File size: 5,021 Bytes
626e1aa | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | """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 # carbonyl oxygen: handled through the carbon rule
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 # nitrile N counted with its carbon
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))
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