Collections:
"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?
✍: FYIcenter.com
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
2020-07-22, 780👍, 0💬
Popular Posts:
How to Download and Install the latest version of JSME? You can follow this tutorial to download and...
How to convert Convert SDF to SVG (Scalable Vector Graphics) using "sdf2svg" PHP script? I want to s...
What are the differences between "babel" and "obabel" commands? "babel" and "obabel" commands are tw...
Molecule Summary: ID: FYI-1000172 SMILES: COc1cc(/C=C/c2cc(/C=C/c3 ccc(O)c(OC)c3)[nH]n2)ccc 1OReceive...
What Is "obenergy" command? How to use it to Calculate Molecule Energy? "obenergy" command is a comm...