residues

In this example we will see how to reorder atoms/residues/molecules

import os
import pyxmolpp2

Let's create a frame to work with

pdb_filename = os.path.join(os.environ["TEST_DATA_PATH"], "pdb/rcsb/1UBQ.pdb")
pdb_file = pyxmolpp2.PdbFile(pdb_filename)

frame = pdb_file.frames()[0]

print([a.id for a in frame.atoms])

[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661]

First we need to define new order of atoms. For sake of simplicity let's number them in reverse order

atoms = frame.atoms

for i, a in enumerate(atoms):
    a.id = atoms.size - i

# New atom ids:
print([a.id for a in frame.atoms])

[660, 659, 658, 657, 656, 655, 654, 653, 652, 651, 650, 649, 648, 647, 646, 645, 644, 643, 642, 641, 640, 639, 638, 637, 636, 635, 634, 633, 632, 631, 630, 629, 628, 627, 626, 625, 624, 623, 622, 621, 620, 619, 618, 617, 616, 615, 614, 613, 612, 611, 610, 609, 608, 607, 606, 605, 604, 603, 602, 601, 600, 599, 598, 597, 596, 595, 594, 593, 592, 591, 590, 589, 588, 587, 586, 585, 584, 583, 582, 581, 580, 579, 578, 577, 576, 575, 574, 573, 572, 571, 570, 569, 568, 567, 566, 565, 564, 563, 562, 561, 560, 559, 558, 557, 556, 555, 554, 553, 552, 551, 550, 549, 548, 547, 546, 545, 544, 543, 542, 541, 540, 539, 538, 537, 536, 535, 534, 533, 532, 531, 530, 529, 528, 527, 526, 525, 524, 523, 522, 521, 520, 519, 518, 517, 516, 515, 514, 513, 512, 511, 510, 509, 508, 507, 506, 505, 504, 503, 502, 501, 500, 499, 498, 497, 496, 495, 494, 493, 492, 491, 490, 489, 488, 487, 486, 485, 484, 483, 482, 481, 480, 479, 478, 477, 476, 475, 474, 473, 472, 471, 470, 469, 468, 467, 466, 465, 464, 463, 462, 461, 460, 459, 458, 457, 456, 455, 454, 453, 452, 451, 450, 449, 448, 447, 446, 445, 444, 443, 442, 441, 440, 439, 438, 437, 436, 435, 434, 433, 432, 431, 430, 429, 428, 427, 426, 425, 424, 423, 422, 421, 420, 419, 418, 417, 416, 415, 414, 413, 412, 411, 410, 409, 408, 407, 406, 405, 404, 403, 402, 401, 400, 399, 398, 397, 396, 395, 394, 393, 392, 391, 390, 389, 388, 387, 386, 385, 384, 383, 382, 381, 380, 379, 378, 377, 376, 375, 374, 373, 372, 371, 370, 369, 368, 367, 366, 365, 364, 363, 362, 361, 360, 359, 358, 357, 356, 355, 354, 353, 352, 351, 350, 349, 348, 347, 346, 345, 344, 343, 342, 341, 340, 339, 338, 337, 336, 335, 334, 333, 332, 331, 330, 329, 328, 327, 326, 325, 324, 323, 322, 321, 320, 319, 318, 317, 316, 315, 314, 313, 312, 311, 310, 309, 308, 307, 306, 305, 304, 303, 302, 301, 300, 299, 298, 297, 296, 295, 294, 293, 292, 291, 290, 289, 288, 287, 286, 285, 284, 283, 282, 281, 280, 279, 278, 277, 276, 275, 274, 273, 272, 271, 270, 269, 268, 267, 266, 265, 264, 263, 262, 261, 260, 259, 258, 257, 256, 255, 254, 253, 252, 251, 250, 249, 248, 247, 246, 245, 244, 243, 242, 241, 240, 239, 238, 237, 236, 235, 234, 233, 232, 231, 230, 229, 228, 227, 226, 225, 224, 223, 222, 221, 220, 219, 218, 217, 216, 215, 214, 213, 212, 211, 210, 209, 208, 207, 206, 205, 204, 203, 202, 201, 200, 199, 198, 197, 196, 195, 194, 193, 192, 191, 190, 189, 188, 187, 186, 185, 184, 183, 182, 181, 180, 179, 178, 177, 176, 175, 174, 173, 172, 171, 170, 169, 168, 167, 166, 165, 164, 163, 162, 161, 160, 159, 158, 157, 156, 155, 154, 153, 152, 151, 150, 149, 148, 147, 146, 145, 144, 143, 142, 141, 140, 139, 138, 137, 136, 135, 134, 133, 132, 131, 130, 129, 128, 127, 126, 125, 124, 123, 122, 121, 120, 119, 118, 117, 116, 115, 114, 113, 112, 111, 110, 109, 108, 107, 106, 105, 104, 103, 102, 101, 100, 99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 89, 88, 87, 86, 85, 84, 83, 82, 81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67, 66, 65, 64, 63, 62, 61, 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1]

As you can see id does not affect atom order in selections.

