Signature Cavities & Channels in Cavitracer - #2267
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August 11, 2026 21:55
…e detection Superpose homologous structures onto a reference via ProDy's own CE-align, auto-discover homologues via DALI when none are given, and compute a consensus signature cavity/channel across the ensemble. The reference is colored by per-residue Shannon entropy, computed either from an auto-built MSA or a user-supplied one (msa_fasta). DALI's discovery filter cutoffs are overridable via dali_filter_kwargs. 18 tests in prody/tests/proteins/test_channels.py, all local-fixture-seeded (no network required).
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Added calcSignatureCavities/calcSignatureChannels for ensemble signature detection.
It would superpose homologous structures onto a reference via ProDy's own CE-align, auto-discover homologues via DALI when none are given, and compute a consensus signature cavity/channel across the ensemble mapped onto of the reference. The reference is colored by per-residue Shannon entropy, computed either from an auto-built MSA or a user-supplied one (msa_fasta). DALI's discovery filter cutoffs are overridable via dali_filter_kwargs.
prody/tests/proteins/test_channels.py