| 1 | #define _FILE_OFFSET_BITS 64 | 
| 2 |  | 
| 3 | #include <stdio.h> | 
| 4 | #include <stdlib.h> | 
| 5 | #include <string.h> | 
| 6 | #include <math.h> | 
| 7 |  | 
| 8 | #include "pov_writer.h" | 
| 9 | #include "atom_parser.h" | 
| 10 |  | 
| 11 | struct bond{ | 
| 12 | int i; | 
| 13 | int j; | 
| 14 | }; | 
| 15 |  | 
| 16 | struct linked_bond_list{ | 
| 17 | struct bond the_bond; | 
| 18 | struct linked_bond_list *next; | 
| 19 | }; | 
| 20 |  | 
| 21 | void make_bonds(struct coords *, int); | 
| 22 |  | 
| 23 | struct linked_bond_list *bl_head; | 
| 24 |  | 
| 25 | void clean_bonds(void); | 
| 26 |  | 
| 27 | void initBondList(void){ | 
| 28 | bl_head = NULL; | 
| 29 | } | 
| 30 |  | 
| 31 | void pov_write(FILE *out_file, struct coords *the_coords, int n_atoms, | 
| 32 | int d_hydrogens, int d_bonds, int d_atoms, int d_vectors){ | 
| 33 |  | 
| 34 | int i,j; /*loop counters */ | 
| 35 | int skip_atom, skip_bond, test1, test2; /*booleans */ | 
| 36 | int gb_atom, gbdp_atom; | 
| 37 | double dx, dy, dz; /* used in making the bonds */ | 
| 38 |  | 
| 39 | struct linked_bond_list *current_bond; /*keeps track of the linked list*/ | 
| 40 |  | 
| 41 | for(i = 0; i < n_atoms; i++){ | 
| 42 | update_types(the_coords[i].name); | 
| 43 | } | 
| 44 |  | 
| 45 | if(d_atoms){ | 
| 46 |  | 
| 47 | fprintf(out_file, | 
| 48 | "//************************************************************\n" | 
| 49 | "// The list of atoms\n" | 
| 50 | "//************************************************************\n" | 
| 51 | "\n" | 
| 52 | "\n"); | 
| 53 |  | 
| 54 | for(i = 0; i < n_atoms; i++){ | 
| 55 |  | 
| 56 | skip_atom = 0; | 
| 57 |  | 
| 58 | if(!d_hydrogens){ | 
| 59 | skip_atom = !strcmp("H", the_coords[i].name); | 
| 60 | } | 
| 61 |  | 
| 62 | if(!skip_atom){ | 
| 63 |  | 
| 64 | gb_atom = !strcmp("GB", the_coords[i].name); | 
| 65 | gbdp_atom = !strcmp("GBDP", the_coords[i].name); | 
| 66 |  | 
| 67 | if (gb_atom) { | 
| 68 | fprintf(out_file, | 
| 69 | "make_%s_ellipse( %lf, %lf, %lf, %lf, %lf, %lf, %lf)\n", | 
| 70 | the_coords[i].name, | 
| 71 | the_coords[i].x, | 
| 72 | the_coords[i].z, | 
| 73 | the_coords[i].y, | 
| 74 | the_coords[i].charge, | 
| 75 | the_coords[i].ux, | 
| 76 | the_coords[i].uz, | 
| 77 | the_coords[i].uy); | 
| 78 | } else { | 
| 79 | if (gbdp_atom) { | 
| 80 | fprintf(out_file, | 
| 81 | "make_%s_shaded_ellipse( %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf, %lf)\n", | 
| 82 | the_coords[i].name, | 
| 83 | the_coords[i].x, | 
| 84 | the_coords[i].z, | 
| 85 | the_coords[i].y, | 
| 86 | the_coords[i].charge, | 
| 87 | the_coords[i].ux, | 
| 88 | the_coords[i].uz, | 
| 89 | the_coords[i].uy, | 
| 90 | the_coords[i].vx, | 
| 91 | the_coords[i].vz, | 
| 92 | the_coords[i].vy); | 
| 93 | } else { | 
| 94 | fprintf(out_file, | 
| 95 | "make_%s_atom( %lf, %lf, %lf )\n", | 
| 96 | the_coords[i].name, | 
| 97 | the_coords[i].x, | 
| 98 | the_coords[i].z, | 
| 99 | the_coords[i].y); | 
| 100 | } | 
| 101 | } | 
| 102 | } | 
| 103 | } | 
| 104 |  | 
| 105 | fprintf(out_file, | 
| 106 | "\n" | 
| 107 | "\n"); | 
