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

Q

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

A

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

⇒ "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

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What options can I use when generating SVG pictures from molecule input data? You can see a list of options supported by Open Babel when generating SVG pictures from molecule input data by running the "babel -H svg" command: fyicenter$ babel -V Open Babel 2.4.1 fyicenter$ babel -H svg svg SVG 2D dep... 2021-07-19, 1545🔥, 0💬

"babel -s ..." Command - Substructure Search
How to use "babel -s ..." command to do substructure search? You can do substructure search using the "-s ..." option of the "babel" command with the following syntax: babel input_section output_section -s smarts_string The smarts_string specifies a SMARTS string that represents a molecule pattern. ... 2020-06-08, 1541🔥, 0💬

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How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp... 2020-07-15, 1481🔥, 0💬

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