| Re: Converting COD2020 to SDF [message #1198 is a reply to message #1196] |
Thu, 28 January 2021 15:36   |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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In case only a few structures are needed, and you are comfortable with the terminal / CLI you might consider the following:
Each COD dataset has its COD ID, a number which may be seen in DataWarrior and which may be used to
access the dataset e.g. on COD's text-based form https://www.crystallography.net/cod/search.html.
The entry «cif» on COD's listed results directs you to the structure's model data set, which you may store on your computer. Among the cod-tools (https://wiki.crystallography.net/cod-tools/) which you may obtain as an archive, or as a bundle package (e.g., Linux Debian, or Ubuntu) is the tool codcif2sdf for the CLI / terminal, which offers the conversion of COD's .cif into the .sdf file. To run successfully, you need OpenBabel which equally is freely available.
The output may be redirected into a permanent record, e.g. calling
codcif2sdf 1505213.cif > example.sdf
Both a COD cif as well its conversion into the .sdf of a typical entry are attached below.
In the past, the conversion a COD .cif into a .sdf only with OpenBabel often was not as good as with codcif2sdf. Alternatively, use a visual program capable to read and write both file formats (e.g., Jmol, or CCDC's Mercury)
Norwid
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Attachment: 1505213.cif
(Size: 13.27KB, Downloaded 374 times)
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Attachment: example.sdf
(Size: 5.01KB, Downloaded 374 times)
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