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| Re: Converting COD2020 to SDF [message #1198 is a reply to message #1196] |
Thu, 28 January 2021 15:36   |
nbehrnd
Messages: 227
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 386 times)
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Attachment: example.sdf
(Size: 5.01KB, Downloaded 386 times)
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| Re: Converting COD2020 to SDF [message #1200 is a reply to message #1199] |
Thu, 28 January 2021 22:56 |
nbehrnd
Messages: 227
Registered: June 2019
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Senior Member |
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Possibly codcif2sdf is part of the tools used for at least two reasons: Using only Openbabel (including release 3.1.0) would not retain the bibliographic information in the .sdf written which show up in DW's display.
An other reason is sometimes both crystallographic motif as well as symmetry of the unit cell are needed to complete the molecule's appearance as one would draw it in a notebook. By choice of the unit cell this may look like the molecule were broken. And it is the reconstruction of intramolecular atom connectivity where OpenBabel may more frequently encounter problems, than codcif2sdf. As an illustration, I attach both COD's .cif about a simple triazine, as well as the rewritten form as .sdf, once by OpenBabel, once by codcif2sdf.
Once the individual entries are rewritten for the organic chemist's eye, they may be stacked into a .sdf of multiple models and read as-such by DataWarrior. Possibly Thomas or/and the maintainer's of COD developed some template scripts to automate the whole process including formatting, and checks for plausibility and consistency. Given the scope and coverage of COD and TCOD often complementary to the ones e.g., by CCDC and ICSD, additional mirrors most likely are welcomed enthusiastically.
Norwid
TCOD, the sibling of COD mentioned: https://www.crystallography.net/tcod/
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| Re: Converting COD2020 to SDF [message #1201 is a reply to message #1200] |
Fri, 29 January 2021 09:36 |
thomas
Messages: 716
Registered: June 2014
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Senior Member |
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Some years ago, when we needed statistical data from crystallographic data for our conformer generation and forcefield algorithms in OpenChemLib, and after getting a veto from Colin Groom to use the CSD for that purpose, we looked for alternatives. As a result we invited one of the COD maintainers (Antanas Vaitkus) to spend parts of his PhD time at Actelion in Switzerland to work on the cif2sdf conversion and especially to improve the calculation of bonds from atom coordinates, which has some issues especially with organo-metallic structures. He did a marvelous job improving the bond calculation logic by looking into lots of original papers, added validation code to produc warnings and errors. After returning to Vilnius he established the conversion as a regularly occurring process that not only creates an SD-file, but also creates a dwar file in their SVN repository.
We download the dwar, remove fishy structures, apply some minor changes, add the organic/metal-organic/inorganic classification, apply a template, and put it on this website for download.
Thomas
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