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Description
Describe the bug
For a complex consisting of chain A and chain B with ipSAE=0, the n0res value is inconsistent across output files:
- In the OUT file, the asymmetric chain pair B→A reports a positive n0res.
- In the OUT2 file, all n0res values are 0, as expected.
Steps to reproduce
- Run the script with a complex of chain A and chain B where ipSAE=0.
- Observe the outputs:
- The OUT file shows a positive n0res for B→A.
- The OUT2 file shows n0res = 0 for all chain pairs.
Expected behavior
If ipSAE = 0, then n0res should be 0 for both asymmetric pairs A→B and B→A in the OUT file — consistent with the OUT2 file.
Proposed solution
Change this line (occurs twice):
valid_pairs_matrix = (chains == chain2) & (pae_matrix < pae_cutoff)
to:
valid_pairs_matrix = np.outer(chains == chain1, chains == chain2) & (pae_matrix < pae_cutoff)
This correction ensures the proper calculation of n0res even when ipSAE=0
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