mmagnus /
rna-tools
| @@ 546-602 (lines=57) @@ | ||
| 543 | color_by_text(txt) |
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| 544 | ||
| 545 | ||
| 546 | def color_obj(rainbow=0): |
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| 547 | ||
| 548 | """ |
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| 549 | stolen from :) |
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| 550 | AUTHOR |
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| 551 | Gareth Stockwell |
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| 552 | ||
| 553 | USAGE |
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| 554 | color_obj(rainbow=0) |
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| 555 | ||
| 556 | This function colours each object currently in the PyMOL heirarchy |
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| 557 | with a different colour. Colours used are either the 22 named |
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| 558 | colours used by PyMOL (in which case the 23rd object, if it exists, |
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| 559 | gets the same colour as the first), or are the colours of the rainbow |
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| 560 | ||
| 561 | """ |
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| 562 | ||
| 563 | # Process arguments |
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| 564 | rainbow = int(rainbow) |
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| 565 | ||
| 566 | # Get names of all PyMOL objects |
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| 567 | obj_list = cmd.get_names('objects') |
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| 568 | ||
| 569 | if rainbow: |
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| 570 | ||
| 571 | print("\nColouring objects as rainbow\n") |
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| 572 | ||
| 573 | nobj = len(obj_list) |
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| 574 | ||
| 575 | # Create colours starting at blue(240) to red(0), using intervals |
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| 576 | # of 240/(nobj-1) |
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| 577 | for j in range(nobj): |
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| 578 | hsv = (240-j*240/(nobj-1), 1, 1) |
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| 579 | # Convert to RGB |
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| 580 | rgb = hsv_to_rgb(hsv) |
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| 581 | # Define the new colour |
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| 582 | cmd.set_color("col" + str(j), rgb) |
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| 583 | print(obj_list[j], rgb) |
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| 584 | # Colour the object |
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| 585 | cmd.color("col" + str(j), obj_list[j]) |
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| 586 | ||
| 587 | else: |
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| 588 | # List of available colours |
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| 589 | colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan', \ |
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| 590 | 'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \ |
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| 591 | 'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate', \ |
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| 592 | 'wheat', 'white', 'grey' ] |
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| 593 | ncolours = len(colours) |
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| 594 | ||
| 595 | # Loop over objects |
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| 596 | i = 0 |
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| 597 | for obj in obj_list: |
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| 598 | print(" ", obj, colours[i]) |
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| 599 | cmd.color(colours[i], obj) |
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| 600 | i = i+1 |
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| 601 | if(i == ncolours): |
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| 602 | i = 0 |
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| 603 | ||
| 604 | ||
| 605 | def names(): |
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| @@ 612-650 (lines=39) @@ | ||
| 609 | print(o) |
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| 610 | ||
| 611 | ||
| 612 | def color_rbw(rainbow=0): |
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| 613 | """ |
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| 614 | similar to color_obj() but this time colors every obect as rainbow |
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| 615 | """ |
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| 616 | rainbow = int(rainbow) |
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| 617 | ||
| 618 | # Get names of all PyMOL objects |
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| 619 | obj_list = cmd.get_names('objects') |
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| 620 | ||
| 621 | if rainbow: |
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| 622 | ||
| 623 | print("\nColouring objects as rainbow\n") |
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| 624 | ||
| 625 | nobj = len(obj_list) |
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| 626 | ||
| 627 | # Create colours starting at blue(240) to red(0), using intervals |
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| 628 | # of 240/(nobj-1) |
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| 629 | for j in range(nobj): |
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| 630 | hsv = (240-j*240/(nobj-1), 1, 1) |
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| 631 | # Convert to RGB |
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| 632 | rgb = hsv_to_rgb(hsv) |
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| 633 | # Define the new colour |
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| 634 | cmd.set_color("col" + str(j), rgb) |
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| 635 | print(obj_list[j], rgb) |
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| 636 | # Colour the object |
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| 637 | cmd.color("col" + str(j), obj_list[j]) |
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| 638 | else: |
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| 639 | colours = ['rainbow'] |
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| 640 | ncolours = len(colours) |
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| 641 | ||
| 642 | # Loop over objects |
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| 643 | i = 0 |
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| 644 | for obj in obj_list: |
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| 645 | print(" ", obj, colours[i]) |
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| 646 | cmd.spectrum('count', colours[i], obj) |
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| 647 | # cmd.color(colours[i], obj) |
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| 648 | i = i+1 |
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| 649 | if(i == ncolours): |
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| 650 | i = 0 |
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| 651 | ||
| 652 | def ino(): |
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| 653 | """Sphare and yellow inorganic, such us Mg. |
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