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Open Babel Options on SDF/Mol Files
What options are offered in Parity Code to support stereoinformation in SDF/Mol V2000 and V3000 files generated by Open Babel?
✍: Guest
Here is the documentation of Open Babel 2.4.1 with options
listed to support stereoinformation in SDF/Mol V2000 and V3000 files:
fyicenter$ obabel -V Open Babel 2.4.1 -- May 25 2020 -- 08:24:13 fyicenter$ obabel -L sdf One of the formats sdf -- MDL MOL format Reads and writes V2000 and V3000 versions Open Babel supports an extension to the MOL file standard that allows cis/trans and tetrahedral stereochemistry to be stored in 0D MOL files. The tetrahedral stereochemistry is stored as the atom parity, while the cis/trans stereochemistry is stored using Up and Down bonds similar to how it is represented in a SMILES string. Use the ``S`` option when reading or writing if you want to avoid storing or interpreting stereochemistry in 0D MOL files. Read Options, e.g. -as s determine chirality from atom parity flags The default setting for 2D and 3D is to ignore atom parity and work out the chirality based on the bond stereochemistry (2D) or coordinates (3D). For 0D the default is already to determine the chirality from the atom parity. S do not read stereochemistry from 0D MOL files Open Babel supports reading and writing cis/trans and tetrahedral stereochemistry to 0D MOL files. This is an extension to the standard which you can turn off using this option. T read title only P read title and properties only When filtering an sdf file on title or properties only, avoid lengthy chemical interpretation by using the ``T`` or ``P`` option together with the :ref:`copy format <Copy_raw_text>`. Write Options, e.g. -x3 3 output V3000 not V2000 (used for >999 atoms/bonds) a write atomclass if available m write no properties w use wedge and hash bonds from input (2D only) S do not store cis/trans stereochemistry in 0D MOL files A output in Alias form, e.g. Ph, if present E add an ASCII depiction of the molecule as a property H use HYD extension (always on if mol contains zero-order bonds)
As you can see, there are 4 options related to stereoinformation.
In order to test the "-as" option, we can create a new SDF/Mol file, L-Alanine-0D.sdf, for the L-Alanine with only 0D stereoinformation:
fyicenter$ cat L-Alanine-0D.sdf L-Alanine FYIcenter.com Stereoinformation in 0D only 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 0 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
Try Open Babel with "-as" option. 0D stereoinformation is detected and converted to 2D stereoinformation in the output. as stereo code in bond lines.
fyicenter$ obabel L-Alanine-0D.sdf -o sdf -as L-Alanine OpenBabel02032116592D Stereoinformation in 0D only 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 $$$$ 1 molecule converted
Try Open Babel without "-as" option. 0D stereoinformation is not detected and no 2D stereoinformation in the output. It also changed the parity code from "2 (even)" to "3 (either)". Could it be another bug?
fyicenter$ obabel L-Alanine-0D.sdf -o sdf L-Alanine OpenBabel02032116572D Stereoinformation in 0D only 6 5 0 0 1 0 0 0 0 0999 V2000 -0.6622 0.5342 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7207 2.0817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 2 5 2 0 0 0 0 2 6 1 0 0 0 0 M ISO 1 3 13 M CHG 2 4 1 6 -1 M END $$$$ 1 molecule converted
In order to test 3D stereoinformation, we can create a new SDF/Mol file, L-Alanine-3D.sdf, for the L-Alanine with only 3D stereoinformation. Notice that z=0.5000 is specified for atom #3, so it upward to the viewer.
fyicenter$ test]$ cat L-Alanine-3D.sdf L-Alanine FYIcenter.com Stereoinformation in 3D only 6 5 0 0 0 0 3 V2000 -0.6622 0.5342 0.0000 C 0 0 0 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 -0.7207 2.0817 0.5000 C 1 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 1 2 1 0 0 0 1 3 1 0 0 0 1 4 1 0 0 0 2 5 2 0 0 0 2 6 1 0 0 0 M CHG 2 4 1 6 -1 M ISO 1 3 13 M END
Try Open Babel with default options. 3D stereoinformation is detected and converted to both 0D and 2D stereoinformation in the output.
fyicenter$ obabel L-Alanine-3D.sdf -o sdf L-Alanine OpenBabel02032117233D Stereoinformation in 3D only 6 5 0 0 0 0 0 0 0 0999 V2000 -0.6622 0.5342 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6622 -0.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7207 2.0817 0.5000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8622 -0.3695 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 0.6220 -1.8037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9464 0.4244 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 1 0 0 0 1 4 1 0 0 0 0 2 5 2 0 0 0 0 2 6 1 0 0 0 0 M ISO 1 3 13 M CHG 2 4 1 6 -1 M END $$$$ 1 molecule converted
⇒ Stereoinformation in SDF/Mol V3000 Files
⇐ Parity and Stereo with Open Babel
2021-03-07, 2121🔥, 0💬
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