Fe database

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 Columns:

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.