rc-foundry 0.1.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- foundry/__init__.py +57 -0
- foundry/callbacks/__init__.py +5 -0
- foundry/callbacks/callback.py +116 -0
- foundry/callbacks/health_logging.py +419 -0
- foundry/callbacks/metrics_logging.py +211 -0
- foundry/callbacks/timing_logging.py +67 -0
- foundry/callbacks/train_logging.py +278 -0
- foundry/common.py +108 -0
- foundry/constants.py +28 -0
- foundry/hydra/resolvers.py +77 -0
- foundry/inference_engines/base.py +235 -0
- foundry/inference_engines/checkpoint_registry.py +66 -0
- foundry/metrics/__init__.py +12 -0
- foundry/metrics/losses.py +30 -0
- foundry/metrics/metric.py +319 -0
- foundry/model/layers/blocks.py +47 -0
- foundry/testing/__init__.py +6 -0
- foundry/testing/fixtures.py +19 -0
- foundry/testing/pytest_hooks.py +15 -0
- foundry/trainers/fabric.py +923 -0
- foundry/training/EMA.py +67 -0
- foundry/training/checkpoint.py +61 -0
- foundry/training/schedulers.py +91 -0
- foundry/utils/alignment.py +86 -0
- foundry/utils/components.py +415 -0
- foundry/utils/datasets.py +405 -0
- foundry/utils/ddp.py +103 -0
- foundry/utils/instantiators.py +72 -0
- foundry/utils/logging.py +279 -0
- foundry/utils/rigid.py +1460 -0
- foundry/utils/rotation_augmentation.py +65 -0
- foundry/utils/squashfs.py +172 -0
- foundry/utils/torch.py +317 -0
- foundry/utils/weights.py +271 -0
- foundry/version.py +34 -0
- foundry_cli/__init__.py +3 -0
- foundry_cli/download_checkpoints.py +281 -0
- mpnn/__init__.py +1 -0
- mpnn/collate/feature_collator.py +265 -0
- mpnn/inference.py +53 -0
- mpnn/inference_engines/mpnn.py +549 -0
- mpnn/loss/nll_loss.py +122 -0
- mpnn/metrics/nll.py +369 -0
- mpnn/metrics/sequence_recovery.py +440 -0
- mpnn/model/layers/graph_embeddings.py +2372 -0
- mpnn/model/layers/message_passing.py +332 -0
- mpnn/model/layers/position_wise_feed_forward.py +44 -0
- mpnn/model/layers/positional_encoding.py +98 -0
- mpnn/model/mpnn.py +2632 -0
- mpnn/pipelines/mpnn.py +162 -0
- mpnn/samplers/samplers.py +167 -0
- mpnn/train.py +341 -0
- mpnn/trainers/mpnn.py +193 -0
- mpnn/transforms/feature_aggregation/mpnn.py +184 -0
- mpnn/transforms/feature_aggregation/polymer_ligand_interface.py +76 -0
- mpnn/transforms/feature_aggregation/token_encodings.py +132 -0
- mpnn/transforms/feature_aggregation/user_settings.py +347 -0
- mpnn/transforms/polymer_ligand_interface.py +164 -0
- mpnn/utils/inference.py +2397 -0
- mpnn/utils/probability.py +37 -0
- mpnn/utils/weights.py +309 -0
- rc_foundry-0.1.1.dist-info/METADATA +239 -0
- rc_foundry-0.1.1.dist-info/RECORD +180 -0
- rc_foundry-0.1.1.dist-info/WHEEL +4 -0
- rc_foundry-0.1.1.dist-info/entry_points.txt +5 -0
- rc_foundry-0.1.1.dist-info/licenses/LICENSE.md +28 -0
- rf3/__init__.py +3 -0
- rf3/_version.py +33 -0
- rf3/alignment.py +79 -0
- rf3/callbacks/dump_validation_structures.py +101 -0
- rf3/callbacks/metrics_logging.py +324 -0
- rf3/chemical.py +1529 -0
- rf3/cli.py +77 -0
- rf3/data/cyclic_transform.py +78 -0
- rf3/data/extra_xforms.py +36 -0
- rf3/data/ground_truth_template.py +463 -0
- rf3/data/paired_msa.py +206 -0
- rf3/data/pipeline_utils.py +128 -0
- rf3/data/pipelines.py +558 -0
- rf3/diffusion_samplers/inference_sampler.py +222 -0
- rf3/inference.py +65 -0
- rf3/inference_engines/__init__.py +5 -0
- rf3/inference_engines/rf3.py +735 -0
- rf3/kinematics.py +354 -0
- rf3/loss/af3_confidence_loss.py +515 -0
- rf3/loss/af3_losses.py +655 -0
- rf3/loss/loss.py +179 -0
- rf3/metrics/chiral.py +179 -0
- rf3/metrics/clashing_chains.py +68 -0
- rf3/metrics/distogram.py +421 -0
- rf3/metrics/lddt.py +523 -0
- rf3/metrics/metadata.py +43 -0
- rf3/metrics/metric_utils.py +192 -0
- rf3/metrics/predicted_error.py +134 -0
- rf3/metrics/rasa.py +108 -0
- rf3/metrics/selected_distances.py +91 -0
- rf3/model/RF3.py +527 -0
- rf3/model/RF3_blocks.py +92 -0
- rf3/model/RF3_structure.py +303 -0
- rf3/model/layers/af3_auxiliary_heads.py +255 -0
- rf3/model/layers/af3_diffusion_transformer.py +544 -0
- rf3/model/layers/attention.py +313 -0
- rf3/model/layers/layer_utils.py +127 -0
- rf3/model/layers/mlff.py +118 -0
- rf3/model/layers/outer_product.py +59 -0
- rf3/model/layers/pairformer_layers.py +783 -0
- rf3/model/layers/structure_bias.py +56 -0
- rf3/scoring.py +1787 -0
- rf3/symmetry/resolve.py +284 -0
- rf3/train.py +194 -0
- rf3/trainers/rf3.py +570 -0
- rf3/util_module.py +47 -0
- rf3/utils/frames.py +109 -0
- rf3/utils/inference.py +665 -0
- rf3/utils/io.py +198 -0
- rf3/utils/loss.py +72 -0
- rf3/utils/predict_and_score.py +165 -0
- rf3/utils/predicted_error.py +673 -0
- rf3/utils/recycling.py +42 -0
- rf3/validate.py +140 -0
