| 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 |
double dx, dy, dz; /* used in making the bonds */ |
| 37 |
|
| 38 |
struct linked_bond_list *current_bond; /*keeps track of the linked list*/ |
| 39 |
|
| 40 |
for(i = 0; i < n_atoms; i++){ |
| 41 |
update_types(the_coords[i].name); |
| 42 |
} |
| 43 |
|
| 44 |
if(d_atoms){ |
| 45 |
|
| 46 |
fprintf(out_file, |
| 47 |
"//************************************************************\n" |
| 48 |
"// The list of atoms\n" |
| 49 |
"//************************************************************\n" |
| 50 |
"\n" |
| 51 |
"\n"); |
| 52 |
|
| 53 |
for(i = 0; i < n_atoms; i++){ |
| 54 |
|
| 55 |
skip_atom = 0; |
| 56 |
|
| 57 |
if(!d_hydrogens){ |
| 58 |
skip_atom = !strcmp("H", the_coords[i].name); |
| 59 |
} |
| 60 |
|
| 61 |
if(!skip_atom){ |
| 62 |
|
| 63 |
fprintf(out_file, |
| 64 |
"make_%s_atom( %lf, %lf, %lf )\n", |
| 65 |
the_coords[i].name, |
| 66 |
the_coords[i].x, |
| 67 |
the_coords[i].z, |
| 68 |
the_coords[i].y); |
| 69 |
} |
| 70 |
} |
| 71 |
|
| 72 |
fprintf(out_file, |
| 73 |
"\n" |
| 74 |
"\n"); |
| 75 |
} |
| 76 |
|
| 77 |
|
| 78 |
if (d_vectors) { |
| 79 |
|
| 80 |
fprintf(out_file, |
| 81 |
"//************************************************************\n" |
| 82 |
"// The list of vectors\n" |
| 83 |
"//************************************************************\n" |
| 84 |
"\n" |
| 85 |
"\n"); |
| 86 |
|
| 87 |
for(i = 0; i < n_atoms; i++){ |
| 88 |
|
| 89 |
if (the_coords[i].hasVector) { |
| 90 |
fprintf(out_file, |
| 91 |
"make_%s_vector(%lf, %lf, %lf, %lf, %lf, %lf)\n", |
| 92 |
the_coords[i].name, |
| 93 |
the_coords[i].x, |
| 94 |
the_coords[i].z, |
| 95 |
the_coords[i].y, |
| 96 |
the_coords[i].ux, |
| 97 |
the_coords[i].uz, |
| 98 |
the_coords[i].uy); |
| 99 |
} |
| 100 |
} |
| 101 |
|
| 102 |
fprintf(out_file, |
| 103 |
"\n" |
| 104 |
"\n"); |
| 105 |
} |
| 106 |
|
| 107 |
if(d_bonds){ |
| 108 |
|
| 109 |
fprintf(out_file, |
| 110 |
"//************************************************************\n" |
| 111 |
"// The list of bonds\n" |
| 112 |
"//************************************************************\n" |
| 113 |
"\n" |
| 114 |
"\n"); |
| 115 |
|
| 116 |
if( bl_head == NULL ) make_bonds(the_coords, n_atoms); |
| 117 |
|
| 118 |
current_bond = bl_head->next; |
| 119 |
|
| 120 |
while(current_bond != NULL){ |
| 121 |
|
| 122 |
skip_bond = 0; |
| 123 |
|
| 124 |
i = current_bond->the_bond.i; |
| 125 |
j = current_bond->the_bond.j; |
| 126 |
|
| 127 |
if(!d_hydrogens){ |
| 128 |
|
| 129 |
test1 = !strcmp("H", the_coords[i].name); |
| 130 |
test2 = !strcmp("H", the_coords[j].name); |
| 131 |
|
| 132 |
skip_bond = (test1 || test2); |
| 133 |
} |
| 134 |
|
| 135 |
if(!skip_bond){ |
| 136 |
|
| 137 |
dx = (the_coords[j].x - the_coords[i].x) / 2.0; |
| 138 |
dy = (the_coords[j].y - the_coords[i].y) / 2.0; |
| 139 |
dz = (the_coords[j].z - the_coords[i].z) / 2.0; |
| 140 |
|
| 141 |
fprintf(out_file, |
| 142 |
"make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", |
| 143 |
the_coords[i].name, |
| 144 |
the_coords[i].x, |
| 145 |
the_coords[i].z, |
| 146 |
the_coords[i].y, |
| 147 |
(the_coords[i].x + dx), |
| 148 |
(the_coords[i].z + dz), |
| 149 |
(the_coords[i].y + dy)); |
| 150 |
|
| 151 |
fprintf(out_file, |
| 152 |
"make_%s_bond( %lf, %lf, %lf, %lf, %lf, %lf )\n", |
