfloat s = (mc->mode == 1 - ? mc->mode_tick / (80 / speed) - : ((80 / speed) - mc->mode_tick + 1) / (80 / speed)); - glScalef (s, s, s); - } - - glPushMatrix(); - glCallList (mc->molecule_dlist); - - 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); -#ifndef HAVE_ANDROID /* Doesn't work -- causes whole scene to be black */ - print_texture_label (mi->dpy, mc->title_font, - mi->xgwa.width, mi->xgwa.height, - 1, m->label); -#endif - } - } - 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); -} - - -ENTRYPOINT void -free_molecule (ModeInfo *mi) -{ - molecule_configuration *mc = &mcs[MI_SCREEN(mi)]; - int i, j; - - if (!mc->glx_context) return; - glXMakeCurrent(MI_DISPLAY(mi), MI_WINDOW(mi), *mc->glx_context); - - for (i = 0; i < mc->nmolecules; i++) { - molecule *m = &mc->molecules[i]; - for (j = 0; j < m->natoms; j++) - free (m->atoms[j].label); - free (m->atoms); - free (m->bonds); - free (m->label); - } - if (mc->molecules) free (mc->molecules); - if (mc->trackball) gltrackball_free (mc->trackball); - if (mc->rot) free_rotator (mc->rot); - if (mc->atom_font) free_texture_font (mc->atom_font); - if (mc->title_font) free_texture_font (mc->title_font); - - if (glIsList(mc->molecule_dlist)) glDeleteLists(mc->molecule_dlist, 1); - if (glIsList(mc->shell_dlist)) glDeleteLists(mc->shell_dlist, 1); - if (glIsList(mc->molecule_dlist)) glDeleteLists(mc->molecule_dlist, 1); -} - -XSCREENSAVER_MODULE ("Molecule", molecule) - -#endif /* USE_GL */ |