We can create a new Frame with altered atom order within residue.

from pyxmolpp2 import Frame

# create empty frame with index=0
new_frame = Frame()

for mol in frame.molecules:
    # create empty chain with same name
    new_mol = new_frame.add_molecule()
    new_mol.name = mol.name
    for residue in frame.residues:
        # create empty residue with same name and id
        new_residue = new_mol.add_residue()
        new_residue.name, new_residue.id = residue.name, residue.id
        for a in sorted(list(residue.atoms), key=lambda a: a.id):
            new_atom = new_residue.add_atom()
            new_atom.r, new_atom.id, new_atom.name = a.r, a.id, a.name

# New frame atoms ids:
print([a.id for a in new_frame.atoms])

[653, 654, 655, 656, 657, 658, 659, 660, 644, 645, 646, 647, 648, 649, 650, 651, 652, 636, 637, 638, 639, 640, 641, 642, 643, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 618, 619, 620, 621, 622, 623, 624, 609, 610, 611, 612, 613, 614, 615, 616, 617, 602, 603, 604, 605, 606, 607, 608, 594, 595, 596, 597, 598, 599, 600, 601, 587, 588, 589, 590, 591, 592, 593, 583, 584, 585, 586, 574, 575, 576, 577, 578, 579, 580, 581, 582, 567, 568, 569, 570, 571, 572, 573, 559, 560, 561, 562, 563, 564, 565, 566, 552, 553, 554, 555, 556, 557, 558, 544, 545, 546, 547, 548, 549, 550, 551, 535, 536, 537, 538, 539, 540, 541, 542, 543, 528, 529, 530, 531, 532, 533, 534, 519, 520, 521, 522, 523, 524, 525, 526, 527, 512, 513, 514, 515, 516, 517, 518, 506, 507, 508, 509, 510, 511, 498, 499, 500, 501, 502, 503, 504, 505, 491, 492, 493, 494, 495, 496, 497, 483, 484, 485, 486, 487, 488, 489, 490, 474, 475, 476, 477, 478, 479, 480, 481, 482, 466, 467, 468, 469, 470, 471, 472, 473, 459, 460, 461, 462, 463, 464, 465, 450, 451, 452, 453, 454, 455, 456, 457, 458, 445, 446, 447, 448, 449, 436, 437, 438, 439, 440, 441, 442, 443, 444, 428, 429, 430, 431, 432, 433, 434, 435, 419, 420, 421, 422, 423, 424, 425, 426, 427, 411, 412, 413, 414, 415, 416, 417, 418, 402, 403, 404, 405, 406, 407, 408, 409, 410, 393, 394, 395, 396, 397, 398, 399, 400, 401, 389, 390, 391, 392, 381, 382, 383, 384, 385, 386, 387, 388, 374, 375, 376, 377, 378, 379, 380, 367, 368, 369, 370, 371, 372, 373, 359, 360, 361, 362, 363, 364, 365, 366, 350, 351, 352, 353, 354, 355, 356, 357, 358, 341, 342, 343, 344, 345, 346, 347, 348, 349, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 322, 323, 324, 325, 326, 327, 328, 329, 314, 315, 316, 317, 318, 319, 320, 321, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 298, 299, 300, 301, 302, 294, 295, 296, 297, 285, 286, 287, 288, 289, 290, 291, 292, 293, 276, 277, 278, 279, 280, 281, 282, 283, 284, 268, 269, 270, 271, 272, 273, 274, 275, 259, 260, 261, 262, 263, 264, 265, 266, 267, 251, 252, 253, 254, 255, 256, 257, 258, 247, 248, 249, 250, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 229, 230, 231, 232, 233, 234, 235, 221, 222, 223, 224, 225, 226, 227, 228, 215, 216, 217, 218, 219, 220, 207, 208, 209, 210, 211, 212, 213, 214, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 187, 188, 189, 190, 191, 192, 193, 194, 179, 180, 181, 182, 183, 184, 185, 186, 170, 171, 172, 173, 174, 175, 176, 177, 178, 161, 162, 163, 164, 165, 166, 167, 168, 169, 152, 153, 154, 155, 156, 157, 158, 159, 160, 146, 147, 148, 149, 150, 151, 139, 140, 141, 142, 143, 144, 145, 131, 132, 133, 134, 135, 136, 137, 138, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 