| """Export chemistry-preserving AlphaFold 3 jobs and parse confidence records.""" |
| from __future__ import annotations |
| from .schema import Molecule, Target |
|
|
|
|
| def af3_input(name: str, proteins: list[Target], peptide: Molecule, seeds=(2027,2028,2029)): |
| if peptide.n_terminus!="free" or peptide.c_terminus!="free": |
| raise ValueError("terminal chemistry requires explicit CCD residues before AF3 export") |
| molecules=[t.molecule for t in proteins]+[peptide] |
| if len(molecules)>26:raise ValueError("too many chains") |
| sequences=[];bonds=[] |
| for index,mol in enumerate(molecules): |
| if mol.n_terminus!="free" or mol.c_terminus!="free": |
| raise ValueError("unencoded terminal chemistry") |
| chain=chr(65+index) |
| entry={"id":chain,"sequence":mol.sequence} |
| if mol.modifications: |
| entry["modifications"]=[{"ptmType":m.ccd,"ptmPosition":m.position} for m in mol.modifications] |
| sequences.append({"protein":entry}) |
| for i,ai,j,aj in mol.bonds:bonds.append([[chain,i,ai],[chain,j,aj]]) |
| result={"name":name,"modelSeeds":list(seeds),"sequences":sequences,"dialect":"alphafold3","version":3} |
| if bonds:result["bondedAtomPairs"]=bonds |
| return result |
|
|
|
|
| def ternary_interface_features(chain_pair_iptm, peptide_index=2): |
| """Retain both peptide interfaces; the weaker interface is the bottleneck.""" |
| import numpy as np |
| a=np.asarray(chain_pair_iptm,float) |
| if a.shape!=(3,3) or peptide_index not in range(3):raise ValueError("expected three-chain matrix") |
| others=[i for i in range(3) if i!=peptide_index] |
| vals=[float(a[peptide_index,i]) for i in others] |
| if not all(np.isfinite(vals)):raise ValueError("missing interface confidence") |
| return {"peptide_partner_1":vals[0],"peptide_partner_2":vals[1],"weakest_interface":min(vals)} |
|
|
