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Parity and Stereo with Open Babel
Cam Open Babel support stereoinformation represented by the Parity Code and Stereo Code in SDF/Mol files?
✍: Guest
Yes. Open Babel can support stereoinformation represented by the Parity Code and Stereo Code
in SDF/Mol files.
But you should use Open Babel 2.4.1 and newer versions. Open Babel 2.3.1 seems to have a bug that reads the Stereo Code incorrectly. See the difference of two SVG diagrams generated by Open Babel 2.4.1 (left) and Open Babel 2.3.1 (right).
new$ obabel -V Open Babel 2.4.1 -- May 25 2020 -- 08:24:13 fyicenter$ obabel L-Alanine.sdf -o svg -O L1.svg -xi --title "v2.4.1" old$ obabel -V Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:48 fyicenter$ obabel L-Alanine.sdf -o svg -O L2.svg -xi --title "v2.3.1"
As you can see, Open Babel 2.3.1 shows the wedge on bond #1, but the stereo code is given on bond #2 in the SDF/Mol file, L-Alanine.sdf:
fyicenter$ cat L-Alanine.sdf L-Alanine CTFile Formats, 2003 123456789012345678901234567890123456789012345678901234567890 6 5 0 0 1 0 3 V2000 -0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 1 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 1 2 1 0 0 0 1 3 1 1 0 0 1 4 1 0 0 0 2 5 2 0 0 0 2 6 1 0 0 0 M CHG 2 4 1 6 -1 M ISO 1 3 13 M END
We can see the same bug in Open Babel 2.3.1, when writing the stereoinformation to SDF/MOl files. The Stereo code is written incorrectly on bond #1 instead of #2.
old$ obabel -V Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:48 old$ obabel L-Alanine.sdf -o sdf L-Alanine OpenBabel02032111492D 123456789012345678901234567890123456789012345678901234567890 6 5 0 0 1 0 0 0 0 0999 V2000 -0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 1 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 2 5 2 0 0 0 0 2 6 1 0 0 0 0 M ISO 1 3 13 M CHG 2 4 1 6 -1 M END $$$$ 1 molecule converted
With Open Babel 2.4.1, the bug is fixed.
new$ obabel -V Open Babel 2.4.1 -- May 25 2020 -- 08:24:13 new$ obabel L-Alanine.sdf -o sdf L-Alanine OpenBabel02032111482D 123456789012345678901234567890123456789012345678901234567890 6 5 0 0 1 0 0 0 0 0999 V2000 -0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 1 0 0 0 1 4 1 0 0 0 0 2 5 2 0 0 0 0 2 6 1 0 0 0 0 M ISO 1 3 13 M CHG 2 4 1 6 -1 M END $$$$ 1 molecule converted
⇒ Open Babel Options on SDF/Mol Files
⇐ Stereoinformation Presentation in SDF/Mol File
2021-03-07, 432👍, 0💬
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