- rfd3/.gitignore +7 -0
- rfd3/Makefile +76 -0
- rfd3/__init__.py +12 -0
- rfd3/callbacks.py +66 -0
- rfd3/cli.py +41 -0
- rfd3/constants.py +212 -0
- rfd3/engine.py +543 -0
- rfd3/inference/datasets.py +193 -0
- rfd3/inference/input_parsing.py +1123 -0
- rfd3/inference/legacy_input_parsing.py +717 -0
- rfd3/inference/parsing.py +165 -0
- rfd3/inference/symmetry/atom_array.py +298 -0
- rfd3/inference/symmetry/checks.py +241 -0
- rfd3/inference/symmetry/contigs.py +63 -0
- rfd3/inference/symmetry/frames.py +355 -0
- rfd3/inference/symmetry/symmetry_utils.py +398 -0
- rfd3/metrics/design_metrics.py +465 -0
- rfd3/metrics/hbonds_hbplus_metrics.py +308 -0
- rfd3/metrics/hbonds_metrics.py +389 -0
- rfd3/metrics/losses.py +325 -0
- rfd3/metrics/metrics_utils.py +118 -0
- rfd3/metrics/sidechain_metrics.py +349 -0
- rfd3/model/RFD3.py +105 -0
- rfd3/model/RFD3_diffusion_module.py +387 -0
- rfd3/model/cfg_utils.py +81 -0
- rfd3/model/inference_sampler.py +635 -0
- rfd3/model/layers/attention.py +577 -0
- rfd3/model/layers/block_utils.py +580 -0
- rfd3/model/layers/blocks.py +777 -0
- rfd3/model/layers/chunked_pairwise.py +377 -0
- rfd3/model/layers/encoders.py +417 -0
- rfd3/model/layers/layer_utils.py +197 -0
- rfd3/model/layers/pairformer_layers.py +128 -0
- rfd3/run_inference.py +45 -0
- rfd3/testing/debug.py +139 -0
- rfd3/testing/debug_utils.py +73 -0
- rfd3/testing/testing_utils.py +356 -0
- rfd3/train.py +194 -0
- rfd3/trainer/dump_validation_structures.py +154 -0
- rfd3/trainer/fabric_trainer.py +923 -0
- rfd3/trainer/recycling.py +42 -0
- rfd3/trainer/rfd3.py +485 -0
- rfd3/trainer/trainer_utils.py +502 -0
- rfd3/transforms/conditioning_base.py +508 -0
- rfd3/transforms/conditioning_utils.py +200 -0
- rfd3/transforms/design_transforms.py +807 -0
- rfd3/transforms/dna_crop.py +523 -0
- rfd3/transforms/hbonds.py +407 -0
- rfd3/transforms/hbonds_hbplus.py +246 -0
- rfd3/transforms/ncaa_transforms.py +153 -0
- rfd3/transforms/pipelines.py +632 -0
- rfd3/transforms/ppi_transforms.py +541 -0
- rfd3/transforms/rasa.py +116 -0
- rfd3/transforms/symmetry.py +76 -0
- rfd3/transforms/training_conditions.py +552 -0
- rfd3/transforms/util_transforms.py +498 -0
- rfd3/transforms/virtual_atoms.py +305 -0
- rfd3/utils/inference.py +648 -0
- rfd3/utils/io.py +245 -0
- rfd3/utils/vizualize.py +276 -0
rf3/chemical.py
ADDED
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# TODO: Deprecate in favor of AtomWorks
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# (This code is a holdover from previous frameworks)
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import os
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import torch
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script_dir = os.path.dirname(os.path.realpath(__file__)) + "/"
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NHEAVY = 23
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NTOTAL = 36
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NNAPROTAAS = 32
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NAATOKENS = 20 + 2 + 10 + 1 + 47 # 20 AAs, UNK, MASK, 8 NAs,HIS_D, 47 atoms
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costgtNA = -0.2744
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aa2long = [
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( # 0 ala
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), # 0 ala
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None,
|
|
241
|
+
None,
|
|
242
|
+
None,
|
|
243
|
+
None,
|
|
244
|
+
), # 5 gln
|
|
245
|
+
(
|
|
246
|
+
" N ",
|
|
247
|
+
" CA ",
|
|
248
|
+
" C ",
|
|
249
|
+
" O ",
|
|
250
|
+
" CB ",
|
|
251
|
+
" CG ",
|
|
252
|
+
" CD ",
|
|
253
|
+
" OE1",
|
|
254
|
+
" OE2",
|
|
255
|
+
None,
|
|
256
|
+
None,
|
|
257
|
+
None,
|
|
258
|
+
None,
|
|
259
|
+
None,
|
|
260
|
+
None,
|
|
261
|
+
None,
|
|
262
|
+
None,
|
|
263
|
+
None,
|
|
264
|
+
None,
|
|
265
|
+
None,
|
|
266
|
+
None,
|
|
267
|
+
None,
|
|
268
|
+
None,
|
|
269
|
+
" H ",
|
|
270
|
+
" HA ",
|
|
271
|
+
"1HB ",
|
|
272
|
+
"2HB ",
|
|
273
|
+
"1HG ",
|
|
274
|
+
"2HG ",
|
|
275
|
+
None,
|
|
276
|
+
None,
|
|
277
|
+
None,
|
|
278
|
+
None,
|
|
279
|
+
None,
|
|
280
|
+
None,
|
|
281
|
+
None,
|
|
282
|
+
), # 6 glu
|
|
283
|
+
(
|
|
284
|
+
" N ",
|
|
285
|
+
" CA ",
|
|
286
|
+
" C ",
|
|
287
|
+
" O ",
|
|
288
|
+
None,
|
|
289
|
+
None,
|
|
290
|
+
None,
|
|
291
|
+
None,
|
|
292
|
+
None,
|
|
293
|
+
None,
|
|
294
|
+
None,
|
|
295
|
+
None,
|
|
296
|
+
None,
|
|
297
|
+
None,
|
|
298
|
+
None,
|
|
299
|
+
None,
|
|
300
|
+
None,
|
|
301
|
+
None,
|
|
302
|
+
None,
|
|
303
|
+
None,
|
|
304
|
+
None,
|
|
305
