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 |
|
|