| 108 | } | 
| 109 |  | 
| 110 |  | 
| 111 | if (d_vectors) { | 
| 112 |  | 
| 113 | fprintf(out_file, | 
| 114 | "//************************************************************\n" | 
| 115 | "// The list of vectors\n" | 
| 116 | "//************************************************************\n" | 
| 117 | "\n" | 
| 118 | "\n"); | 
| 119 |  | 
| 120 | for(i = 0; i < n_atoms; i++){ | 
| 121 |  | 
| 122 | if (the_coords[i].hasVector) { | 
| 123 | fprintf(out_file, | 
| 124 | "make_%s_vector(%lf, %lf, %lf, %lf, %lf, %lf)\n", | 
| 125 | the_coords[i].name, | 
| 126 | the_coords[i].x, | 
| 127 | the_coords[i].z, | 
| 128 | the_coords[i].y, | 
| 129 | the_coords[i].ux, | 
| 130 | the_coords[i].uz, | 
| 131 | the_coords[i].uy); | 
| 132 | } | 
| 133 | } | 
| 134 |  | 
| 135 | fprintf(out_file, | 
| 136 | "\n" | 
| 137 | "\n"); | 
| 138 | } | 
| 139 |  | 
| 140 | if(d_bonds){ | 
| 141 |  | 
| 142 | fprintf(out_file, | 
| 143 | "//************************************************************\n" | 
| 144 | "// The list of bonds\n" | 
| 145 | "//************************************************************\n" | 
| 146 | "\n" | 
| 147 | "\n"); | 
| 148 |  | 
| 149 | if( bl_head == NULL ) make_bonds(the_coords, n_atoms); | 
| 150 |  | 
| 151 | current_bond = bl_head->next; | 
| 152 |  | 
| 153 | while(current_bond != NULL){ | 
| 154 |  | 
| 155 | skip_bond = 0; | 
| 156 |  | 
| 157 | i = current_bond->the_bond.i; | 
| 158 | j = current_bond->the_bond.j; | 
| 159 |  | 
| 160 | if(!d_hydrogens){ | 
| 161 |  | 
| 162 | test1 = !strcmp("H", the_coords[i].name); | 
| 163 | test2 = !strcmp("H", the_coords[j].name); | 
| 164 |  | 
| 165 | skip_bond = (test1 || test2); | 
| 166 | } | 
| 167 |  | 
| 168 | if(!skip_bond){ | 
| 169 |  | 
| 170 | dx = (the_coords[j].x - the_coords[i].x) / 2.0; | 
| 171 | dy = (the_coords[j].y - the_coords[i].y) / 2.0; | 
| 172 | dz = (the_coords[j].z - the_coords[i].z) / 2.0; | 
| 173 |  | 
| 174 | fprintf(out_file, | 
| 175 | "make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", | 
| 176 | the_coords[i].name, | 
| 177 | the_coords[i].x, | 
| 178 | the_coords[i].z, | 
| 179 | the_coords[i].y, | 
| 180 | (the_coords[i].x + dx), | 
| 181 | (the_coords[i].z + dz), | 
| 182 | (the_coords[i].y + dy)); | 
| 183 |  | 
| 184 | fprintf(out_file, | 
| 185 | "make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", | 
| 186 | the_coords[j].name, | 
| 187 | the_coords[j].x, | 
| 188 | the_coords[j].z, | 
| 189 | the_coords[j].y, | 
| 190 | (the_coords[j].x - dx), | 
| 191 | (the_coords[j].z - dz), | 
| 192 | (the_coords[j].y - dy)); | 
| 193 |  | 
| 194 | fprintf(out_file, "\n"); | 
| 195 | } | 
| 196 |  | 
| 197 | current_bond = current_bond->next; | 
| 198 | } | 
| 199 |  | 
| 200 | if( regenerateBonds )clean_bonds(); | 
| 201 | } | 
| 202 | } | 
| 203 |  | 
| 204 |  | 
| 205 | void make_bonds(struct coords *the_coords, int n_atoms){ | 
| 206 |  | 
| 207 | int i, j; /*counters */ | 
| 208 | struct linked_bond_list *temp_bond; /*bond place holder */ | 
| 209 |  | 
| 210 | const double bond_fudge = 1.12; // a fudge factor | 
