Fix: correct n0res calculation for complexes with ipSAE=0 (#15) #16
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Description:
This PR addresses the inconsistency in n0res values reported in the OUT file versus the OUT2 file for complexes with ipSAE=0.
Problem:
For chain pairs in complexes where ipSAE=0, the OUT file reports a positive n0res value for the asymmetric chain pair B→A, while the OUT2 file correctly shows n0res = 0 for all pairs.
Solution:
Update the calculation of valid_pairs_matrix in two places by changing:
valid_pairs_matrix = (chains == chain2) & (pae_matrix < pae_cutoff)to
valid_pairs_matrix = np.outer(chains == chain1, chains == chain2) & (pae_matrix < pae_cutoff)This change ensures consistent n0res values when ipSAE=0.
Fixes: #15