Bug fix: resolved the issue where some identical chains in a homo-oli…#140
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yx0516 wants to merge 1 commit intoHannesStark:mainfrom
Open
Bug fix: resolved the issue where some identical chains in a homo-oli…#140yx0516 wants to merge 1 commit intoHannesStark:mainfrom
yx0516 wants to merge 1 commit intoHannesStark:mainfrom
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…gomeric structure were ignored during design.
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When designing specific residues in a known homooligomer, the pipeline occasionally outputs a structure that contains only one copy of the identical chains, triggering an error.
For example, the below structure has five chains: A, B, C, D, E, where A, B and C form a homooligomer. After the first design step, the returned model keeps only chains A, D and E, while chains B and C are silently dropped. The resulting error message is as follows:
File "/data/PRG/tools/boltz/apps/boltzgen/src/boltzgen/task/predict/data_from_generated.py", line 321, in getitem_from_paths
feat = self.get_feat(generated_path, design_mask, ss_type, binding_type)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/PRG/tools/boltz/apps/boltzgen/src/boltzgen/task/predict/data_from_generated.py", line 379, in get_feat
design_chains = np.unique(asym_id[chain_design_mask])
~~~~~~~^^^^^^^^^^^^^^^^^^^
IndexError: boolean index did not match indexed array along axis 0; size of axis is 391 but size of corresponding boolean axis is 715
The yaml file are as following:
design_spec.yaml
The reason is that: in the parse_pdb function (src/boltzgen/data/parse/pdb_parser.py), label_seq was assigned only to the first sub-chain (chain A) of an entity, while the remaining identical sub-chains (B and C) were left without label_seq.
After adding the corresponding fix, the issue was resolved.