|
+
None,
|
|
306
|
+
None,
|
|
307
|
+
" H ",
|
|
308
|
+
"1HA ",
|
|
309
|
+
"2HA ",
|
|
310
|
+
None,
|
|
311
|
+
None,
|
|
312
|
+
None,
|
|
313
|
+
None,
|
|
314
|
+
None,
|
|
315
|
+
None,
|
|
316
|
+
None,
|
|
317
|
+
None,
|
|
318
|
+
None,
|
|
319
|
+
None,
|
|
320
|
+
), # 7 gly
|
|
321
|
+
(
|
|
322
|
+
" N ",
|
|
323
|
+
" CA ",
|
|
324
|
+
" C ",
|
|
325
|
+
" O ",
|
|
326
|
+
" CB ",
|
|
327
|
+
" CG ",
|
|
328
|
+
" ND1",
|
|
329
|
+
" CD2",
|
|
330
|
+
" CE1",
|
|
331
|
+
" NE2",
|
|
332
|
+
None,
|
|
333
|
+
None,
|
|
334
|
+
None,
|
|
335
|
+
None,
|
|
336
|
+
None,
|
|
337
|
+
None,
|
|
338
|
+
None,
|
|
339
|
+
None,
|
|
340
|
+
None,
|
|
341
|
+
None,
|
|
342
|
+
None,
|
|
343
|
+
None,
|
|
344
|
+
None,
|
|
345
|
+
" H ",
|
|
346
|
+
" HA ",
|
|
347
|
+
"1HB ",
|
|
348
|
+
"2HB ",
|
|
349
|
+
"2HD ",
|
|
350
|
+
"1HE ",
|
|
351
|
+
"2HE ",
|
|
352
|
+
None,
|
|
353
|
+
None,
|
|
354
|
+
None,
|
|
355
|
+
None,
|
|
356
|
+
None,
|
|
357
|
+
None,
|
|
358
|
+
), # 8 his
|
|
359
|
+
(
|
|
360
|
+
" N ",
|
|
361
|
+
" CA ",
|
|
362
|
+
" C ",
|
|
363
|
+
" O ",
|
|
364
|
+
" CB ",
|
|
365
|
+
" CG1",
|
|
366
|
+
" CG2",
|
|
367
|
+
" CD1",
|
|
368
|
+
None,
|
|
369
|
+
None,
|
|
370
|
+
None,
|
|
371
|
+
None,
|
|
372
|
+
None,
|
|
373
|
+
None,
|
|
374
|
+
None,
|
|
375
|
+
None,
|
|
376
|
+
None,
|
|
377
|
+
None,
|
|
378
|
+
None,
|
|
379
|
+
None,
|
|
380
|
+
None,
|
|
381
|
+
None,
|
|
382
|
+
None,
|
|
383
|
+
" H ",
|
|
384
|
+
" HA ",
|
|
385
|
+
" HB ",
|
|
386
|
+
"1HG2",
|
|
387
|
+
"2HG2",
|
|
388
|
+
"3HG2",
|
|
389
|
+
"1HG1",
|
|
390
|
+
"2HG1",
|
|
391
|
+
"1HD1",
|
|
392
|
+
"2HD1",
|
|
393
|
+
"3HD1",
|
|
394
|
+
None,
|
|
395
|
+
None,
|
|
396
|
+
), # 9 ile
|
|
397
|
+
(
|
|
398
|
+
" N ",
|
|
399
|
+
" CA ",
|
|
400
|
+
" C ",
|
|
401
|
+
" O ",
|
|
402
|
+
" CB ",
|
|
403
|
+
" CG ",
|
|
404
|
+
" CD1",
|
|
405
|
+
" CD2",
|
|
406
|
+
None,
|
|
407
|
+
None,
|
|
408
|
+
None,
|
|
409
|
+
None,
|
|
410
|
+
None,
|
|
411
|
+
None,
|
|
412
|
+
None,
|
|
413
|
+
None,
|
|
414
|
+
None,
|
|
415
|
+
None,
|
|
416
|
+
None,
|
|
417
|
+
None,
|
|
418
|
+
None,
|
|
419
|
+
None,
|
|
420
|
+
None,
|
|
421
|
+
" H ",
|
|
422
|
+
" HA ",
|
|
423
|
+
"1HB ",
|
|
424
|
+
"2HB ",
|
|
425
|
+
" HG ",
|
|
426
|
+
"1HD1",
|
|
427
|
+
"2HD1",
|
|
428
|
+
"3HD1",
|
|
429
|
+
"1HD2",
|
|
430
|
+
"2HD2",
|
|
431
|
+
"3HD2",
|
|
432
|
+
None,
|
|
433
|
+
None,
|
|
434
|
+
), # 10 leu
|
|
435
|
+
(
|
|
436
|
+
" N ",
|
|
437
|
+
" CA ",
|
|
438
|
+
" C ",
|
|
439
|
+
" O ",
|
|
440
|
+
" CB ",
|
|
441
|
+
" CG ",
|
|
442
|
+
" CD ",
|
|
443
|
+
" CE ",
|
|
444
|
+
" NZ ",
|
|
445
|
+
None,
|
|
446
|
+
None,
|
|
447
|
+
None,
|
|
448
|
+
None,
|
|
449
|
+
None,
|
|
450
|
+
None,
|
|
451
|
+
None,
|
|
452
|
+
None,
|
|
453
|
+
None,
|
|
454
|
+
None,
|
|
455
|
+
None,
|
|
456
|
+
None,
|
|
457
|
+
None,
|
|
458
|
+
None,
|
|
459
|
+
" H ",
|
|
460
|
+
" HA ",
|
|
461
|
+
"1HB ",
|
|
462
|
+
"2HB ",
|
|
463
|
+
"1HG ",
|
|
464
|
+
"2HG ",
|
|
465
|
+
"1HD ",
|
|
466
|
+
"2HD ",
|
|
467
|
+
"1HE ",
|
|
468
|
+
"2HE ",
|
|
469
|
+
"1HZ ",
|
|
470
|
+
"2HZ ",
|
|
471
|
+
"3HZ ",
|
|
472
|
+
), # 11 lys
|
|
473
|
+
(
|
|
474
|
+
" N ",
|
|
475
|
+
" CA ",
|
|
476
|
+
" C ",
|
|
477
|
+
" O ",
|
|
478
|
+
" CB ",
|
|
479
|
+
" CG ",
|
|
480
|
+
" SD ",
|
|
481
|
+
" CE ",
|
|
482
|
+
None,
|
|
483
|
+
None,
|
|
484
|
+
None,
|
|
485
|
+
None,
|
|
486
|
+
None,
|
|
487
|
+
None,
|
|
488
|
+
None,
|
|
489
|
+
None,
|
|
490
|
+
None,
|
|
491
|
+
None,
|
|
492
|
+
None,
|
|
493
|
+
None,
|
|
494
|
+
None,
|
|
495
|
+
None,
|
|
496
|
+
None,
|
|
497
|
+
" H ",
|
|
498
|
+
" HA ",
|
|
499
|
+
"1HB ",
|
|
500
|
+
"2HB ",
|
|
501
|
+
"1HG ",
|
|
502
|
+
"2HG ",
|
|
503
|
+
"1HE ",
|
|
504
|
+
"2HE ",
|
|
505
|
+
"3HE ",
|
|
506
|
+
None,
|
|
507
|
+
None,
|
|
508
|
+
None,
|
|
509
|
+
None,
|
|
510
|
+
), # 12 met
|
|
511
|
+
(
|
|
512
|
+
" N ",
|
|
513
|
+
" CA ",
|
|
514
|
+
" C ",
|
|
515
|
+
" O ",
|
|
516
|
+
" CB ",
|
|
517
|
+
" CG ",
|
|
518
|
+
" CD1",
|
|
519
|
+
" CD2",
|
|
520
|
+
" CE1",
|
|
521
|
+
" CE2",
|
|
522
|
+
" CZ ",
|
|
523
|
+
None,
|
|
524
|
+
None,
|
|
525
|
+
None,
|
|
526
|
+
None,
|
|
527
|
+
None,
|
|
528
|
+
None,
|
|
529
|
+
None,
|
|
530
|
+
None,
|
|
531
|
+
None,
|
|
532
|
+
None,
|
|
533
|
+
None,
|
|
534
|
+
None,
|
|
535
|
+
" H ",
|
|
536
|
+
" HA ",
|
|
537
|
+
"1HB ",
|
|
538
|
+
"2HB ",
|
|
539
|
+
"1HD ",
|
|
540
|
+
"2HD ",
|
|
541
|
+
"1HE ",
|
|
542
|
+
"2HE ",
|
|
543
|
+
" HZ ",
|
|
544
|
+
None,
|
|
545
|
+
None,
|
|
546
|
+
None,
|
|
547
|
+
None,
|
|
548
|
+
), # 13 phe
|
|
549
|
+
(
|
|
550
