Add iLIS interface score (sqrt(LIS × cLIS), AFM-LIS)

[DimaMolod]

Summary

Adds the iLIS interface score (integrated Local Interaction Score; Kim et al., AFM-LIS — github.com/flyark/AFM-LIS) to AlphaJudge.

iLIS = √(LIS × cLIS), where:

• LIS (already in AlphaJudge) = the (12 − PAE)/12 confidence transform averaged over inter-chain residue pairs with PAE < 12 Å.
• cLIS (new) = the same transform averaged only over residue pairs that are also in direct physical contact (representative atom CB-else-CA, within contact_thresh; default 8 Å, matching AFM-LIS's Cβ–Cβ ≤ 8 Å).
• The geometric mean forces the score to 0 unless an interface has both broad PAE confidence and confident direct contacts.

cLIS reuses the existing Interface contact set (_pairs), so no new geometry/IO is introduced. Both chain directions are averaged, mirroring the existing lis().

Changes

• src/alphajudge/interface.py: new Interface.clis() and Interface.ilis().
• src/alphajudge/runner.py: emit interface_cLIS and interface_iLIS in the per-run CSV (next to interface_LIS).
• test/test_parsers_and_runner.py: add both columns to the expected output schema + a deterministic test_clis_ilis_math_is_deterministic.

Validation

Cross-checked against the official AFM-LIS lis.py on benchmark dimers — LIS, cLIS and iLIS agree to 4 decimal places:

Dimer (E. coli, AF2 best model)	LIS	cLIS	iLIS
P0ACD8+P69741	0.7467	0.8980	0.8189
P18775+P18776	0.6444	0.8921	0.7582

(official vs AlphaJudge identical at 4 dp; cLIS differs only ~2e-5, from the strict <8 Å vs inclusive ≤8 Å contact boundary.)

Not added to the frozen interface metascore — kept as a standalone score.

🤖 Generated with Claude Code