"babel ... -o svg -xi" - Show Atom Indices in SVG


How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string.

✍: FYIcenter.com


The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the order of atoms in the SMILES string.

For example, the following command generate a SVG picture of the tyrosine molecule from a SMILES string:

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o svg -O tyrosine-i.svg -xi

1 molecule converted

Open the output file, tyrosine-i.svg, in a Web browser, you see tyrosine molecule structure displayed with SMILES index number on each atom.

Open Babel SVG Picture - Tyrosine Molecule with Indeces
Open Babel SVG Picture - Tyrosine Molecule with Indeces


"babel ... -o svg -xS" - Ball/Stick Depiction in SVG

"obabel ... -o svg" Command - Generate SVG from SMILES

"babel ... -o svg" - Generating SVG Pictures

⇑⇑ Open Babel Tutorials

2021-02-04, 294👍, 0💬