"babel ... -o svg -xX" - Hide Implicit H in SVG

Q

How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command?

✍: FYIcenter.com

A

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 documebnt: "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:

Tyrosine Molecule without and with Hydrogen Symbols
Tyrosine Molecule without and with Hydrogen Symbols

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

⇑⇑ Open Babel Tutorials

2020-07-22, 328👍, 0💬