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Fix IndexError in kaggle_submission.py for sequences exceeding max_length #11

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drqsatoshi merged 2 commits into from
Jan 31, 2026
Merged

Fix IndexError in kaggle_submission.py for sequences exceeding max_length #11

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Copilot Jan 31, 2026
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Fix IndexError for sequences longer than max_length in kaggle_submiss…
Copilot Jan 31, 2026
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4 changes: 2 additions & 2 deletions kaggle_submission.py
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@drqsatoshi drqsatoshi Jan 31, 2026

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def create_submission(predictions, output_path, num_structures=5):
"""
Create submission file from predictions.

Args:
    predictions: dict with 'coords' (N, L, num_structures, 3) and 'sequences'
    output_path: path to save submission.csv
    num_structures: number of structures to predict (default 5)
"""
coords = predictions['coords']  # Expected shape: (num_seq, max_len, num_struct, 3)
sequences = predictions['sequences']

rows = []
residue_idx = 0

for seq_idx in range(len(sequences)):
    seq = sequences[seq_idx]
    for pos, nucleotide in enumerate(seq):
        row = {
            'id': residue_idx,
            'resname': nucleotide,
            'resid': pos + 1
        }
        
        # Add coordinates for each structure
        for struct_idx in range(num_structures):
            x, y, z = coords[seq_idx, pos, struct_idx, :]
            
            row[f'x_{struct_idx + 1}'] = x
            row[f'y_{struct_idx + 1}'] = y
            row[f'z_{struct_idx + 1}'] = z
        
        rows.append(row)
        residue_idx += 1

df = pd.DataFrame(rows)
df.to_csv(output_path, index=False)
print(f"Saved submission to {output_path}")
return df

Original file line number Diff line number Diff line change
Expand Up @@ -150,9 +150,9 @@ def predict_structures(

# Store predictions
for j, (idx, row) in enumerate(batch_df.iterrows()):
seq_len = len(row['sequence'])
seq_len = min(len(row['sequence']), max_length)
target_id = row['target_id']
sequence = row['sequence']
sequence = row['sequence'][:max_length] # Truncate sequence to max_length
Comment on lines +153 to +155
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Copilot AI Jan 31, 2026

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This change fixes the IndexError for sequences longer than max_length, but there is no automated test covering the case where len(row['sequence']) > max_length for the predict_structures → create_submission pipeline; adding a regression test that constructs a sequence longer than max_length and asserts that submission generation completes without index errors (and that only the first max_length residues are emitted) would help prevent this bug from reappearing.

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coords = pred_coords[j, :seq_len, :, :]

predictions.append({
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