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2026-03-30T17:54:40Z

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← Older revision		Revision as of 17:54, 30 March 2026
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	** I tried to break up sets of molecules small enough that we never have more than 5000 mols in one directory.		** I tried to break up sets of molecules small enough that we never have more than 5000 mols in one directory.
	** but I have not been completely successful. I am still working on that.		** but I have not been completely successful. I am still working on that.


			* In Bioactive, in addition to "inVitro", "inVivo", "natural", there is also "user"
			* the idea is that people can upload a set of molecules by date and name to "user"
			* then overnight, or following some cron job schedule, we compute exactly the same reports as we do for bioactive compounds from the literature for compounds that users upload.


	[[Category:ZINC26]		[[Category:ZINC26]

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2026-03-30T17:50:21Z

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New page

These are notes for the developers of ZINC26.

* root directory is /nfs/exk/newdbpublic
* Bioact - bioactives directory. These are sourced from public websites and curated manually.
* Purch - purchasable chemistry. Sourced from public sources and curated manually.
* We generate smallworld and arthor indexes for all of the above directories. Stored on /nfs/db5/newdb/
* Purchbioact - this directory is entirely computed
** first pass: for each molecule in each bioactive catalog, we search it in each purchasable catalog.
** if there are no hits, it gets deleted.
** files are of the form <mol_id>.<cat_id>.txt

** second pass: In each directory, where molecules live (.smi) for each molecule e.g. HMDB0001881
** we generate a report e.g. in /nfs/exk/newdbpublic/Purchbioact/invivo/hmdb/hmdbcosmetic/cc we run
** python /nfs/exk/newdbpublic/Purchbioact/bin/script2a.py HMDB0037790
** (try script1 also. try script2 also. still working out the kinks.)
** it is these reports that I want to form the basis of a "molecule detail report"

** third pass: Once we generate a molecule detail report for every bioactive molecule, I want to prepare
** summary reports that give overall answers for all bioactive catalogs.
**
** there is more, but this is a good start.

** the calculations of the first pass are still running, but there is now tons of data to process
** I tried to break up sets of molecules small enough that we never have more than 5000 mols in one directory.
** but I have not been completely successful. I am still working on that.

[[Category:ZINC26]

ZINC26:Developer - Revision history

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