mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 22:34:26 +08:00
fc41c1a5eb
- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches - Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features - Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/ - Keep templates enabled; test test__chopped_dimer now passes
58 lines
1.2 KiB
JSON
58 lines
1.2 KiB
JSON
{
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"dialect": "alphafold3",
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"version": 1,
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"name": "test_complex",
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"modelSeeds": [42],
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"sequences": [
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{
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"protein": {
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"id": "A",
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"sequence": "MESAIAEGGASRFSASSGGGGSRGAPQHYPKTAGNSEFLGKTPGQNAQKWIPARSTRRDDNSAA",
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"modifications": [
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{"ptmType": "HY3", "ptmPosition": 1},
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{"ptmType": "P1L", "ptmPosition": 5}
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],
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"unpairedMsa": null,
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"pairedMsa": null,
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"templates": []
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}
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},
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{
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"dna": {
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"id": "B",
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"sequence": "GATTACA",
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"modifications": [
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{"modificationType": "6OG", "basePosition": 1},
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{"modificationType": "6MA", "basePosition": 2}
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]
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}
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},
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{
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"rna": {
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"id": "C",
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"sequence": "AGCU",
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"modifications": [
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{"modificationType": "2MG", "basePosition": 1},
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{"modificationType": "5MC", "basePosition": 4}
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]
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}
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},
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{
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"ligand": {
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"id": "D",
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"ccdCodes": ["ATP"]
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}
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},
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{
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"ligand": {
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"id": "E",
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"ccdCodes": ["HEM"]
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}
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}
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],
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"bondedAtomPairs": [
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[["A", 1, "CA"], ["D", 1, "CHA"]],
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[["A", 5, "SG"], ["E", 1, "C04"]]
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],
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"userCCD": null
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} |