"""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)}