"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command?
If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command.
Here is how the "-xX" option is described in Open Babel help document: "X - All atoms are explicitly declared. Useful if we don't want any extra hydrogens drawn to fill the valence."
For example, the following command generate a SVG picture with no implicit hydrogen symbols for the tyrosine molecule:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-no-hydrogen.svg -xX 1 molecule converted
As a comparison, running the following command generates a SVG picture with implicit hydrogen symbols of the same molecule:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.svg 1 molecule converted
Open both output files, tyrosine.svg and tyrosine-no-hydrogen.svg, in a Web browser, you see the differences:
Note that "-xX" option was added in Open Babel 2.4 for SVG format.
⇒ "babel ... -o svg -xC" - Hide Terminal C in SVG
⇐ "babel ... -o svg -xS" - Ball/Stick Depiction in SVG
⇑ "babel ... -o svg" - Generating SVG Pictures
2020-07-22, 780👍, 0💬
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