| 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*/ |
| 61 |
|
|
| 62 |
|
if(!skip_atom){ |
| 63 |
|
|
| 64 |
< |
fprintf(out_file, |
| 65 |
< |
"make_%s_atom( %lf, %lf, %lf )\n", |
| 66 |
< |
the_coords[i].name, |
| 67 |
< |
the_coords[i].x, |
| 68 |
< |
the_coords[i].z, |
| 69 |
< |
the_coords[i].y); |
| 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 |
< |
|
| 104 |
> |
|
| 105 |
|
fprintf(out_file, |
| 106 |
|
"\n" |
| 107 |
|
"\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" |
| 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" |
| 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 |
|
|