| 211 | struct atom type_i, type_j; /* holds the atom types */ | 
| 212 |  | 
| 213 | int test; /* booleans */ | 
| 214 | double dx, dy, dz, dr2, dcv, dcv2; // used to determine bond existence | 
| 215 |  | 
| 216 |  | 
| 217 | bl_head = (struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); | 
| 218 | bl_head->next = NULL; | 
| 219 |  | 
| 220 | for(i = 0; i < (n_atoms - 1); i++){ | 
| 221 |  | 
| 222 | for(j = (i+1); j < n_atoms; j++){ | 
| 223 |  | 
| 224 | dx = the_coords[j].x - the_coords[i].x; | 
| 225 | dy = the_coords[j].y - the_coords[i].y; | 
| 226 | dz = the_coords[j].z - the_coords[i].z; | 
| 227 |  | 
| 228 | dr2 = dx * dx + dy * dy + dz * dz; | 
| 229 |  | 
| 230 | test = !findAtomType(the_coords[i].name, &type_i); | 
| 231 | if(test){ | 
| 232 | fprintf(stderr, "Atom Type %s, not found!\n", | 
| 233 | the_coords[i].name); | 
| 234 | exit(8); | 
| 235 | } | 
| 236 |  | 
| 237 | test = !findAtomType(the_coords[j].name, &type_j); | 
| 238 | if(test){ | 
| 239 | fprintf(stderr, "Atom Type %s, not found!\n", | 
| 240 | the_coords[j].name); | 
| 241 | exit(8); | 
| 242 | } | 
| 243 |  | 
| 244 |  | 
| 245 | dcv = bond_fudge * (type_i.covalentRadii + type_j.covalentRadii); | 
| 246 | dcv2 = dcv * dcv; | 
| 247 |  | 
| 248 | if(dr2 <= dcv2){ | 
| 249 |  | 
| 250 | temp_bond = | 
| 251 | (struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); | 
| 252 |  | 
| 253 | bl_head->the_bond.i = i; | 
| 254 | bl_head->the_bond.j = j; | 
| 255 |  | 
| 256 | temp_bond->next = bl_head; | 
| 257 | bl_head = temp_bond; | 
| 258 | } | 
| 259 | } | 
| 260 | } | 
| 261 | } | 
| 262 |  | 
| 263 |  | 
| 264 | void clean_bonds(){ | 
| 265 | struct linked_bond_list *current_bond; | 
| 266 | struct linked_bond_list *next_bond; /* place holders */ | 
| 267 |  | 
| 268 |  | 
| 269 | current_bond = bl_head->next; | 
| 270 |  | 
| 271 | while(current_bond != NULL){ | 
| 272 |  | 
| 273 | next_bond = current_bond->next; | 
| 274 | free(current_bond); | 
| 275 | current_bond = next_bond; | 
| 276 | } | 
| 277 |  | 
| 278 | bl_head->next = NULL; | 
| 279 | free( bl_head ); | 
| 280 | bl_head = NULL; | 
| 281 | } | 
| 282 |  | 
| 283 |  | 
| 284 | void make_header_macros(FILE *out_file){ | 
| 285 |  | 
| 286 | struct linked_atom *type_list;  // list of all atom types | 
| 287 | struct linked_atom *current_type; // current atom type | 
| 288 |  | 
| 289 | char *name; | 
| 290 | double red, green, blue; | 
| 291 | double radius; | 
| 292 |  | 
| 293 | type_list = get_type_list(); | 
| 294 | current_type = type_list->next; | 
| 295 |  | 
| 296 | while(current_type != NULL){ | 
| 297 |  | 
| 298 | name = current_type->myAtom.name; | 
| 299 | radius = current_type->myAtom.vanDerWallRadii; | 
| 300 | red = ((double)current_type->myAtom.red) / 255.0; | 
| 301 | green =  ((double)current_type->myAtom.green) / 255.0; | 
| 302 | blue =  ((double)current_type->myAtom.blue) / 255.0; | 
| 303 |  | 
| 304 |  | 
| 305 |  | 
| 306 | fprintf(out_file, | 
| 307 | "//****************************************************\n" | 
| 308 | "// DEFINE %s MACROS\n" | 
