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girke-lab / chemminetools

ChemMine Tools: open source web framework for small molecule analysis
http://chemmine.ucr.edu
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ChemMine Hierarchical Clustering #226

Open LaurenJoe opened 2 years ago

LaurenJoe commented 2 years ago

Hello,

I was wondering if there was an automated way for me to change all the names of 'My Compounds'? I have many compounds and manually changing the names of each would be rather tedious.

Thank you for your time and help!

austinleong commented 2 years ago

Hello Lauren,

ChemMine Tools currently doesn't have a way to facilitate a bulk-renaming of compounds, but I can consider it as a feature request. In the meantime, if you have the option of importing your compounds as SDF, see if you can find a way to have the compound name attached as an associated data item. It'll look something like:

> <NAME>
CAFFEINE

and will be somewhere between the "M END" after the compound data, and the "$$$$" record separator. If your SDF source has that feature, you can bypass ChemMine Tool's limitations entirely.

In any case, I'll let you know if I can put something together to help out. If you have any suggestions on how such a tool/interface would look like, that'd be helpful as well.

austinleong commented 2 years ago

Edit: Fixed code formatting in previous post.

(I'm not sure if GitHub pushes notifications for comment edits, so I'm posting a new comment to make sure that happens)

LaurenJoe commented 2 years ago

Thanks for the help Austin.

I was wondering if you could help me with some other inquiries as well.

I'm looking to generate a hierarchical clustering based on bacterial strains X chemical compounds - with the strains on one axis and compounds on the other. Then I was hoping to colour coat based on how the chemicals affect growth. Is this possible with ChemMine tools? And if so, how would I achieve this?