| 153 |
the_coords[j].name, |
| 154 |
the_coords[j].x, |
| 155 |
the_coords[j].z, |
| 156 |
the_coords[j].y, |
| 157 |
(the_coords[j].x - dx), |
| 158 |
(the_coords[j].z - dz), |
| 159 |
(the_coords[j].y - dy)); |
| 160 |
|
| 161 |
fprintf(out_file, "\n"); |
| 162 |
} |
| 163 |
|
| 164 |
current_bond = current_bond->next; |
| 165 |
} |
| 166 |
|
| 167 |
if( regenerateBonds )clean_bonds(); |
| 168 |
} |
| 169 |
} |
| 170 |
|
| 171 |
|
| 172 |
void make_bonds(struct coords *the_coords, int n_atoms){ |
| 173 |
|
| 174 |
int i, j; /*counters */ |
| 175 |
struct linked_bond_list *temp_bond; /*bond place holder */ |
| 176 |
|
| 177 |
const double bond_fudge = 1.12; // a fudge factor |
| 178 |
struct atom type_i, type_j; /* holds the atom types */ |
| 179 |
|
| 180 |
int test; /* booleans */ |
| 181 |
double dx, dy, dz, dr2, dcv, dcv2; // used to determine bond existence |
| 182 |
|
| 183 |
|
| 184 |
bl_head = (struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); |
| 185 |
bl_head->next = NULL; |
| 186 |
|
| 187 |
for(i = 0; i < (n_atoms - 1); i++){ |
| 188 |
|
| 189 |
for(j = (i+1); j < n_atoms; j++){ |
| 190 |
|
| 191 |
dx = the_coords[j].x - the_coords[i].x; |
| 192 |
dy = the_coords[j].y - the_coords[i].y; |
| 193 |
dz = the_coords[j].z - the_coords[i].z; |
| 194 |
|
| 195 |
dr2 = dx * dx + dy * dy + dz * dz; |
| 196 |
|
| 197 |
test = !findAtomType(the_coords[i].name, &type_i); |
| 198 |
if(test){ |
| 199 |
fprintf(stderr, "Atom Type %s, not found!\n", |
| 200 |
the_coords[i].name); |
| 201 |
exit(8); |
| 202 |
} |
| 203 |
|
| 204 |
test = !findAtomType(the_coords[j].name, &type_j); |
| 205 |
if(test){ |
| 206 |
fprintf(stderr, "Atom Type %s, not found!\n", |
| 207 |
the_coords[j].name); |
| 208 |
exit(8); |
| 209 |
} |
| 210 |
|
| 211 |
|
| 212 |
dcv = bond_fudge * (type_i.covalentRadii + type_j.covalentRadii); |
| 213 |
dcv2 = dcv * dcv; |
| 214 |
|
| 215 |
if(dr2 <= dcv2){ |
| 216 |
|
| 217 |
temp_bond = |
| 218 |
(struct linked_bond_list *)malloc(sizeof(struct linked_bond_list)); |
| 219 |
|
| 220 |
bl_head->the_bond.i = i; |
| 221 |
bl_head->the_bond.j = j; |
| 222 |
|
| 223 |
temp_bond->next = bl_head; |
| 224 |
bl_head = temp_bond; |
| 225 |
} |
| 226 |
} |
| 227 |
} |
| 228 |
} |
| 229 |
|
| 230 |
|
| 231 |
void clean_bonds(){ |
| 232 |
struct linked_bond_list *current_bond; |
| 233 |
struct linked_bond_list *next_bond; /* place holders */ |
| 234 |
|
| 235 |
|
| 236 |
current_bond = bl_head->next; |
| 237 |
|
| 238 |
while(current_bond != NULL){ |
| 239 |
|
| 240 |
next_bond = current_bond->next; |
| 241 |
free(current_bond); |
| 242 |
current_bond = next_bond; |
| 243 |
} |
| 244 |
|
| 245 |
bl_head->next = NULL; |
| 246 |
free( bl_head ); |
| 247 |
bl_head = NULL; |
| 248 |
} |
| 249 |
|
| 250 |
|
| 251 |
void make_header_macros(FILE *out_file){ |
| 252 |
|
| 253 |
struct linked_atom *type_list; // list of all atom types |
| 254 |
struct linked_atom *current_type; // current atom type |
| 255 |
|
| 256 |
char *name; |
| 257 |
double red, green, blue; |
| 258 |
double radius; |
| 259 |
|
| 260 |
type_list = get_type_list(); |
| 261 |
current_type = type_list->next; |
| 262 |
|
| 263 |
while(current_type != NULL){ |
| 264 |
|
| 265 |
name = current_type->myAtom.name; |
| 266 |
radius = current_type->myAtom.vanDerWallRadii; |