|
+
" N ",
|
|
551
|
+
" CA ",
|
|
552
|
+
" C ",
|
|
553
|
+
" O ",
|
|
554
|
+
" CB ",
|
|
555
|
+
" CG ",
|
|
556
|
+
" CD ",
|
|
557
|
+
None,
|
|
558
|
+
None,
|
|
559
|
+
None,
|
|
560
|
+
None,
|
|
561
|
+
None,
|
|
562
|
+
None,
|
|
563
|
+
None,
|
|
564
|
+
None,
|
|
565
|
+
None,
|
|
566
|
+
None,
|
|
567
|
+
None,
|
|
568
|
+
None,
|
|
569
|
+
None,
|
|
570
|
+
None,
|
|
571
|
+
None,
|
|
572
|
+
None,
|
|
573
|
+
" HA ",
|
|
574
|
+
"1HB ",
|
|
575
|
+
"2HB ",
|
|
576
|
+
"1HG ",
|
|
577
|
+
"2HG ",
|
|
578
|
+
"1HD ",
|
|
579
|
+
"2HD ",
|
|
580
|
+
None,
|
|
581
|
+
None,
|
|
582
|
+
None,
|
|
583
|
+
None,
|
|
584
|
+
None,
|
|
585
|
+
None,
|
|
586
|
+
), # 14 pro
|
|
587
|
+
(
|
|
588
|
+
" N ",
|
|
589
|
+
" CA ",
|
|
590
|
+
" C ",
|
|
591
|
+
" O ",
|
|
592
|
+
" CB ",
|
|
593
|
+
" OG ",
|
|
594
|
+
None,
|
|
595
|
+
None,
|
|
596
|
+
None,
|
|
597
|
+
None,
|
|
598
|
+
None,
|
|
599
|
+
None,
|
|
600
|
+
None,
|
|
601
|
+
None,
|
|
602
|
+
None,
|
|
603
|
+
None,
|
|
604
|
+
None,
|
|
605
|
+
None,
|
|
606
|
+
None,
|
|
607
|
+
None,
|
|
608
|
+
None,
|
|
609
|
+
None,
|
|
610
|
+
None,
|
|
611
|
+
" H ",
|
|
612
|
+
" HG ",
|
|
613
|
+
" HA ",
|
|
614
|
+
"1HB ",
|
|
615
|
+
"2HB ",
|
|
616
|
+
None,
|
|
617
|
+
None,
|
|
618
|
+
None,
|
|
619
|
+
None,
|
|
620
|
+
None,
|
|
621
|
+
None,
|
|
622
|
+
None,
|
|
623
|
+
None,
|
|
624
|
+
), # 15 ser
|
|
625
|
+
(
|
|
626
|
+
" N ",
|
|
627
|
+
" CA ",
|
|
628
|
+
" C ",
|
|
629
|
+
" O ",
|
|
630
|
+
" CB ",
|
|
631
|
+
" OG1",
|
|
632
|
+
" CG2",
|
|
633
|
+
None,
|
|
634
|
+
None,
|
|
635
|
+
None,
|
|
636
|
+
None,
|
|
637
|
+
None,
|
|
638
|
+
None,
|
|
639
|
+
None,
|
|
640
|
+
None,
|
|
641
|
+
None,
|
|
642
|
+
None,
|
|
643
|
+
None,
|
|
644
|
+
None,
|
|
645
|
+
None,
|
|
646
|
+
None,
|
|
647
|
+
None,
|
|
648
|
+
None,
|
|
649
|
+
" H ",
|
|
650
|
+
" HG1",
|
|
651
|
+
" HA ",
|
|
652
|
+
" HB ",
|
|
653
|
+
"1HG2",
|
|
654
|
+
"2HG2",
|
|
655
|
+
"3HG2",
|
|
656
|
+
None,
|
|
657
|
+
None,
|
|
658
|
+
None,
|
|
659
|
+
None,
|
|
660
|
+
None,
|
|
661
|
+
None,
|
|
662
|
+
), # 16 thr
|
|
663
|
+
(
|
|
664
|
+
" N ",
|
|
665
|
+
" CA ",
|
|
666
|
+
" C ",
|
|
667
|
+
" O ",
|
|
668
|
+
" CB ",
|
|
669
|
+
" CG ",
|
|
670
|
+
" CD1",
|
|
671
|
+
" CD2",
|
|
672
|
+
" CE2",
|
|
673
|
+
" CE3",
|
|
674
|
+
" NE1",
|
|
675
|
+
" CZ2",
|
|
676
|
+
" CZ3",
|
|
677
|
+
" CH2",
|
|
678
|
+
None,
|
|
679
|
+
None,
|
|
680
|
+
None,
|
|
681
|
+
None,
|
|
682
|
+
None,
|
|
683
|
+
None,
|
|
684
|
+
None,
|
|
685
|
+
None,
|
|
686
|
+
None,
|
|
687
|
+
" H ",
|
|
688
|
+
" HA ",
|
|
689
|
+
"1HB ",
|
|
690
|
+
"2HB ",
|
|
691
|
+
"1HD ",
|
|
692
|
+
"1HE ",
|
|
693
|
+
" HZ2",
|
|
694
|
+
" HH2",
|
|
695
|
+
" HZ3",
|
|
696
|
+
" HE3",
|
|
697
|
+
None,
|
|
698
|
+
None,
|
|
699
|
+
None,
|
|
700
|
+
), # 17 trp
|
|
701
|
+
(
|
|
702
|
+
" N ",
|
|
703
|
+
" CA ",
|
|
704
|
+
" C ",
|
|
705
|
+
" O ",
|
|
706
|
+
" CB ",
|
|
707
|
+
" CG ",
|
|
708
|
+
" CD1",
|
|
709
|
+
" CD2",
|
|
710
|
+
" CE1",
|
|
711
|
+
" CE2",
|
|
712
|
+
" CZ ",
|
|
713
|
+
" OH ",
|
|
714
|
+
None,
|
|
715
|
+
None,
|
|
716
|
+
None,
|
|
717
|
+
None,
|
|
718
|
+
None,
|
|
719
|
+
None,
|
|
720
|
+
None,
|
|
721
|
+
None,
|
|
722
|
+
None,
|
|
723
|
+
None,
|
|
724
|
+
None,
|
|
725
|
+
" H ",
|
|
726
|
+
" HA ",
|
|
727
|
+
"1HB ",
|
|
728
|
+
"2HB ",
|
|
729
|
+
"1HD ",
|
|
730
|
+
"1HE ",
|
|
731
|
+
"2HE ",
|
|
732
|
+
"2HD ",
|
|
733
|
+
" HH ",
|
|
734
|
+
None,
|
|
735
|
+
None,
|
|
736
|
+
None,
|
|
737
|
+
None,
|
|
738
|
+
), # 18 tyr
|
|
739
|
+
(
|
|
740
|
+
" N ",
|
|
741
|
+
" CA ",
|
|
742
|
+
" C ",
|
|
743
|
+
" O ",
|
|
744
|
+
" CB ",
|
|
745
|
+
" CG1",
|
|
746
|
+
" CG2",
|
|
747
|
+
None,
|
|
748
|
+
None,
|
|
749
|
+
None,
|
|
750
|
+
None,
|
|
751
|
+
None,
|
|
752
|
+
None,
|
|
753
|
+
None,
|
|
754
|
+
None,
|
|
755
|
+
None,
|
|
756
|
+
None,
|
|
757
|
+
None,
|
|
758
|
+
None,
|
|
759
|
+
None,
|
|
760
|
+
None,
|
|
761
|
+
None,
|
|
762
|
+
None,
|
|
763
|
+
" H ",
|
|
764
|
+
" HA ",
|
|
765
|
+
" HB ",
|
|
766
|
+
"1HG1",
|
|
767
|
+
"2HG1",
|
|
768
|
+
"3HG1",
|
|
769
|
+
"1HG2",
|
|
770
|
+
"2HG2",
|
|
771
|
+
"3HG2",
|
|
772
|
+
None,
|
|
773
|
+
None,
|
|
774
|
+
None,
|
|
775
|
+
None,
|
|
776
|
+
), # 19 val
|
|
777
|
+
(
|
|
778
|
+
" N ",
|
|
779
|
+
" CA ",
|
|
780
|
+
" C ",
|
|
781
|
+
" O ",
|
|
782
|
+
" CB ",
|
|
783
|
+
None,
|
|
784
|
+
None,
|
|
785
|
+
None,
|
|
786
|
+
None,
|
|
787
|
+
None,
|
|
788
|
+
None,
|
|
789
|
+
None,
|
|
790
|
+
None,
|
|
791
|
+
None,
|
|
792
|
+
None,
|
|
793
|
+
None,
|
|
794
|
+
None,
|
|
795
|
+
None,
|
|
796
|
+
