Chemistry translator: Molecule from CDX

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1

Hello all,

Would any of you know of a node that would interpret the CambridgeSoft CDX format into any other molecule format?

Basically, I am reading a CambridgeSoft base 64 CDX and want to use these molecules. I have tried Molecule to Indigo, Molecule to CDK, Molecule Type Cast, OpenBabel, MolConverter (Marvin) and I may forget some.

Your help will be more than welcome,

Fred

2

I suspect you can do this in knime with openbabel. Make sure you have openbabel installed first. Looking on openbabels website it does support CDX format along with Another 112 formats. Knime node doesn’t show all these options in the node but they are supported. See how I did it for inchi strings in this post, I’d be interested to know how you get on.
Will be nice for knime 2.6 to implement open babel a little better and integrate the software in the knime update site instead of downloading separately. Here is the post;
http://tech.knime.org/forum/knime-general/converting-inchi-strings-to-smilessdfs-etc

3

OpenBabel in KNIME 2.6 will show all supported formats by the installed openbabel executable. The binaries can also be installed from the update site, but especially on Linux it may happen that they don't work because of wrong dynamic library versions.

4

Hello,

Thanks a lot Simon! Your procedure successfully forced the OpenBabel node to consider the input as CDX.

However, the node failed to translate the CDX into molecules (mol - MDL MOL format). I believe this is because of the base 64 CDX format.

For info:

  • I took the raw base 64 CDX character string and pasted it into a file, to which I gave a .cdx extension. This opened ok in CambridgeSoft ChemDraw.
  • However, when I took the raw base 64 CDX character string and pasted it into OB, it would not be converted. Nor would the .cdx file.
  • Then, from ChemDraw, I saved the exact same .cdx file I had created manually and gave it a different name (from test.cdx to test2.cdx) and this file gets converted ok by OB.

I guess ChemDraw edits the raw format so that it fits into the original CDX format.

I will crack this one but it is taking time...

It is good news that K2.6 will see the full-fledged version of the OB node. Good work!

Cheers all,

Fred

5

:(

I meet the same request and I failed too. CDX is a binary file and it can not be read correctly by File Reader. So I think the open babel can not get the correct input at all.

If there is an obabel node which read input from file, instead of from input port, will be helpful.

If anyone can give a solution will be appreciated. Thank you.

6

The category Chemistry > Translator contains an OpenBabel node. Make sure you have the chemistry extensions installed from our update site.

7

I found the open babel node. But here is the issue.

The openbabel node read input from the output of previous node. And cdx is a binary file and there is no node which can read the binary file and put the content into one cell directly. Maybe there is but i did not found it.

So i think an open babel reader which read input from file(s) directly is more user-friendly and straightforward.