Collections:
"babel -h" Command - Add Hydrogens to Molecule Data
How to add hydrogen atoms to molecule data during data conversion?
✍: FYIcenter.com
Most molecules contains many hydrogen atoms.
When molecules are written in many data formats, those hydrogen atoms are
removed. We normally can read molecule structure without hydrogen atoms.
But if you want to add those removed hydrogen atoms back during the molecule data conversion process, you can use the "babel" generic option "-h" as shown in the example below:
fyicenter$ obabel -:c1ccccc1 -o sdf --gen2D -h OpenBabel05212009372D 12 12 0 0 0 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5320 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6258 -0.5160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6258 1.5160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5320 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8937 1.5160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8937 -0.5160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 1 2 2 0 0 0 0 1 7 1 0 0 0 0 2 3 1 0 0 0 0 2 8 1 0 0 0 0 3 4 2 0 0 0 0 3 9 1 0 0 0 0 4 5 1 0 0 0 0 4 10 1 0 0 0 0 5 6 2 0 0 0 0 5 11 1 0 0 0 0 6 12 1 0 0 0 0 M END $$$$ 1 molecule converted
As you can see from the output, 6 hydrogen atoms were added back to the benzene molecule, because of the "-h" option. Without the "-h" option, "babel" command converts only carbon atoms of the benzene molecule that are specified in the input SMILES string.
As a comparison, here is the output of the above "babel" command without the "-h" option:
fyicenter$ obabel -:c1ccccc1 -o sdf --gen2D OpenBabel05212009382D 6 6 0 0 0 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 M END $$$$ 1 molecule converted
⇒ "babel -d" Command - Delete Hydrogens from Molecule Data
⇐ "babel ... -f # -l #" - Split Large Molecule File
2020-07-15, 1270👍, 0💬
Popular Posts:
Where to find molecule FAQ (Frequently Asked Questions)? I want to learn more about molecules. Here ...
How to convert SMILES to SDF/Mol file and view the molecule 2D or 3D structure? To help you converti...
What Is Molecular Formula? A Molecule Formula is an expression of element symbols and numbers of ato...
How to build my own JSME editor Web Page? If you want to build your Web page and offer JSME as a mol...
Where to find FAQ (Frequently Asked Questions) on JSME JavaScript API? Here is a list of tutorials t...