| 309 | "//****************************************************\n" | 
| 310 | "\n" | 
| 311 | "#macro make_%s_bond " | 
| 312 | "(end_1x, end_1y, end_1z, end_2x, end_2y, end_2z)\n" | 
| 313 | "\n" | 
| 314 | "  #local x1 = end_1x;\n" | 
| 315 | "  #local y1 = end_1y;\n" | 
| 316 | "  #local z1 = end_1z;\n" | 
| 317 | "  #local x2 = end_2x;\n" | 
| 318 | "  #local y2 = end_2y;\n" | 
| 319 | "  #local z2 = end_2z;\n" | 
| 320 | "\n" | 
| 321 | "  #if(ROTATE)\n" | 
| 322 | "    #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" | 
| 323 | "    #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" | 
| 324 | "    #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" | 
| 325 | "\n" | 
| 326 | "    #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" | 
| 327 | "    #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" | 
| 328 | "    #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" | 
| 329 | "\n" | 
| 330 | "  #else\n" | 
| 331 | "    #local x1_new = x1;" | 
| 332 | "    #local y1_new = y1;" | 
| 333 | "    #local z1_new = z1;" | 
| 334 | "\n" | 
| 335 | "    #local x2_new = x2;" | 
| 336 | "    #local y2_new = y2;" | 
| 337 | "    #local z2_new = z2;" | 
| 338 | "\n" | 
| 339 | "  #end\n" | 
| 340 | "\n" | 
| 341 | "  cylinder{\n" | 
| 342 | "    < x1_new, y1_new, z1_new >,\n" | 
| 343 | "    < x2_new, y2_new, z2_new >,\n" | 
| 344 | "    BOND_RADIUS\n" | 
| 345 | "    texture{\n" | 
| 346 | "      pigment{ rgb < %lf, %lf, %lf > }\n" | 
| 347 | "      finish{\n" | 
| 348 | "        ambient .2\n" | 
| 349 | "        diffuse .6\n" | 
| 350 | "        specular 1\n" | 
| 351 | "        roughness .001\n" | 
| 352 | "        metallic\n" | 
| 353 | "      }\n" | 
| 354 | "    }\n" | 
| 355 | "  }\n" | 
| 356 | "#end\n" | 
| 357 | "#macro make_%s_atom " | 
| 358 | "(center_x, center_y, center_z)\n" | 
| 359 | "\n" | 
| 360 | "  #local x1 = center_x;\n" | 
| 361 | "  #local y1 = center_y;\n" | 
| 362 | "  #local z1 = center_z;\n" | 
| 363 | "\n" | 
| 364 | "  #if(ROTATE)\n" | 
| 365 | "\n" | 
| 366 | "    #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" | 
| 367 | "    #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" | 
| 368 | "    #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" | 
| 369 | "\n" | 
| 370 | "  #else\n" | 
| 371 | "\n" | 
| 372 | "    #local x1_new = x1;" | 
| 373 | "    #local y1_new = y1;" | 
| 374 | "    #local z1_new = z1;" | 
| 375 | "\n" | 
| 376 | "  #end\n" | 
| 377 | "\n" | 
| 378 | "  sphere{\n" | 
| 379 | "    < x1_new, y1_new, z1_new >,\n" | 
| 380 | "    ATOM_SPHERE_FACTOR * %lf\n" | 
| 381 | "    texture{\n" | 
| 382 | "      pigment{ rgb < %lf, %lf, %lf > }\n" | 
| 383 | "      finish{\n" | 
| 384 | "        ambient .2\n" | 
| 385 | "        diffuse .6\n" | 
| 386 | "        specular 1\n" | 
| 387 | "        roughness .001\n" | 
| 388 | "        metallic\n" | 
| 389 | "      }\n" | 
| 390 | "    }\n" | 
| 391 | "  }\n" | 
| 392 | "#end\n" | 
| 393 | "#macro make_%s_ellipse " | 
| 394 | "(center_x, center_y, center_z, ecc, u_x, u_y, u_z)\n" | 
| 395 | "\n" | 
