| """Effective carbon number (ECN) for flame-ionisation-detector response, from a SMILES string. |
| |
| Rules after Scanlon & Willis, J. Chromatogr. Sci. 23 (1985) 333 (aliphatic/aromatic C 1.0, olefinic 0.95, |
| acetylenic 1.30, carbonyl C 0, nitrile C 0.3, ether O -1.0, primary/secondary/tertiary alcohol O |
| -0.6/-0.75/-0.25, ester single-bonded O -0.25, carboxylic-acid OH -0.6 treated like a primary alcohol, amine N |
| -0.6/-0.75/-0.25 by substitution, halogen on aliphatic C -0.12, on olefinic C +0.05). Atoms with no rule (S, P, |
| nitro N, ...) contribute 0. The result is an approximation of published response factors, so every consumer |
| tags it ``computed_ecn_scanlon_willis_1985``. |
| """ |
| from __future__ import annotations |
|
|
| from rdkit import Chem |
|
|
|
|
| def effective_carbon_number(smiles: str) -> dict: |
| mol = Chem.MolFromSmiles(smiles) |
| if mol is None: |
| raise ValueError(f"bad SMILES {smiles!r}") |
| total = 0.0 |
| detail: dict[str, float] = {} |
|
|
| def add(label: str, v: float): |
| nonlocal total |
| total += v |
| detail[label] = detail.get(label, 0.0) + v |
|
|
| for atom in mol.GetAtoms(): |
| z = atom.GetAtomicNum() |
| if z == 6: |
| nbrs = atom.GetNeighbors() |
| dbl_o = any(b.GetBondType() == Chem.BondType.DOUBLE and b.GetOtherAtom(atom).GetAtomicNum() == 8 for b in atom.GetBonds()) |
| triple_n = any(b.GetBondType() == Chem.BondType.TRIPLE and b.GetOtherAtom(atom).GetAtomicNum() == 7 for b in atom.GetBonds()) |
| if dbl_o: |
| add("carbonyl_C", 0.0) |
| elif triple_n: |
| add("nitrile_C", 0.3) |
| elif atom.GetIsAromatic(): |
| add("aromatic_C", 1.0) |
| elif any(b.GetBondType() == Chem.BondType.TRIPLE for b in atom.GetBonds()): |
| add("acetylenic_C", 1.30) |
| elif any(b.GetBondType() == Chem.BondType.DOUBLE and b.GetOtherAtom(atom).GetAtomicNum() == 6 for b in atom.GetBonds()): |
| add("olefinic_C", 0.95) |
| else: |
| add("aliphatic_C", 1.0) |
| elif z == 8: |
| if any(b.GetBondType() == Chem.BondType.DOUBLE for b in atom.GetBonds()): |
| continue |
| heavy = [n for n in atom.GetNeighbors() if n.GetAtomicNum() > 1] |
| if atom.GetTotalNumHs() == 1 and len(heavy) == 1: |
| c = heavy[0] |
| acid = any(b.GetBondType() == Chem.BondType.DOUBLE and b.GetOtherAtom(c).GetAtomicNum() == 8 for b in c.GetBonds()) |
| if acid: |
| add("acid_OH", -0.6) |
| elif c.GetIsAromatic(): |
| add("phenol_OH", -0.6) |
| else: |
| subs = sum(1 for n in c.GetNeighbors() if n.GetAtomicNum() == 6) |
| add({1: "primary_OH", 2: "secondary_OH"}.get(subs, "tertiary_OH"), {1: -0.6, 2: -0.75}.get(subs, -0.25)) |
| elif len(heavy) == 2: |
| ester = any(any(b.GetBondType() == Chem.BondType.DOUBLE and b.GetOtherAtom(c).GetAtomicNum() == 8 for b in c.GetBonds()) for c in heavy) |
| add("ester_O" if ester else "ether_O", -0.25 if ester else -1.0) |
| else: |
| add("other_O", 0.0) |
| elif z == 7: |
| if any(n.GetAtomicNum() == 8 for n in atom.GetNeighbors()): |
| add("nitro_N", 0.0) |
| elif any(b.GetBondType() == Chem.BondType.TRIPLE for b in atom.GetBonds()): |
| continue |
| elif atom.GetIsAromatic(): |
| add("aromatic_N", -0.6) |
| elif any(b.GetBondType() == Chem.BondType.DOUBLE for b in atom.GetBonds()): |
| add("imine_N", -0.6) |
| else: |
| heavy = sum(1 for n in atom.GetNeighbors() if n.GetAtomicNum() > 1) |
| amide = any(any(b.GetBondType() == Chem.BondType.DOUBLE and b.GetOtherAtom(n).GetAtomicNum() == 8 for b in n.GetBonds()) for n in atom.GetNeighbors() if n.GetAtomicNum() == 6) |
| if amide: |
| add("amide_N", -0.6) |
| else: |
| add({1: "primary_N", 2: "secondary_N"}.get(heavy, "tertiary_N"), {1: -0.6, 2: -0.75}.get(heavy, -0.25)) |
| elif z in (9, 17, 35, 53): |
| c = next((n for n in atom.GetNeighbors() if n.GetAtomicNum() == 6), None) |
| olefinic = c is not None and (c.GetIsAromatic() or any(b.GetBondType() == Chem.BondType.DOUBLE for b in c.GetBonds())) |
| add("halogen_on_olefinic_C" if olefinic else "halogen_on_aliphatic_C", 0.05 if olefinic else -0.12) |
| else: |
| add(f"no_rule_{atom.GetSymbol()}", 0.0) |
| n_carbon = sum(1 for a in mol.GetAtoms() if a.GetAtomicNum() == 6) |
| return {"ecn": round(max(total, 0.0), 3), "n_carbon": n_carbon, "contributions": {k: round(v, 3) for k, v in detail.items()}} |
|
|
|
|
| if __name__ == "__main__": |
| for s in ("CCCCCCC", "CCO", "CC(=O)O", "CCOC(=O)C", "c1ccccc1", "CC(C)=O", "ClC(Cl)Cl", "O"): |
| print(s, effective_carbon_number(s)) |
|
|
