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"babel -i sdf -o svg" - Custom Atom Positions
How to create a molecule structure with custom atom positions?
✍: FYIcenter.com
You can create a molecule structure
with custom atom positions using "obabel -i sdf -o svg" command
as shown below.
1. Create a SDF file for your molecule structure. Take the L-Alanin-2D.sdf file used in other tutorials as an example.
2. Edit the SDF file by changing the coordinates of the 3rd and 5th atoms.
L-Alanin - Stretched FYICenter.com 2D Stereoinformation: Stereo Code 6 5 0 0 1 0 0 0 0 0999 V2000 3.6373 2.1000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.4249 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4249 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2124 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2124 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 3 2 1 0 0 0 0 4 2 1 0 0 0 0 5 4 2 0 0 0 0 6 4 1 0 0 0 0 M END
3. Generate the SVG diagram with "obabel -i sdf -o svg" command.
fyicenter$ obabel L-Alanin-2D.sdf -O output.svg -xd
4. View output.svg, you will see a molecule diagram with 2 atoms stretched out.
⇒ "babel ... -o svg" - Two "svg" Tag Levels
⇐ "babel ... -o svg -xC" - Hide Terminal C in SVG
2021-12-01, 1262👍, 0💬
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