| 396 | "  #local x1 = center_x;\n" | 
| 397 | "  #local y1 = center_y;\n" | 
| 398 | "  #local z1 = center_z;\n" | 
| 399 | "  #local x2 = u_x;\n" | 
| 400 | "  #local y2 = u_y;\n" | 
| 401 | "  #local z2 = u_z;\n" | 
| 402 | "\n" | 
| 403 | "  #if(ROTATE)\n" | 
| 404 | "\n" | 
| 405 | "    #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" | 
| 406 | "    #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" | 
| 407 | "    #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" | 
| 408 | "\n" | 
| 409 | "    #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" | 
| 410 | "    #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" | 
| 411 | "    #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" | 
| 412 | "\n" | 
| 413 | "  #else\n" | 
| 414 | "\n" | 
| 415 | "    #local x1_new = x1;" | 
| 416 | "    #local y1_new = y1;" | 
| 417 | "    #local z1_new = z1;" | 
| 418 | "\n" | 
| 419 | "    #local x2_new = x2;" | 
| 420 | "    #local y2_new = y2;" | 
| 421 | "    #local z2_new = z2;" | 
| 422 | "\n" | 
| 423 | "  #end\n" | 
| 424 | "\n" | 
| 425 | "    #local myUlen = sqrt(x2_new*x2_new + y2_new*y2_new + z2_new*z2_new);\n" | 
| 426 | "    #local uux = x2_new / myUlen;\n" | 
| 427 | "    #local uuy = y2_new / myUlen;\n" | 
| 428 | "    #local uuz = z2_new / myUlen;\n" | 
| 429 | "    #local myTheta = -degrees(acos(uuz));\n" | 
| 430 | "    #local myPsi = -degrees(atan(uux/uuy));\n" | 
| 431 | "    #local myScale = ATOM_SPHERE_FACTOR * %lf;\n" | 
| 432 | "\n" | 
| 433 | "  sphere{\n" | 
| 434 | "    < 0, 0, 0 >, 1\n" | 
| 435 | "    texture{\n" | 
| 436 | "      pigment{\n" | 
| 437 | "        average\n" | 
| 438 | "        pigment_map{\n" | 
| 439 | "          [1.0 grad1]\n" | 
| 440 | "          [1.0 grad2]\n" | 
| 441 | "          [1.0 grad3]\n" | 
| 442 | "          [5.0 gradz]\n" | 
| 443 | "        }\n" | 
| 444 | "      }\n" | 
| 445 | "      finish{\n" | 
| 446 | "        ambient .2\n" | 
| 447 | "        diffuse .6\n" | 
| 448 | "        specular 1\n" | 
| 449 | "        roughness .001\n" | 
| 450 | "        metallic\n" | 
| 451 | "      }\n" | 
| 452 | "    }\n" | 
| 453 | "    scale<myScale,myScale,ecc*myScale>\n" | 
| 454 | "    rotate<myTheta,0,myPsi>\n" | 
| 455 | "    translate< x1_new, y1_new, z1_new>\n" | 
| 456 | "  }\n" | 
| 457 | "#end\n" | 
| 458 | "#macro make_%s_shaded_ellipse " | 
| 459 | "(center_x, center_y, center_z, ecc, u_x, u_y, u_z, v_x, v_y, v_z)\n" | 
| 460 | "\n" | 
| 461 | "  #local x1 = center_x;\n" | 
| 462 | "  #local y1 = center_y;\n" | 
| 463 | "  #local z1 = center_z;\n" | 
| 464 | "  #local x2 = u_x;\n" | 
| 465 | "  #local y2 = u_y;\n" | 
| 466 | "  #local z2 = u_z;\n" | 
| 467 | "  #local x3 = v_x;\n" | 
| 468 | "  #local y3 = v_y;\n" | 
| 469 | "  #local z3 = v_z;\n" | 
| 470 | "\n" | 
| 471 | "  #if(ROTATE)\n" | 
| 472 | "\n" | 
| 473 | "    #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" | 
| 474 | "    #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" | 
| 475 | "    #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" | 
| 476 | "\n" | 