| 267 |
red = ((double)current_type->myAtom.red) / 255.0; |
| 268 |
green = ((double)current_type->myAtom.green) / 255.0; |
| 269 |
blue = ((double)current_type->myAtom.blue) / 255.0; |
| 270 |
|
| 271 |
|
| 272 |
|
| 273 |
fprintf(out_file, |
| 274 |
"//****************************************************\n" |
| 275 |
"// DEFINE %s MACROS\n" |
| 276 |
"//****************************************************\n" |
| 277 |
"\n" |
| 278 |
"#macro make_%s_bond " |
| 279 |
"(end_1x, end_1y, end_1z, end_2x, end_2y, end_2z)\n" |
| 280 |
"\n" |
| 281 |
" #local x1 = end_1x;\n" |
| 282 |
" #local y1 = end_1y;\n" |
| 283 |
" #local z1 = end_1z;\n" |
| 284 |
" #local x2 = end_2x;\n" |
| 285 |
" #local y2 = end_2y;\n" |
| 286 |
" #local z2 = end_2z;\n" |
| 287 |
"\n" |
| 288 |
" #if(ROTATE)\n" |
| 289 |
" #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" |
| 290 |
" #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" |
| 291 |
" #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" |
| 292 |
"\n" |
| 293 |
" #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" |
| 294 |
" #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" |
| 295 |
" #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" |
| 296 |
"\n" |
| 297 |
" #else\n" |
| 298 |
" #local x1_new = x1;" |
| 299 |
" #local y1_new = y1;" |
| 300 |
" #local z1_new = z1;" |
| 301 |
"\n" |
| 302 |
" #local x2_new = x2;" |
| 303 |
" #local y2_new = y2;" |
| 304 |
" #local z2_new = z2;" |
| 305 |
"\n" |
| 306 |
" #end\n" |
| 307 |
"\n" |
| 308 |
" cylinder{\n" |
| 309 |
" < x1_new, y1_new, z1_new >,\n" |
| 310 |
" < x2_new, y2_new, z2_new >,\n" |
| 311 |
" BOND_RADIUS\n" |
| 312 |
" texture{\n" |
| 313 |
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 314 |
" finish{\n" |
| 315 |
" ambient .2\n" |
| 316 |
" diffuse .6\n" |
| 317 |
" specular 1\n" |
| 318 |
" roughness .001\n" |
| 319 |
" metallic\n" |
| 320 |
" }\n" |
| 321 |
" }\n" |
| 322 |
" }\n" |
| 323 |
"#end\n" |
| 324 |
"#macro make_%s_atom " |
| 325 |
"(center_x, center_y, center_z)\n" |
| 326 |
"\n" |
| 327 |
" #local x1 = center_x;\n" |
| 328 |
" #local y1 = center_y;\n" |
| 329 |
" #local z1 = center_z;\n" |
| 330 |
"\n" |
| 331 |
" #if(ROTATE)\n" |
| 332 |
"\n" |
| 333 |
" #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" |
| 334 |
" #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" |
| 335 |
" #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" |
| 336 |
"\n" |
| 337 |
" #else\n" |
| 338 |
"\n" |
| 339 |
" #local x1_new = x1;" |
| 340 |
" #local y1_new = y1;" |
| 341 |
" #local z1_new = z1;" |
| 342 |
"\n" |
| 343 |
" #end\n" |
| 344 |
"\n" |
| 345 |
" sphere{\n" |
| 346 |
" < x1_new, y1_new, z1_new >,\n" |
| 347 |
" ATOM_SPHERE_FACTOR * %lf\n" |
| 348 |
" texture{\n" |
| 349 |
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 350 |
" finish{\n" |
| 351 |
" ambient .2\n" |
| 352 |
" diffuse .6\n" |
| 353 |
" specular 1\n" |
| 354 |
" roughness .001\n" |
| 355 |
" metallic\n" |
| 356 |
" }\n" |
| 357 |
" }\n" |
| 358 |
" }\n" |
| 359 |
"#end\n" |
| 360 |
"#macro make_%s_vector " |
| 361 |
"(center_x, center_y, center_z, ux, uy, uz)\n" |
| 362 |
"\n" |
| 363 |
" #local vx = VECTOR_SCALE * ux;\n" |
| 364 |
" #local vy = VECTOR_SCALE * uy;\n" |
| 365 |
" #local vz = VECTOR_SCALE * uz;\n" |