None,
|
|
797
|
+
None,
|
|
798
|
+
None,
|
|
799
|
+
None,
|
|
800
|
+
None,
|
|
801
|
+
" H ",
|
|
802
|
+
" HA ",
|
|
803
|
+
"1HB ",
|
|
804
|
+
"2HB ",
|
|
805
|
+
"3HB ",
|
|
806
|
+
None,
|
|
807
|
+
None,
|
|
808
|
+
None,
|
|
809
|
+
None,
|
|
810
|
+
None,
|
|
811
|
+
None,
|
|
812
|
+
None,
|
|
813
|
+
None,
|
|
814
|
+
), # 20 unk
|
|
815
|
+
(
|
|
816
|
+
" N ",
|
|
817
|
+
" CA ",
|
|
818
|
+
" C ",
|
|
819
|
+
" O ",
|
|
820
|
+
" CB ",
|
|
821
|
+
None,
|
|
822
|
+
None,
|
|
823
|
+
None,
|
|
824
|
+
None,
|
|
825
|
+
None,
|
|
826
|
+
None,
|
|
827
|
+
None,
|
|
828
|
+
None,
|
|
829
|
+
None,
|
|
830
|
+
None,
|
|
831
|
+
None,
|
|
832
|
+
None,
|
|
833
|
+
None,
|
|
834
|
+
None,
|
|
835
|
+
None,
|
|
836
|
+
None,
|
|
837
|
+
None,
|
|
838
|
+
None,
|
|
839
|
+
" H ",
|
|
840
|
+
" HA ",
|
|
841
|
+
"1HB ",
|
|
842
|
+
"2HB ",
|
|
843
|
+
"3HB ",
|
|
844
|
+
None,
|
|
845
|
+
None,
|
|
846
|
+
None,
|
|
847
|
+
None,
|
|
848
|
+
None,
|
|
849
|
+
None,
|
|
850
|
+
None,
|
|
851
|
+
None,
|
|
852
|
+
), # 21 mask
|
|
853
|
+
(
|
|
854
|
+
" O4'",
|
|
855
|
+
" C1'",
|
|
856
|
+
" C2'",
|
|
857
|
+
" OP1",
|
|
858
|
+
" P ",
|
|
859
|
+
" OP2",
|
|
860
|
+
" O5'",
|
|
861
|
+
" C5'",
|
|
862
|
+
" C4'",
|
|
863
|
+
" C3'",
|
|
864
|
+
" O3'",
|
|
865
|
+
" N9 ",
|
|
866
|
+
" C4 ",
|
|
867
|
+
" N3 ",
|
|
868
|
+
" C2 ",
|
|
869
|
+
" N1 ",
|
|
870
|
+
" C6 ",
|
|
871
|
+
" C5 ",
|
|
872
|
+
" N7 ",
|
|
873
|
+
" C8 ",
|
|
874
|
+
" N6 ",
|
|
875
|
+
None,
|
|
876
|
+
None,
|
|
877
|
+
"H5''",
|
|
878
|
+
" H5'",
|
|
879
|
+
" H4'",
|
|
880
|
+
" H3'",
|
|
881
|
+
"H2''",
|
|
882
|
+
" H2'",
|
|
883
|
+
" H1'",
|
|
884
|
+
" H2 ",
|
|
885
|
+
" H61",
|
|
886
|
+
" H62",
|
|
887
|
+
" H8 ",
|
|
888
|
+
None,
|
|
889
|
+
None,
|
|
890
|
+
), # 22 DA
|
|
891
|
+
(
|
|
892
|
+
" O4'",
|
|
893
|
+
" C1'",
|
|
894
|
+
" C2'",
|
|
895
|
+
" OP1",
|
|
896
|
+
" P ",
|
|
897
|
+
" OP2",
|
|
898
|
+
" O5'",
|
|
899
|
+
" C5'",
|
|
900
|
+
" C4'",
|
|
901
|
+
" C3'",
|
|
902
|
+
" O3'",
|
|
903
|
+
" N1 ",
|
|
904
|
+
" C2 ",
|
|
905
|
+
" O2 ",
|
|
906
|
+
" N3 ",
|
|
907
|
+
" C4 ",
|
|
908
|
+
" N4 ",
|
|
909
|
+
" C5 ",
|
|
910
|
+
" C6 ",
|
|
911
|
+
None,
|
|
912
|
+
None,
|
|
913
|
+
None,
|
|
914
|
+
None,
|
|
915
|
+
"H5''",
|
|
916
|
+
" H5'",
|
|
917
|
+
" H4'",
|
|
918
|
+
" H3'",
|
|
919
|
+
"H2''",
|
|
920
|
+
" H2'",
|
|
921
|
+
" H1'",
|
|
922
|
+
" H42",
|
|
923
|
+
" H41",
|
|
924
|
+
" H5 ",
|
|
925
|
+
" H6 ",
|
|
926
|
+
None,
|
|
927
|
+
None,
|
|
928
|
+
), # 23 DC
|
|
929
|
+
(
|
|
930
|
+
" O4'",
|
|
931
|
+
" C1'",
|
|
932
|
+
" C2'",
|
|
933
|
+
" OP1",
|
|
934
|
+
" P ",
|
|
935
|
+
" OP2",
|
|
936
|
+
" O5'",
|
|
937
|
+
" C5'",
|
|
938
|
+
" C4'",
|
|
939
|
+
" C3'",
|
|
940
|
+
" O3'",
|
|
941
|
+
" N9 ",
|
|
942
|
+
" C4 ",
|
|
943
|
+
" N3 ",
|
|
944
|
+
" C2 ",
|
|
945
|
+
" N1 ",
|
|
946
|
+
" C6 ",
|
|
947
|
+
" C5 ",
|
|
948
|
+
" N7 ",
|
|
949
|
+
" C8 ",
|
|
950
|
+
" N2 ",
|
|
951
|
+
" O6 ",
|
|
952
|
+
None,
|
|
953
|
+
"H5''",
|
|
954
|
+
" H5'",
|
|
955
|
+
" H4'",
|
|
956
|
+
" H3'",
|
|
957
|
+
"H2''",
|
|
958
|
+
" H2'",
|
|
959
|
+
" H1'",
|
|
960
|
+
" H1 ",
|
|
961
|
+
" H22",
|
|
962
|
+
" H21",
|
|
963
|
+
" H8 ",
|
|
964
|
+
None,
|
|
965
|
+
None,
|
|
966
|
+
), # 24 DG
|
|
967
|
+
(
|
|
968
|
+
" O4'",
|
|
969
|
+
" C1'",
|
|
970
|
+
" C2'",
|
|
971
|
+
" OP1",
|
|
972
|
+
" P ",
|
|
973
|
+
" OP2",
|
|
974
|
+
" O5'",
|
|
975
|
+
" C5'",
|
|
976
|
+
" C4'",
|
|
977
|
+
" C3'",
|
|
978
|
+
" O3'",
|
|
979
|
+
" N1 ",
|
|
980
|
+
" C2 ",
|
|
981
|
+
" O2 ",
|
|
982
|
+
" N3 ",
|
|
983
|
+
" C4 ",
|
|
984
|
+
" O4 ",
|
|
985
|
+
" C5 ",
|
|
986
|
+
" C7 ",
|
|
987
|
+
" C6 ",
|
|
988
|
+
None,
|
|
989
|
+
None,
|
|
990
|
+
None,
|
|
991
|
+
"H5''",
|
|
992
|
+
" H5'",
|
|
993
|
+
" H4'",
|
|
994
|
+
" H3'",
|
|
995
|
+
"H2''",
|
|
996
|
+
" H2'",
|
|
997
|
+
" H1'",
|
|
998
|
+
" H3 ",
|
|
999
|
+
" H71",
|
|
1000
|
+
" H72",
|
|
1001
|
+
" H73",
|
|
1002
|
+
" H6 ",
|
|
1003
|
+
None,
|
|
1004
|
+
), # 25 DT
|
|
1005
|
+
(
|
|
1006
|
+
" O4'",
|
|
1007
|
+
" C1'",
|
|
1008
|
+
" C2'",
|
|
1009
|
+
" OP1",
|
|
1010
|
+
" P ",
|
|
1011
|
+
" OP2",
|
|
1012
|
+
" O5'",
|
|
1013
|
+
" C5'",
|
|
1014
|
+
" C4'",
|
|
1015
|
+
" C3'",
|
|
1016
|
+
" O3'",
|
|
1017
|
+
None,
|
|
1018
|
+
None,
|
|
1019
|
+
None,
|
|
1020
|
+
None,
|
|
1021
|
+
None,
|
|
1022
|
+
None,
|
|
1023
|
+
None,
|
|
1024
|
+
None,
|
|
1025
|
+
None,
|
|
1026
|
+
None,
|
|
1027
|
+
None,
|
|
1028
|
+
None,
|
|
1029
|
+
"H5''",
|
|
1030
|
+
" H5'",
|
|
1031
|
+
" H4'",
|
|
1032
|
+
" H3'",
|
|
1033
|
+
"H2''",
|
|
1034