| 477 | "    #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" | 
| 478 | "    #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" | 
| 479 | "    #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" | 
| 480 | "\n" | 
| 481 | "    #local x3_new = rotatePointX + A11 * (x3-rotatePointX) + A12 * (y3-rotatePointY) + A13 * (z3-rotatePointZ);\n" | 
| 482 | "    #local y3_new = rotatePointY + A21 * (x3-rotatePointX) + A22 * (y3-rotatePointY) + A23 * (z3-rotatePointZ);\n" | 
| 483 | "    #local z3_new = rotatePointZ + A31 * (x3-rotatePointX) + A32 * (y3-rotatePointY) + A33 * (z3-rotatePointZ);\n" | 
| 484 | "\n" | 
| 485 | "  #else\n" | 
| 486 | "\n" | 
| 487 | "    #local x1_new = x1;" | 
| 488 | "    #local y1_new = y1;" | 
| 489 | "    #local z1_new = z1;" | 
| 490 | "\n" | 
| 491 | "    #local x2_new = x2;" | 
| 492 | "    #local y2_new = y2;" | 
| 493 | "    #local z2_new = z2;" | 
| 494 | "\n" | 
| 495 | "    #local x3_new = x3;" | 
| 496 | "    #local y3_new = y3;" | 
| 497 | "    #local z3_new = z3;" | 
| 498 | "\n" | 
| 499 | "  #end\n" | 
| 500 | "\n" | 
| 501 | "    #local myUlen = sqrt(x2_new*x2_new + y2_new*y2_new + z2_new*z2_new);\n" | 
| 502 | "    #local uux = x2_new / myUlen;\n" | 
| 503 | "    #local uuy = y2_new / myUlen;\n" | 
| 504 | "    #local uuz = z2_new / myUlen;\n" | 
| 505 | "    #local myVlen = sqrt(x3_new*x3_new + y3_new*y3_new + z3_new*z3_new);\n" | 
| 506 | "    #local vvx = x3_new / myVlen;\n" | 
| 507 | "    #local vvy = y3_new / myVlen;\n" | 
| 508 | "    #local vvz = z3_new / myVlen;\n" | 
| 509 | "\n" | 
| 510 | "    #local myTheta = degrees(acos(uuz));\n" | 
| 511 | "    #local myPsi = -degrees(atan(uux/uuy));\n" | 
| 512 | "    #local myPhi = degrees(acos(vvz));\n" | 
| 513 | "    #local myScale = ATOM_SPHERE_FACTOR * %lf;\n" | 
| 514 | "\n" | 
| 515 | "  sphere{\n" | 
| 516 | "    < 0, 0, 0 >, 1\n" | 
| 517 | "    texture{\n" | 
| 518 | "      pigment{\n" | 
| 519 | "        average\n" | 
| 520 | "        pigment_map{\n" | 
| 521 | "          [1.0 grad1]\n" | 
| 522 | "          [1.0 grad2]\n" | 
| 523 | "          [1.0 grad3]\n" | 
| 524 | "          [5.0 gradz]\n" | 
| 525 | "        }\n" | 
| 526 | "      }\n" | 
| 527 | "      finish{\n" | 
| 528 | "        ambient .2\n" | 
| 529 | "        diffuse .6\n" | 
| 530 | "        specular 1\n" | 
| 531 | "        roughness .001\n" | 
| 532 | "        metallic\n" | 
| 533 | "      }\n" | 
| 534 | "    }\n" | 
| 535 | "    scale<myScale,myScale,ecc*myScale>\n" | 
| 536 | "    rotate<myTheta,myPhi,myPsi>\n" | 
| 537 | "    translate< x1_new, y1_new, z1_new>\n" | 
| 538 | "  }\n" | 
| 539 | "#end\n" | 
| 540 | "#macro make_%s_vector " | 
| 541 | "(center_x, center_y, center_z, ux, uy, uz)\n" | 
| 542 | "\n" | 
| 543 | "  #local vx = VECTOR_SCALE * ux;\n" | 
| 544 | "  #local vy = VECTOR_SCALE * uy;\n" | 
| 545 | "  #local vz = VECTOR_SCALE * uz;\n" | 
| 546 | "  #local x1 = center_x - 0.5 * vx;\n" | 
| 547 | "  #local y1 = center_y - 0.5 * vy;\n" | 
| 548 | "  #local z1 = center_z - 0.5 * vz;\n" | 
| 549 | "  #local x2 = center_x + 0.5 * vx;\n" | 
| 550 | "  #local y2 = center_y + 0.5 * vy;\n" | 
