Fe database: Difference between revisions
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==Organization in Fe Files== | ==Organization in Fe Files== | ||
1st | Tab separated: | ||
2nd | 1st column: Enumerated compound | ||
3rd | 2nd column: Generated enumerated compound ID consisting of reaction ID, library, and building block IDs used to make compound | ||
4+ | 3rd column: Tranch or HAC/logP of enumerated compound | ||
4+ columns: Starting building blocks | |||
==Useful Commands== | ==Useful Commands== | ||
Revision as of 19:24, 14 June 2024
Accessing Fe/Iron
Fe, which is the Enumeration of the Hartenfeller and other reliable reactions, can be found
on our cluster at
/nfs/exj/Fe/
Using Chemspace Building Blocks (480K) the enumerations are in
/mnt/nfs/exj/Fe/Chemspace0324/ChemspaceBB_enumerated
there are also some in /mnt/nfs/exj/Fe/Chemspace0324/170split
Some molecules are also available on Wynton
/wynton/group/bks/iron-24/ and /wynton/group/bks/Fe-stage
They are also available on AWS.
aws:///zinc3d/Fe/
Reaction Codes
You can find the corresponding reaction to reaction id in: commons.docking.org
Organization in Fe Files
Tab separated:
1st column: Enumerated compound 2nd column: Generated enumerated compound ID consisting of reaction ID, library, and building block IDs used to make compound 3rd column: Tranch or HAC/logP of enumerated compound 4+ columns: Starting building blocks
Useful Commands
find . -name "*.txt.gz" -print
Is a general command that can be used to find all the files with enumerated compounds at the top level directories
find . -name "*.txt.gz" -print -exec zcat {} \; | tail -n +3 > all_files.txt
Is a command that is run to string the files all together into one. When zcating the first line is incorrect and this command foregoes the first incorrect line when cating them all.