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Bug: Inconsistent n0res in OUT and OUT2 files for complex with ipSAE=0 #15

@liuqqq2019

Description

@liuqqq2019

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

  1. Run the script with a complex of chain A and chain B where ipSAE=0.
  2. 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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