| 366 |
" #local x1 = center_x - 0.5 * vx;\n" |
| 367 |
" #local y1 = center_y - 0.5 * vy;\n" |
| 368 |
" #local z1 = center_z - 0.5 * vz;\n" |
| 369 |
" #local x2 = center_x + 0.5 * vx;\n" |
| 370 |
" #local y2 = center_y + 0.5 * vy;\n" |
| 371 |
" #local z2 = center_z + 0.5 * vz;\n" |
| 372 |
" #local v2 = vx*vx + vy*vy + vz*vz;\n" |
| 373 |
" #local vl = sqrt(v2);\n" |
| 374 |
" #local x3 = x1 + vx * (1.0 - CONE_FRACTION);\n" |
| 375 |
" #local y3 = y1 + vy * (1.0 - CONE_FRACTION);\n" |
| 376 |
" #local z3 = z1 + vz * (1.0 - CONE_FRACTION);\n" |
| 377 |
"\n" |
| 378 |
" #if(ROTATE)\n" |
| 379 |
" #local x1_new = rotatePointX + A11 * (x1-rotatePointX) + A12 * (y1-rotatePointY) + A13 * (z1-rotatePointZ);\n" |
| 380 |
" #local y1_new = rotatePointY + A21 * (x1-rotatePointX) + A22 * (y1-rotatePointY) + A23 * (z1-rotatePointZ);\n" |
| 381 |
" #local z1_new = rotatePointZ + A31 * (x1-rotatePointX) + A32 * (y1-rotatePointY) + A33 * (z1-rotatePointZ);\n" |
| 382 |
"\n" |
| 383 |
" #local x2_new = rotatePointX + A11 * (x2-rotatePointX) + A12 * (y2-rotatePointY) + A13 * (z2-rotatePointZ);\n" |
| 384 |
" #local y2_new = rotatePointY + A21 * (x2-rotatePointX) + A22 * (y2-rotatePointY) + A23 * (z2-rotatePointZ);\n" |
| 385 |
" #local z2_new = rotatePointZ + A31 * (x2-rotatePointX) + A32 * (y2-rotatePointY) + A33 * (z2-rotatePointZ);\n" |
| 386 |
"\n" |
| 387 |
" #local x3_new = rotatePointX + A11 * (x3-rotatePointX) + A12 * (y3-rotatePointY) + A13 * (z3-rotatePointZ);\n" |
| 388 |
" #local y3_new = rotatePointY + A21 * (x3-rotatePointX) + A22 * (y3-rotatePointY) + A23 * (z3-rotatePointZ);\n" |
| 389 |
" #local z3_new = rotatePointZ + A31 * (x3-rotatePointX) + A32 * (y3-rotatePointY) + A33 * (z3-rotatePointZ);\n" |
| 390 |
"\n" |
| 391 |
" #else\n" |
| 392 |
" #local x1_new = x1;" |
| 393 |
" #local y1_new = y1;" |
| 394 |
" #local z1_new = z1;" |
| 395 |
"\n" |
| 396 |
" #local x2_new = x2;" |
| 397 |
" #local y2_new = y2;" |
| 398 |
" #local z2_new = z2;" |
| 399 |
"\n" |
| 400 |
" #local x3_new = x3;" |
| 401 |
" #local y3_new = y3;" |
| 402 |
" #local z3_new = z3;" |
| 403 |
"\n" |
| 404 |
" #end\n" |
| 405 |
"\n" |
| 406 |
" cylinder{\n" |
| 407 |
" < x1_new, y1_new, z1_new >,\n" |
| 408 |
" < x3_new, y3_new, z3_new >,\n" |
| 409 |
" STICK_RADIUS\n" |
| 410 |
" texture{\n" |
| 411 |
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 412 |
" finish{\n" |
| 413 |
" ambient .2\n" |
| 414 |
" diffuse .6\n" |
| 415 |
" specular 1\n" |
| 416 |
" roughness .001\n" |
| 417 |
" metallic\n" |
| 418 |
" }\n" |
| 419 |
" }\n" |
| 420 |
" }\n" |
| 421 |
" cone{\n" |
| 422 |
" < x2_new, y2_new, z2_new >, 0.0\n" |
| 423 |
" < x3_new, y3_new, z3_new >, CONE_RADIUS\n" |
| 424 |
" texture{\n" |
| 425 |
" pigment{ rgb < %lf, %lf, %lf > }\n" |
| 426 |
" finish{\n" |
| 427 |
" ambient .2\n" |
| 428 |
" diffuse .6\n" |
| 429 |
" specular 1\n" |
| 430 |
" roughness .001\n" |
| 431 |
" metallic\n" |
| 432 |
" }\n" |
| 433 |
" }\n" |
| 434 |
" }\n" |
| 435 |
"#end\n" |
| 436 |
"\n" |
| 437 |
"\n", |
| 438 |
name, |
| 439 |
name, |
| 440 |
red, green, blue, |
| 441 |
name, |
| 442 |
radius, |
| 443 |
red, green, blue, |
| 444 |
name, |
| 445 |
red, green, blue, |
| 446 |
red, green, blue); |
| 447 |
|
| 448 |
current_type = current_type->next; |
| 449 |
} |
| 450 |
} |