| 551 | "  #local z2 = center_z + 0.5 * vz;\n" | 
| 552 | "  #local v2 = vx*vx + vy*vy + vz*vz;\n" | 
| 553 | "  #local vl  = sqrt(v2);\n" | 
| 554 | "  #local x3 = x1 + vx * (1.0 - CONE_FRACTION);\n" | 
| 555 | "  #local y3 = y1 + vy * (1.0 - CONE_FRACTION);\n" | 
| 556 | "  #local z3 = z1 + vz * (1.0 - CONE_FRACTION);\n" | 
| 557 | "\n" | 
| 558 | "  #if(ROTATE)\n" | 
| 559 | "    #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" | 
| 560 | "    #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" | 
| 561 | "    #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" | 
| 562 | "\n" | 
| 563 | "    #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" | 
| 564 | "    #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" | 
| 565 | "    #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" | 
| 566 | "\n" | 
| 567 | "    #local x3_new = rotatePointX + A11 * (x3-rotatePointX) + A12 * (y3-rotatePointY) + A13 * (z3-rotatePointZ);\n" | 
| 568 | "    #local y3_new = rotatePointY + A21 * (x3-rotatePointX) + A22 * (y3-rotatePointY) + A23 * (z3-rotatePointZ);\n" | 
| 569 | "    #local z3_new = rotatePointZ + A31 * (x3-rotatePointX) + A32 * (y3-rotatePointY) + A33 * (z3-rotatePointZ);\n" | 
| 570 | "\n" | 
| 571 | "  #else\n" | 
| 572 | "    #local x1_new = x1;" | 
| 573 | "    #local y1_new = y1;" | 
| 574 | "    #local z1_new = z1;" | 
| 575 | "\n" | 
| 576 | "    #local x2_new = x2;" | 
| 577 | "    #local y2_new = y2;" | 
| 578 | "    #local z2_new = z2;" | 
| 579 | "\n" | 
| 580 | "    #local x3_new = x3;" | 
| 581 | "    #local y3_new = y3;" | 
| 582 | "    #local z3_new = z3;" | 
| 583 | "\n" | 
| 584 | "  #end\n" | 
| 585 | "\n" | 
| 586 | "  cylinder{\n" | 
| 587 | "    < x1_new, y1_new, z1_new >,\n" | 
| 588 | "    < x3_new, y3_new, z3_new >,\n" | 
| 589 | "    STICK_RADIUS\n" | 
| 590 | "    texture{\n" | 
| 591 | "      pigment{ rgb < %lf, %lf, %lf > }\n" | 
| 592 | "      finish{\n" | 
| 593 | "        ambient .2\n" | 
| 594 | "        diffuse .6\n" | 
| 595 | "        specular 1\n" | 
| 596 | "        roughness .001\n" | 
| 597 | "        metallic\n" | 
| 598 | "      }\n" | 
| 599 | "    }\n" | 
| 600 | "  }\n" | 
| 601 | "  cone{\n" | 
| 602 | "    < x2_new, y2_new, z2_new >, 0.0\n" | 
| 603 | "    < x3_new, y3_new, z3_new >, CONE_RADIUS\n" | 
| 604 | "    texture{\n" | 
| 605 | "      pigment{ rgb < %lf, %lf, %lf > }\n" | 
| 606 | "      finish{\n" | 
| 607 | "        ambient .2\n" | 
| 608 | "        diffuse .6\n" | 
| 609 | "        specular 1\n" | 
| 610 | "        roughness .001\n" | 
| 611 | "        metallic\n" | 
| 612 | "      }\n" | 
| 613 | "    }\n" | 
| 614 | "  }\n" | 
| 615 | "#end\n" | 
| 616 | "\n" | 
| 617 | "\n", | 
| 618 | name, | 
| 619 | name, | 
| 620 | red, green, blue, | 
| 621 | name, | 
| 622 | radius, | 
| 623 | red, green, blue, | 
| 624 | name, | 
| 625 | radius, | 
| 626 | name, | 
| 627 | radius, | 
| 628 | name, | 
| 629 | red, green, blue, | 
| 630 | red, green, blue); | 
| 631 |  | 
| 632 | current_type = current_type->next; | 
| 633 | } | 
| 634 | } |