Collections:
"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command?
✍: FYIcenter.com
If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command.
For example, the following command generate a ball and stick depiction of of the tyrosine molecule in SVG format:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-ball-stick.svg -xS 1 molecule converted
As a comparison, running the following command generates a normal skeleton depiction of of the same molecule in SVG format:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-skeleton.svg 1 molecule converted
Open both output files, tyrosine-skeleton.svg and tyrosine-ball-stick.svg, in a Web browser, you see the differences:
Note that "-xS" option was added in Open Babel 2.4 for SVG format.
⇒ "babel ... -o svg -xX" - Hide Implicit H in SVG
⇐ "babel ... -o svg -xi" - Show Atom Indices in SVG
2020-07-15, 860🔥, 0💬
Popular Posts:
What Is Molecular Formula? A Molecule Formula is an expression of element symbols and numbers of ato...
Molecule Summary: ID: FYI-1002255 Names: InChIKey: AHDDXXVFDWAUGA-UHFFFAOYS A-NSMILES: CCc1cc(O)c8c6...
Molecule Summary: ID: FYI-1001997 SMILES: CCCCCCCCCCCOC(=O)CCCCCN( CCCCCCCC(=O)OC(CCCCCCCC) CCCCCCCC)C...
How to get help information on Open Babel Fingerprints? You can use the "babel -H fpt" command to ge...
Molecule Summary: ID: FYI-1002257 Names: InChIKey: AVYKQOAMZCAHRG-UHFFFAOYS A-NSMILES: CCO[Si](CCC(F...