Collections:
"babel -d" Command - Delete Hydrogens from Molecule Data
How to delete hydrogen atoms from molecule data during data conversion?
✍: FYIcenter.com
If hydrogen atoms of a molecule are included in the input data source,
you can use the "babel" generic option "-d" remove those hydrogen atoms
during the molecule data conversion process.
Here is an example of using the "-d" option in the "babel" command.
1. Generate a benzene molecule with hydrogen atoms included and stored in a "sdf" file.
fyicenter$ obabel -:c1ccccc1 -o sdf -O benzene.sdf --gen2D -h 1 molecule converted fyicenter$ more benzene.sdf OpenBabel05212009392D 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 $$$$
2. Convert the benzene molecule from "sdf" format to "svg" format with hydrogen atoms deleted using the "-d" option:
fyicenter$ babel benzene.sdf -o svg -d <?xml version="1.0"?> <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cml="http://www.xml-cml.org/schema" width="149.283" height="159.999" x="0" y="0" font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="1" stroke-linecap="round"> <rect x="0%" y="0%" width="100%" height="100%" stroke-width="0" fill="rgb(255,255,255)" /> <line x1="74.6" y1="120.0" x2="40.0" y2="100.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="73.0" y1="110.8" x2="48.8" y2="96.8" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="40.0" y1="100.0" x2="40.0" y2="60.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="40.0" y1="60.0" x2="74.6" y2="40.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="48.8" y1="63.2" x2="73.0" y2="49.2" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="74.6" y1="40.0" x2="109.3" y2="60.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="109.3" y1="60.0" x2="109.3" y2="100.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="102.1" y1="66.0" x2="102.1" y2="94.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="109.3" y1="100.0" x2="74.6" y2="120.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <text font-size="18.000000" fill ="black" font-family="sans-serif" x="10.000000" y="20.000000" ></text> <title> - OBDepict</title> </svg>
As you can see from the output, 6 hydrogen atoms were deleted from the benzene molecule, because of the "-d" option.
As a comparison, here is the output of the above "babel" command without the "-d" option:
fyicenter$ babel benzene.sdf -o svg <?xml version="1.0"?> <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cml="http://www.xml-cml.org/schema" width="218.564" height="240.001" x="0" y="0" font-family="sans-serif" stroke="rgb(0,0,0)" stroke-width="1" stroke-linecap="round"> <rect x="0%" y="0%" width="100%" height="100%" stroke-width="0" fill="rgb(255,255,255)" /> <line x1="109.3" y1="159.4" x2="109.3" y2="187.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="75.2" y1="139.7" x2="51.3" y2="153.5" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="75.2" y1="100.3" x2="51.3" y2="86.5" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="109.3" y1="80.6" x2="109.3" y2="53.0" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="143.4" y1="100.3" x2="167.3" y2="86.5" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="143.4" y1="139.7" x2="167.3" y2="153.5" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="109.3" y1="159.4" x2="75.2" y2="139.7" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="107.7" y1="150.1" x2="84.0" y2="136.4" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="75.2" y1="139.7" x2="75.2" y2="100.3" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="75.2" y1="100.3" x2="109.3" y2="80.6" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="84.0" y1="103.6" x2="107.7" y2="89.9" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="109.3" y1="80.6" x2="143.4" y2="100.3" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="143.4" y1="100.3" x2="143.4" y2="139.7" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="136.2" y1="106.3" x2="136.2" y2="133.7" stroke="rgb(0,0,0)" stroke-width="1.0"/> <line x1="143.4" y1="139.7" x2="109.3" y2="159.4" stroke="rgb(0,0,0)" stroke-width="1.0"/> <text x="103.283733" y="208.000619" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text x="34.000000" y="168.000464" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text x="34.000000" y="88.000155" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text x="103.283733" y="48.000000" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text x="172.563528" y="88.000155" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text x="172.563528" y="168.000464" fill="rgb(191,191,191)" stroke="rgb(191,191,191)" stroke-width="1" font-size="16" >H</text> <text font-size="18.000000" fill ="black" font-family="sans-serif" x="10.000000" y="20.000000" ></text> <title> - OBDepict</title> </svg>
⇒ "babel --append ..." Command - Calculate Molecule Properties
⇐ "babel -h" Command - Add Hydrogens to Molecule Data
2020-07-15, 575👍, 0💬
Popular Posts:
Molecule Summary: ID: FYI-1000186 SMILES: CCC/C=C/C=O Received at FYIcenter.com on: 2020-11-09
Molecule Summary: ID: FYI-1000180 SMILES: O=C1N[C@H](C)CNC2=C1SC(C =C3)=C2C4=C3N=C(OC5=NC(C l)=NC=C5CO...
How to download and install PyMol Open Source edition on macOS? If you want to try the open source e...
Where to find FAQ (Frequently Asked Questions) on running Open Babel on CentOS? Here is a list of tu...
How to perform exact match in fastsearch index file using a "babel" command? If you want to perform ...