Selecting tranches in ZINC22: Difference between revisions
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Current method to select tranches to dock in ZINC 22 . | Current method to select tranches to dock in ZINC 22 . | ||
== platforms == | |||
We support three platforms: | We support three platforms: | ||
* our cluster, .txt suffix | * our cluster, .txt suffix | ||
* Wynton, .wyn suffix | * Wynton, .wyn suffix | ||
* AWS, .s3 suffix | * AWS, .s3 suffix | ||
If you are on another platform, we suggest using and adapting one of these three. | |||
== Prepared subsets in "sets" == | |||
* by HAC by number of atoms | |||
* by calculated LogP within 0.1 units. | |||
* by charge -4 to +4. | |||
Look in /nfs/exd/zinc-22/sets/ | |||
e.g. to dock neutrals (N), H17, lead-like, on Wynton, you would use | |||
/nfs/exd/ | /wynton/group/bks/sets/N-H17.lead-like.wyn | ||
similarly, to dock mono cations, H23-H25, lead-like, on our cluster, use | |||
/nfs/exd/sets/O-H2[345].lead-like.txt | |||
and to dock all charges of fragment-like, H07 to H16, on AWS, use | |||
sets/?-H0[789].frag-like.s3 sets/?-H1[0-6].frag-like.s3 | |||
== more granularity use "dirs" == | |||
Thus, use /wynton/group/bks/sets/dirs/ or /nfs/exd/sets/dirs. | |||
* | The format is <charge>-<logPbin>-<Hbin>.<layer>.<suffix> | ||
where | |||
* suffix is one of s3, wyn, txt | |||
* layer is a-z see [[ZINC22:Layers]] | |||
* Hbin is H04 to H49 | |||
* charge is N=0, O=+1, M=-1, etc from J to R. | |||
* logP bin is | |||
** P359 = LogP 3.5 to 3.99 | |||
** P304 = logP 3.0 to 3.49 | |||
** P012 = LogP 0-2 | |||
** M = LogP < 0 | |||
** P4 = LogP 4.0 to 4.99 | |||
** P56789 = logP > 5.0 | |||
You can learn about how the sets were assembled using make-sets.csh | |||
make-sets.csh in turn uses files in /nfs/exd/jjiwork/dirs/ | |||
these in turn are created using make-files2.csh in /nfs/exd/jjiwork/ | |||
We can adjust these subsets based on what people want. It is easy, we just need to do it. | |||
[[Category:ZINC22]] | [[Category:ZINC22]] | ||
[[Category:DOCK3.8]] | [[Category:DOCK3.8]] | ||
Latest revision as of 17:56, 12 June 2024
Current method to select tranches to dock in ZINC 22 .
platforms
We support three platforms:
- our cluster, .txt suffix
- Wynton, .wyn suffix
- AWS, .s3 suffix
If you are on another platform, we suggest using and adapting one of these three.
Prepared subsets in "sets"
- by HAC by number of atoms
- by calculated LogP within 0.1 units.
- by charge -4 to +4.
Look in /nfs/exd/zinc-22/sets/
e.g. to dock neutrals (N), H17, lead-like, on Wynton, you would use
/wynton/group/bks/sets/N-H17.lead-like.wyn
similarly, to dock mono cations, H23-H25, lead-like, on our cluster, use
/nfs/exd/sets/O-H2[345].lead-like.txt
and to dock all charges of fragment-like, H07 to H16, on AWS, use
sets/?-H0[789].frag-like.s3 sets/?-H1[0-6].frag-like.s3
more granularity use "dirs"
Thus, use /wynton/group/bks/sets/dirs/ or /nfs/exd/sets/dirs.
The format is <charge>-<logPbin>-<Hbin>.<layer>.<suffix> where
- suffix is one of s3, wyn, txt
- layer is a-z see ZINC22:Layers
- Hbin is H04 to H49
- charge is N=0, O=+1, M=-1, etc from J to R.
- logP bin is
- P359 = LogP 3.5 to 3.99
- P304 = logP 3.0 to 3.49
- P012 = LogP 0-2
- M = LogP < 0
- P4 = LogP 4.0 to 4.99
- P56789 = logP > 5.0
You can learn about how the sets were assembled using make-sets.csh make-sets.csh in turn uses files in /nfs/exd/jjiwork/dirs/ these in turn are created using make-files2.csh in /nfs/exd/jjiwork/
We can adjust these subsets based on what people want. It is easy, we just need to do it.