113, 114, 115, 116, 117, 118, 119, 120, 106, 107, 108, 109, 110, 111, 112, 98, 99, 100, 101, 102, 103, 104, 105, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 79, 80, 81, 82, 83, 84, 85, 86, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 64, 65, 66, 67, 59, 60, 61, 62, 63, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 653, 654, 655, 656, 657, 658, 659, 660, 644, 645, 646, 647, 648, 649, 650, 651, 652, 636, 637, 638, 639, 640, 641, 642, 643, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 618, 619, 620, 621, 622, 623, 624, 609, 610, 611, 612, 613, 614, 615, 616, 617, 602, 603, 604, 605, 606, 607, 608, 594, 595, 596, 597, 598, 599, 600, 601, 587, 588, 589, 590, 591, 592, 593, 583, 584, 585, 586, 574, 575, 576, 577, 578, 579, 580, 581, 582, 567, 568, 569, 570, 571, 572, 573, 559, 560, 561, 562, 563, 564, 565, 566, 552, 553, 554, 555, 556, 557, 558, 544, 545, 546, 547, 548, 549, 550, 551, 535, 536, 537, 538, 539, 540, 541, 542, 543, 528, 529, 530, 531, 532, 533, 534, 519, 520, 521, 522, 523, 524, 525, 526, 527, 512, 513, 514, 515, 516, 517, 518, 506, 507, 508, 509, 510, 511, 498, 499, 500, 501, 502, 503, 504, 505, 491, 492, 493, 494, 495, 496, 497, 483, 484, 485, 486, 487, 488, 489, 490, 474, 475, 476, 477, 478, 479, 480, 481, 482, 466, 467, 468, 469, 470, 471, 472, 473, 459, 460, 461, 462, 463, 464, 465, 450, 451, 452, 453, 454, 455, 456, 457, 458, 445, 446, 447, 448, 449, 436, 437, 438, 439, 440, 441, 442, 443, 444, 428, 429, 430, 431, 432, 433, 434, 435, 419, 420, 421, 422, 423, 424, 425, 426, 427, 411, 412, 413, 414, 415, 416, 417, 418, 402, 403, 404, 405, 406, 407, 408, 409, 410, 393, 394, 395, 396, 397, 398, 399, 400, 401, 389, 390, 391, 392, 381, 382, 383, 384, 385, 386, 387, 388, 374, 375, 376, 377, 378, 379, 380, 367, 368, 369, 370, 371, 372, 373, 359, 360, 361, 362, 363, 364, 365, 366, 350, 351, 352, 353, 354, 355, 356, 357, 358, 341, 342, 343, 344, 345, 346, 347, 348, 349, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 322, 323, 324, 325, 326, 327, 328, 329, 314, 315, 316, 317, 318, 319, 320, 321, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 298, 299, 300, 301, 302, 294, 295, 296, 297, 285, 286, 287, 288, 289, 290, 291, 292, 293, 276, 277, 278, 279, 280, 281, 282, 283, 284, 268, 269, 270, 271, 272, 273, 274, 275, 259, 260, 261, 262, 263, 264, 265, 266, 267, 251, 252, 253, 254, 255, 256, 257, 258, 247, 248, 249, 250, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 229, 230, 231, 232, 233, 234, 235, 221, 222, 223, 224, 225, 226, 227, 228, 215, 216, 217, 218, 219, 220, 207, 208, 209, 210, 211, 212, 213, 214, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 187, 188, 189, 190, 191, 192, 193, 194, 179, 180, 181, 182, 183, 184, 185, 186, 170, 171, 172, 173, 174, 175, 176, 177, 178, 161, 162, 163, 164, 165, 166, 167, 168, 169, 152, 153, 154, 155, 156, 157, 158, 159, 160, 146, 147, 148, 149, 150, 151, 139, 140, 141, 142, 143, 144, 145, 131, 132, 133, 134, 135, 136, 137, 138, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 113, 114, 115, 116, 117, 118, 119, 120, 106, 107, 108, 109, 110, 111, 112, 98, 99, 100, 101, 102, 103, 104, 105, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 79, 80, 81, 82, 83, 84, 85, 86, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 64, 65, 66, 67, 59, 60, 61, 62, 63, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1]