BioPhi inputs and parameters
VH/VL sequences, mode, target humanness, and residues to preserve for BioPhi.
You provide a heavy-chain variable-region sequence (and optionally the light chain), and which BioPhi tool you call decides the mode: biophi_humanness only reads the sequence, while biophi_humanize and biophi_graft rewrite it. When you humanize with biophi_humanize, keeping binding-residue preservation on is your guardrail against breaking the binding site.
Sequences
vh_sequencestringrequiredHeavy-chain variable-region amino acid sequence.
vl_sequencestringLight-chain variable-region amino acid sequence.
Mode: which tool you call
toolstringdefault: biophi_humannessbiophi_humanness (score only), biophi_humanize (Sapiens deep-learning humanization), or biophi_graft (CDR grafting). Each calls the same backend with its mode fixed — there is no separate mode argument to set.
Humanization controls
These apply to biophi_humanize and biophi_graft.
target_humannessfloatdefault: 0.85Target humanness score to humanize toward (0.0–1.0). Accepted by both biophi_humanize and biophi_graft.
preserve_binding_residuesbooldefault: truebiophi_humanize only. Toggles whether known binding residues are held fixed during Sapiens humanization — it is an on/off switch, not a list of positions to name yourself. biophi_graft has no equivalent control.
Classification
oasis_percentile_thresholdfloatdefault: 80.0OASis percentile threshold for the humanness classification (0.0–100.0). Accepted by biophi_humanness and biophi_humanize; biophi_graft doesn't take it.
From a therapeutic name
All three tools also accept a therapeutic_name — name a known antibody and the platform resolves its VH/VL from Thera-SAbDab before scoring or humanizing.
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