|
+
" H2'",
|
|
1035
|
+
" H1'",
|
|
1036
|
+
None,
|
|
1037
|
+
None,
|
|
1038
|
+
None,
|
|
1039
|
+
None,
|
|
1040
|
+
None,
|
|
1041
|
+
None,
|
|
1042
|
+
), # 26 DX (unk DNA)
|
|
1043
|
+
(
|
|
1044
|
+
" O4'",
|
|
1045
|
+
" C1'",
|
|
1046
|
+
" C2'",
|
|
1047
|
+
" OP1",
|
|
1048
|
+
" P ",
|
|
1049
|
+
" OP2",
|
|
1050
|
+
" O5'",
|
|
1051
|
+
" C5'",
|
|
1052
|
+
" C4'",
|
|
1053
|
+
" C3'",
|
|
1054
|
+
" O3'",
|
|
1055
|
+
" O2'",
|
|
1056
|
+
" N1 ",
|
|
1057
|
+
" C2 ",
|
|
1058
|
+
" N3 ",
|
|
1059
|
+
" C4 ",
|
|
1060
|
+
" C5 ",
|
|
1061
|
+
" C6 ",
|
|
1062
|
+
" N6 ",
|
|
1063
|
+
" N7 ",
|
|
1064
|
+
" C8 ",
|
|
1065
|
+
" N9 ",
|
|
1066
|
+
None,
|
|
1067
|
+
" H5'",
|
|
1068
|
+
"H5''",
|
|
1069
|
+
" H4'",
|
|
1070
|
+
" H3'",
|
|
1071
|
+
" H2'",
|
|
1072
|
+
"HO2'",
|
|
1073
|
+
" H1'",
|
|
1074
|
+
" H2 ",
|
|
1075
|
+
" H61",
|
|
1076
|
+
" H62",
|
|
1077
|
+
" H8 ",
|
|
1078
|
+
None,
|
|
1079
|
+
None,
|
|
1080
|
+
), # 27 A
|
|
1081
|
+
(
|
|
1082
|
+
" O4'",
|
|
1083
|
+
" C1'",
|
|
1084
|
+
" C2'",
|
|
1085
|
+
" OP1",
|
|
1086
|
+
" P ",
|
|
1087
|
+
" OP2",
|
|
1088
|
+
" O5'",
|
|
1089
|
+
" C5'",
|
|
1090
|
+
" C4'",
|
|
1091
|
+
" C3'",
|
|
1092
|
+
" O3'",
|
|
1093
|
+
" O2'",
|
|
1094
|
+
" N1 ",
|
|
1095
|
+
" C2 ",
|
|
1096
|
+
" O2 ",
|
|
1097
|
+
" N3 ",
|
|
1098
|
+
" C4 ",
|
|
1099
|
+
" N4 ",
|
|
1100
|
+
" C5 ",
|
|
1101
|
+
" C6 ",
|
|
1102
|
+
None,
|
|
1103
|
+
None,
|
|
1104
|
+
None,
|
|
1105
|
+
" H5'",
|
|
1106
|
+
"H5''",
|
|
1107
|
+
" H4'",
|
|
1108
|
+
" H3'",
|
|
1109
|
+
" H2'",
|
|
1110
|
+
"HO2'",
|
|
1111
|
+
" H1'",
|
|
1112
|
+
" H42",
|
|
1113
|
+
" H41",
|
|
1114
|
+
" H5 ",
|
|
1115
|
+
" H6 ",
|
|
1116
|
+
None,
|
|
1117
|
+
None,
|
|
1118
|
+
), # 28 C
|
|
1119
|
+
(
|
|
1120
|
+
" O4'",
|
|
1121
|
+
" C1'",
|
|
1122
|
+
" C2'",
|
|
1123
|
+
" OP1",
|
|
1124
|
+
" P ",
|
|
1125
|
+
" OP2",
|
|
1126
|
+
" O5'",
|
|
1127
|
+
" C5'",
|
|
1128
|
+
" C4'",
|
|
1129
|
+
" C3'",
|
|
1130
|
+
" O3'",
|
|
1131
|
+
" O2'",
|
|
1132
|
+
" N1 ",
|
|
1133
|
+
" C2 ",
|
|
1134
|
+
" N2 ",
|
|
1135
|
+
" N3 ",
|
|
1136
|
+
" C4 ",
|
|
1137
|
+
" C5 ",
|
|
1138
|
+
" C6 ",
|
|
1139
|
+
" O6 ",
|
|
1140
|
+
" N7 ",
|
|
1141
|
+
" C8 ",
|
|
1142
|
+
" N9 ",
|
|
1143
|
+
" H5'",
|
|
1144
|
+
"H5''",
|
|
1145
|
+
" H4'",
|
|
1146
|
+
" H3'",
|
|
1147
|
+
" H2'",
|
|
1148
|
+
"HO2'",
|
|
1149
|
+
" H1'",
|
|
1150
|
+
" H1 ",
|
|
1151
|
+
" H22",
|
|
1152
|
+
" H21",
|
|
1153
|
+
" H8 ",
|
|
1154
|
+
None,
|
|
1155
|
+
None,
|
|
1156
|
+
), # 29 G
|
|
1157
|
+
(
|
|
1158
|
+
" O4'",
|
|
1159
|
+
" C1'",
|
|
1160
|
+
" C2'",
|
|
1161
|
+
" OP1",
|
|
1162
|
+
" P ",
|
|
1163
|
+
" OP2",
|
|
1164
|
+
" O5'",
|
|
1165
|
+
" C5'",
|
|
1166
|
+
" C4'",
|
|
1167
|
+
" C3'",
|
|
1168
|
+
" O3'",
|
|
1169
|
+
" O2'",
|
|
1170
|
+
" N1 ",
|
|
1171
|
+
" C2 ",
|
|
1172
|
+
" O2 ",
|
|
1173
|
+
" N3 ",
|
|
1174
|
+
" C4 ",
|
|
1175
|
+
" O4 ",
|
|
1176
|
+
" C5 ",
|
|
1177
|
+
" C6 ",
|
|
1178
|
+
None,
|
|
1179
|
+
None,
|
|
1180
|
+
None,
|
|
1181
|
+
" H5'",
|
|
1182
|
+
"H5''",
|
|
1183
|
+
" H4'",
|
|
1184
|
+
" H3'",
|
|
1185
|
+
" H2'",
|
|
1186
|
+
"HO2'",
|
|
1187
|
+
" H1'",
|
|
1188
|
+
" H3 ",
|
|
1189
|
+
" H5 ",
|
|
1190
|
+
" H6 ",
|
|
1191
|
+
None,
|
|
1192
|
+
None,
|
|
1193
|
+
None,
|
|
1194
|
+
), # 30 U
|
|
1195
|
+
(
|
|
1196
|
+
" O4'",
|
|
1197
|
+
" C1'",
|
|
1198
|
+
" C2'",
|
|
1199
|
+
" OP1",
|
|
1200
|
+
" P ",
|
|
1201
|
+
" OP2",
|
|
1202
|
+
" O5'",
|
|
1203
|
+
" C5'",
|
|
1204
|
+
" C4'",
|
|
1205
|
+
" C3'",
|
|
1206
|
+
" O3'",
|
|
1207
|
+
" O2'",
|
|
1208
|
+
None,
|
|
1209
|
+
None,
|
|
1210
|
+
None,
|
|
1211
|
+
None,
|
|
1212
|
+
None,
|
|
1213
|
+
None,
|
|
1214
|
+
None,
|
|
1215
|
+
None,
|
|
1216
|
+
None,
|
|
1217
|
+
None,
|
|
1218
|
+
None,
|
|
1219
|
+
" H5'",
|
|
1220
|
+
"H5''",
|
|
1221
|
+
" H4'",
|
|
1222
|
+
" H3'",
|
|
1223
|
+
" H2'",
|
|
1224
|
+
"HO2'",
|
|
1225
|
+
" H1'",
|
|
1226
|
+
None,
|
|
1227
|
+
None,
|
|
1228
|
+
None,
|
|
1229
|
+
None,
|
|
1230
|
+
None,
|
|
1231
|
+
None,
|
|
1232
|
+
), # 31 RX (unk RNA)
|
|
1233
|
+
(
|
|
1234
|
+
" N ",
|
|
1235
|
+
" CA ",
|
|
1236
|
+
" C ",
|
|
1237
|
+
" O ",
|
|
1238
|
+
" CB ",
|
|
1239
|
+
" CG ",
|
|
1240
|
+
" NE2",
|
|
1241
|
+
" CD2",
|
|
1242
|
+
" CE1",
|
|
1243
|
+
" ND1",
|
|
1244
|
+
None,
|
|
1245
|
+
None,
|
|
1246
|
+
None,
|
|
1247
|
+
None,
|
|
1248
|
+
None,
|
|
1249
|
+
None,
|
|
1250
|
+
None,
|
|
1251
|
+
None,
|
|
1252
|
+
None,
|
|
1253
|
+
None,
|
|
1254
|
+
None,
|
|
1255
|
+
None,
|
|
1256
|
+
None,
|
|
1257
|
+
" H ",
|
|
1258
|
+
" HA ",
|
|
1259
|
+
"1HB ",
|
|
1260
