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Fix two verbose route oversights (#293)
* Update inputs.py * Update inputs.py
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alphafold3_pytorch/inputs.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2822,6 +2822,7 @@ def load_msa_from_msa_dir(
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# (since we don't have a precise mapping from AFDB UniProt accession IDs to PDB chain IDs), whereas for the original
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# PDB examples, we can directly identify the corresponding MSAs.
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msa_fpaths = []
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msa_fpath_pattern = ""
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if exists(msa_dir):
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msa_fpath_pattern = (
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os.path.join(msa_dir, f"{pdb_id.split('-assembly1')[0]}_*", "a3m", "*.a3m")
@@ -2880,7 +2881,7 @@ def load_msa_from_msa_dir(
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if chain_id not in msas:
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if verbose:
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logger.warning(
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f"Failed to load any MSAs for chain {chain_id} of file {file_id} due to: {e}. A dummy MSA will be installed for this chain."
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f"Failed to load any MSAs for chain {chain_id} of file {file_id}. A dummy MSA will be installed for this chain."
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)
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msas[chain_id] = dummy_msa
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@@ -2948,6 +2949,7 @@ def load_templates_from_templates_dir(
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# (since we don't have a precise mapping from AFDB UniProt accession IDs to PDB chain IDs),
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# whereas for the original PDB examples, we can directly identify the corresponding templates.
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template_fpaths = []
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template_fpath_pattern = ""
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if exists(templates_dir):
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template_fpath_pattern = (
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os.path.join(

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