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Preserve user-supplied templates in batched MMseqs2-GPU path #25

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Preserve user-supplied templates in batched MMseqs2-GPU path #25

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Preserve user-supplied templates in batched MMseqs2-GPU path
seanwangsalad May 20, 2026
34d788a
Preserve user-supplied templates in batched MMseqs2-GPU path
seanwangsalad May 20, 2026
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5 changes: 4 additions & 1 deletion src/alphafold3/data/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1709,12 +1709,15 @@ def process_batch(
for hit, struc in template_hits.get_hits_with_structures()
]

# Preserve any user-supplied templates from the input JSON.
user_templates = list(chain.templates) if chain.templates else []

# Get Foldseek templates and merge
foldseek_tmpls = self._get_foldseek_templates(
chain.sequence
)
templates = self._merge_templates(
pdb_templates, foldseek_tmpls
user_templates + pdb_templates, foldseek_tmpls
)

processed_chain = folding_input.ProteinChain(
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