|
+
"2HB ",
|
|
1261
|
+
"2HD ",
|
|
1262
|
+
"1HE ",
|
|
1263
|
+
"1HD ",
|
|
1264
|
+
None,
|
|
1265
|
+
None,
|
|
1266
|
+
None,
|
|
1267
|
+
None,
|
|
1268
|
+
None,
|
|
1269
|
+
None,
|
|
1270
|
+
), # -1 his_d
|
|
1271
|
+
]
|
|
1272
|
+
|
|
1273
|
+
# frames for generic FAPE
|
|
1274
|
+
##NOTE: 1st entry must be "backbone frame"
|
|
1275
|
+
# fmt: on
|
|
1276
|
+
frames = [
|
|
1277
|
+
[[" N ", " CA ", " C "], [" CA ", " C ", " O "]], # ala
|
|
1278
|
+
[
|
|
1279
|
+
[" N ", " CA ", " C "],
|
|
1280
|
+
[" CA ", " C ", " O "],
|
|
1281
|
+
[" N ", " CA ", " CB "],
|
|
1282
|
+
[" CA ", " CB ", " CG "],
|
|
1283
|
+
[" CB ", " CG ", " CD "],
|
|
1284
|
+
[" CG ", " CD ", " NE "],
|
|
1285
|
+
], # arg
|
|
1286
|
+
[
|
|
1287
|
+
[" N ", " CA ", " C "],
|
|
1288
|
+
[" CA ", " C ", " O "],
|
|
1289
|
+
[" N ", " CA ", " CB "],
|
|
1290
|
+
[" CA ", " CB ", " CG "],
|
|
1291
|
+
], # asn
|
|
1292
|
+
[
|
|
1293
|
+
[" N ", " CA ", " C "],
|
|
1294
|
+
[" CA ", " C ", " O "],
|
|
1295
|
+
[" N ", " CA ", " CB "],
|
|
1296
|
+
[" CA ", " CB ", " CG "],
|
|
1297
|
+
], # asp
|
|
1298
|
+
[
|
|
1299
|
+
[" N ", " CA ", " C "],
|
|
1300
|
+
[" CA ", " C ", " O "],
|
|
1301
|
+
[" N ", " CA ", " CB "],
|
|
1302
|
+
], # cys
|
|
1303
|
+
[
|
|
1304
|
+
[" N ", " CA ", " C "],
|
|
1305
|
+
[" CA ", " C ", " O "],
|
|
1306
|
+
[" N ", " CA ", " CB "],
|
|
1307
|
+
[" CA ", " CB ", " CG "],
|
|
1308
|
+
[" CB ", " CG ", " CD "],
|
|
1309
|
+
], # gln
|
|
1310
|
+
[
|
|
1311
|
+
[" N ", " CA ", " C "],
|
|
1312
|
+
[" CA ", " C ", " O "],
|
|
1313
|
+
[" N ", " CA ", " CB "],
|
|
1314
|
+
[" CA ", " CB ", " CG "],
|
|
1315
|
+
[" CB ", " CG ", " CD "],
|
|
1316
|
+
], # glu
|
|
1317
|
+
[[" N ", " CA ", " C "], [" CA ", " C ", " O "]], # gly
|
|
1318
|
+
[
|
|
1319
|
+
[" N ", " CA ", " C "],
|
|
1320
|
+
[" CA ", " C ", " O "],
|
|
1321
|
+
[" N ", " CA ", " CB "],
|
|
1322
|
+
[" CA ", " CB ", " CG "],
|
|
1323
|
+
], # his
|
|
1324
|
+
[
|
|
1325
|
+
[" N ", " CA ", " C "],
|
|
1326
|
+
[" CA ", " C ", " O "],
|
|
1327
|
+
[" N ", " CA ", " CB "],
|
|
1328
|
+
[" CA ", " CB ", " CG1"],
|
|
1329
|
+
], # ile
|
|
1330
|
+
[
|
|
1331
|
+
[" N ", " CA ", " C "],
|
|
1332
|
+
[" CA ", " C ", " O "],
|
|
1333
|
+
[" N ", " CA ", " CB "],
|
|
1334
|
+
[" CA ", " CB ", " CG "],
|
|
1335
|
+
], # leu
|
|
1336
|
+
[
|
|
1337
|
+
[" N ", " CA ", " C "],
|
|
1338
|
+
[" CA ", " C ", " O "],
|
|
1339
|
+
[" N ", " CA ", " CB "],
|
|
1340
|
+
[" CA ", " CB ", " CG "],
|
|
1341
|
+
[" CB ", " CG ", " CD "],
|
|
1342
|
+
[" CG ", " CD ", " CE "],
|
|
1343
|
+
], # lys
|
|
1344
|
+
[
|
|
1345
|
+
[" N ", " CA ", " C "],
|
|
1346
|
+
[" CA ", " C ", " O "],
|
|
1347
|
+
[" N ", " CA ", " CB "],
|
|
1348
|
+
[" CA ", " CB ", " CG "],
|
|
1349
|
+
[" CB ", " CG ", " SD "],
|
|
1350
|
+
], # met
|
|
1351
|
+
[
|
|
1352
|
+
[" N ", " CA ", " C "],
|
|
1353
|
+
[" CA ", " C ", " O "],
|
|
1354
|
+
[" N ", " CA ", " CB "],
|
|
1355
|
+
[" CA ", " CB ", " CG "],
|
|
1356
|
+
], # phe
|
|
1357
|
+
[
|
|
1358
|
+
[" N ", " CA ", " C "],
|
|
1359
|
+
[" CA ", " C ", " O "],
|
|
1360
|
+
[" N ", " CA ", " CB "],
|
|
1361
|
+
[" CA ", " CB ", " CG "],
|
|
1362
|
+
[" CB ", " CG ", " CD "],
|
|
1363
|
+
], # pro
|
|
1364
|
+
[
|
|
1365
|
+
[" N ", " CA ", " C "],
|
|
1366
|
+
[" CA ", " C ", " O "],
|
|
1367
|
+
[" N ", " CA ", " CB "],
|
|
1368
|
+
[" CA ", " CB ", " OG "],
|
|
1369
|
+
], # ser
|
|
1370
|
+
[
|
|
1371
|
+
[" N ", " CA ", " C "],
|
|
1372
|
+
[" CA ", " C ", " O "],
|
|
1373
|
+
[" N ", " CA ", " CB "],
|
|
1374
|
+
[" CA ", " CB ", " OG1"],
|
|
1375
|
+
], # thr
|
|
1376
|
+
[
|
|
1377
|
+
[" N ", " CA ", " C "],
|
|
1378
|
+
[" CA ", " C ", " O "],
|
|
1379
|
+
[" N ", " CA ", " CB "],
|
|
1380
|
+
[" CA ", " CB ", " CG "],
|
|
1381
|
+
], # trp
|
|
1382
|
+
[
|
|
1383
|
+
[" N ", " CA ", " C "],
|
|
1384
|
+
[" CA ", " C ", " O "],
|
|
1385
|
+
[" N ", " CA ", " CB "],
|
|
1386
|
+
[" CA ", " CB ", " CG "],
|
|
1387
|
+
], # tyr
|
|
1388
|
+
[
|
|
1389
|
+
[" N ", " CA ", " C "],
|
|
1390
|
+
[" CA ", " C ", " O "],
|
|
1391
|
+
[" N ", " CA ", " CB "],
|
|
1392
|
+
], # val
|
|
1393
|
+
[[" N ", " CA ", " C "], [" CA ", " C ", " O "]], # unk
|
|
1394
|
+
[[" N ", " CA ", " C "], [" CA ", " C ", " O "]], # mask
|
|
1395
|
+
[
|
|
1396
|
+
[" O4'", " C1'", " C2'"],
|
|
1397
|
+
[" OP1", " P ", " O5'"],
|
|
1398
|
+
[" P ", " O5'", " C5'"],
|
|
1399
|
+
[" O5'", " C5'", " C4'"],
|
|
1400
|
+
[" C5'", " C4'", " C3'"],
|
|
1401
|
+
[" C5'", " C4'", " O4'"],
|
|
1402
|
+
[" C4'", " O4'", " C1'"],
|
|
1403
|
+
[" C2'", " C1'", " N9 "],
|
|
1404
|
+
