Compound conversion: Add index to output

[hechth]

The compound conversion tool which is part of the chemical toolbox doesn't handle indices etc. for the files which it processes and silently drops lines that are invalid - this makes working with larger files problematic, as the output format can no more be associated with the inputs.

Is there a way to add indices to the files to indicate which output belongs to which input or is the only option to run collections and have one identifier per job?

[bgruening]

@hechth you are talking about that tool? https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/openbabel/ob_convert.xml

Which input format are you using?

[hechth]

@bgruening Indeed!

I'm using a normal list, so the inchi format how it is called.

Some example data is attached.
inchi.zip

[bgruening]

Can you try adding an additional column (https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0) to the inchi file? Is that preserved by openbabel?

[hechth]

I tried using 2 columns separated with ,, that didn't change anything on the specific history (https://umsa.cerit-sc.cz/u/hechth/h/compound-convert-test).

[bgruening]

try adding a new column with a tab using the tool from above

[hechth]

Nope - tried adding a column manually, using tabs, commas, the Galaxy tool, but always the same - no index in the output and invalid data gets dropped silently.

[bgruening]

Maybe @simonbray has an idea?
This tool is using simply openbabel, so if openbabl can not deal with this I think we are out of luck here.

[simonbray]

Can you use a different file format? I think inchi is in general not a good choice for the input.

With smiles or sdf you can specify the index in the molecule name/title.

[hechth]

I explicitly want the inchi, since I want to compute smiles from inchi.

I also don't get why indexing is possible with SMILES and not with inchi? They're both just texts ...

[simonbray]

I also don't get why indexing is possible with SMILES and not with inchi? They're both just texts ...

What I meant is that SMILES has a name/title/label which you can append a index to.

I explicitly want the inchi, since I want to compute smiles from inchi.

I think as @bgruening said we are limited by the underlying software. Maybe you can use a Galaxy workaround like this? https://usegalaxy.eu/u/sbray/h/inchi-index

[hechth]

In this scenario the join works as the inchi doesn't change - but if we actually change specific parts of it, they are no more identical, so the workaround doesn't function.

If I come up with a solution, should I just PR it here? Otherwise, I think I could solve our specific needs with a targeted tool.

Thank you very much for your support and for looking into this!

[simonbray]

Yes, PRs are always welcome, thanks!