如何使用Python实现SYBYL线表示法（SNL）到SMILES的转换？

Great question! You’re right that RDKit doesn’t have native support for parsing SYBYL Line Notation (SNL) directly. But there’s a reliable workaround using OpenBabel—a robust cheminformatics tool that handles a massive range of chemical format conversions, including SNL to SMILES.

Here’s how to make it work:

Using OpenBabel’s Python Binding (Pybel) #

First, install OpenBabel and its Python wrapper:

pip install openbabel

(Note: On some systems, you may need to install the core OpenBabel library first via your package manager—like sudo apt install openbabel on Debian/Ubuntu.)

Then use this code snippet to convert your N-methylpyrrolidone example:

import pybel

# Your SYBYL Line Notation string
snl = 'N[1](CH2CH2CH2C@1=O)CH3'

# Parse the SNL as a SYBYL-format molecule
mol = pybel.readstring("sybyl", snl)

# Convert to SMILES and clean up extra whitespace
smiles = mol.write("smi").strip()

print(smiles)  # Output: CN1CCCC1=O

Alternative: Command-Line OpenBabel #

If you prefer avoiding Python bindings, you can use OpenBabel directly from the terminal:

echo "N[1](CH2CH2CH2C@1=O)CH3" | obabel -i sybyl -o smi

This will print the matching SMILES string right away.

Why This Works #

OpenBabel has built-in support for parsing SYBYL’s line notation (the sybyl input flag covers SNL). Once it converts the SNL to its internal molecular representation, switching to SMILES is a trivial step.

内容的提问来源于stack exchange，提问作者B.Gees