[" C4'", " C3'", " O3'"],
|
|
1405
|
+
], # DA
|
|
1406
|
+
[
|
|
1407
|
+
[" O4'", " C1'", " C2'"],
|
|
1408
|
+
[" OP1", " P ", " O5'"],
|
|
1409
|
+
[" P ", " O5'", " C5'"],
|
|
1410
|
+
[" O5'", " C5'", " C4'"],
|
|
1411
|
+
[" C5'", " C4'", " C3'"],
|
|
1412
|
+
[" C5'", " C4'", " O4'"],
|
|
1413
|
+
[" C4'", " O4'", " C1'"],
|
|
1414
|
+
[" C2'", " C1'", " N1 "],
|
|
1415
|
+
[" C4'", " C3'", " O3'"],
|
|
1416
|
+
], # DC
|
|
1417
|
+
[
|
|
1418
|
+
[" O4'", " C1'", " C2'"],
|
|
1419
|
+
[" OP1", " P ", " O5'"],
|
|
1420
|
+
[" P ", " O5'", " C5'"],
|
|
1421
|
+
[" O5'", " C5'", " C4'"],
|
|
1422
|
+
[" C5'", " C4'", " C3'"],
|
|
1423
|
+
[" C5'", " C4'", " O4'"],
|
|
1424
|
+
[" C4'", " O4'", " C1'"],
|
|
1425
|
+
[" C2'", " C1'", " N9 "],
|
|
1426
|
+
[" C4'", " C3'", " O3'"],
|
|
1427
|
+
], # DG
|
|
1428
|
+
[
|
|
1429
|
+
[" O4'", " C1'", " C2'"],
|
|
1430
|
+
[" OP1", " P ", " O5'"],
|
|
1431
|
+
[" P ", " O5'", " C5'"],
|
|
1432
|
+
[" O5'", " C5'", " C4'"],
|
|
1433
|
+
[" C5'", " C4'", " C3'"],
|
|
1434
|
+
[" C5'", " C4'", " O4'"],
|
|
1435
|
+
[" C4'", " O4'", " C1'"],
|
|
1436
|
+
[" C2'", " C1'", " N1 "],
|
|
1437
|
+
[" C4'", " C3'", " O3'"],
|
|
1438
|
+
], # DT
|
|
1439
|
+
[
|
|
1440
|
+
[" O4'", " C1'", " C2'"],
|
|
1441
|
+
[" OP1", " P ", " O5'"],
|
|
1442
|
+
[" P ", " O5'", " C5'"],
|
|
1443
|
+
[" O5'", " C5'", " C4'"],
|
|
1444
|
+
[" C5'", " C4'", " C3'"],
|
|
1445
|
+
[" C5'", " C4'", " O4'"],
|
|
1446
|
+
[" C4'", " O4'", " C1'"],
|
|
1447
|
+
[" C4'", " C3'", " O3'"],
|
|
1448
|
+
], # DX
|
|
1449
|
+
[
|
|
1450
|
+
[" O4'", " C1'", " C2'"],
|
|
1451
|
+
[" OP1", " P ", " O5'"],
|
|
1452
|
+
[" P ", " O5'", " C5'"],
|
|
1453
|
+
[" O5'", " C5'", " C4'"],
|
|
1454
|
+
[" C5'", " C4'", " C3'"],
|
|
1455
|
+
[" C5'", " C4'", " O4'"],
|
|
1456
|
+
[" C4'", " O4'", " C1'"],
|
|
1457
|
+
[" C2'", " C1'", " N9 "],
|
|
1458
|
+
[" C4'", " C3'", " O3'"],
|
|
1459
|
+
], # A
|
|
1460
|
+
[
|
|
1461
|
+
[" O4'", " C1'", " C2'"],
|
|
1462
|
+
[" OP1", " P ", " O5'"],
|
|
1463
|
+
[" P ", " O5'", " C5'"],
|
|
1464
|
+
[" O5'", " C5'", " C4'"],
|
|
1465
|
+
[" C5'", " C4'", " C3'"],
|
|
1466
|
+
[" C5'", " C4'", " O4'"],
|
|
1467
|
+
[" C4'", " O4'", " C1'"],
|
|
1468
|
+
[" C2'", " C1'", " N1 "],
|
|
1469
|
+
[" C4'", " C3'", " O3'"],
|
|
1470
|
+
], # C
|
|
1471
|
+
[
|
|
1472
|
+
[" O4'", " C1'", " C2'"],
|
|
1473
|
+
[" OP1", " P ", " O5'"],
|
|
1474
|
+
[" P ", " O5'", " C5'"],
|
|
1475
|
+
[" O5'", " C5'", " C4'"],
|
|
1476
|
+
[" C5'", " C4'", " C3'"],
|
|
1477
|
+
[" C5'", " C4'", " O4'"],
|
|
1478
|
+
[" C4'", " O4'", " C1'"],
|
|
1479
|
+
[" C2'", " C1'", " N9 "],
|
|
1480
|
+
[" C4'", " C3'", " O3'"],
|
|
1481
|
+
], # G
|
|
1482
|
+
[
|
|
1483
|
+
[" O4'", " C1'", " C2'"],
|
|
1484
|
+
[" OP1", " P ", " O5'"],
|
|
1485
|
+
[" P ", " O5'", " C5'"],
|
|
1486
|
+
[" O5'", " C5'", " C4'"],
|
|
1487
|
+
[" C5'", " C4'", " C3'"],
|
|
1488
|
+
[" C5'", " C4'", " O4'"],
|
|
1489
|
+
[" C4'", " O4'", " C1'"],
|
|
1490
|
+
[" C2'", " C1'", " N1 "],
|
|
1491
|
+
[" C4'", " C3'", " O3'"],
|
|
1492
|
+
], # U
|
|
1493
|
+
[
|
|
1494
|
+
[" O4'", " C1'", " C2'"],
|
|
1495
|
+
[" OP1", " P ", " O5'"],
|
|
1496
|
+
[" P ", " O5'", " C5'"],
|
|
1497
|
+
[" O5'", " C5'", " C4'"],
|
|
1498
|
+
[" C5'", " C4'", " C3'"],
|
|
1499
|
+
[" C5'", " C4'", " O4'"],
|
|
1500
|
+
[" C4'", " O4'", " C1'"],
|
|
1501
|
+
[" C4'", " C3'", " O3'"],
|
|
1502
|
+
], # RX
|
|
1503
|
+
]
|
|
1504
|
+
# fmt: on
|
|
1505
|
+
NFRAMES = max([len(f) for f in frames])
|
|
1506
|
+
|
|
1507
|
+
# general FAPE parameters
|
|
1508
|
+
frame_indices = torch.full((NAATOKENS, NFRAMES, 3, 2), 0, dtype=torch.long)
|
|
1509
|
+
for i in range(NNAPROTAAS):
|
|
1510
|
+
i_l = aa2long[i]
|
|
1511
|
+
for j, x in enumerate(frames[i]):
|
|
1512
|
+
if x is not None:
|
|
1513
|
+
# frames are stored as (residue offset, atom position)
|
|
1514
|
+
frame_indices[i, j, 0] = torch.tensor((0, i_l.index(x[0])))
|
|
1515
|
+
frame_indices[i, j, 1] = torch.tensor((0, i_l.index(x[1])))
|
|
1516
|
+
frame_indices[i, j, 2] = torch.tensor((0, i_l.index(x[2])))
|
|
1517
|
+
|
|
1518
|
+
|
|
1519
|
+
allatom_mask = torch.zeros((NAATOKENS, NTOTAL), dtype=torch.bool)
|
|
1520
|
+
long2alt = torch.zeros((NAATOKENS, NTOTAL), dtype=torch.long)
|
|
1521
|
+
for i in range(NNAPROTAAS):
|
|
1522
|
+
for j, a in enumerate(aa2long[i]):
|
|
1523
|
+
if a is not None:
|
|
1524
|
+
allatom_mask[i, j] = True
|
|
1525
|
+
|
|
1526
|
+
allatom_mask[NNAPROTAAS:, 1] = True
|
|
1527
|
+
allatom_mask[:, 1] = True
|
|
1528
|
+
heavyatom_mask = allatom_mask.clone()
|
|
1529
|
+
heavyatom_mask[:, NHEAVY:] = False
|