Fe database: Difference between revisions

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==Accessing Fe/Iron==
Fe, which is the Enumeration of the Hartenfeller and other reliable reactions, can be found  
Fe, which is the Enumeration of the Hartenfeller and other reliable reactions, can be found  


on our cluster at  
on our cluster at  
/nfs/exj/Fe/
/nfs/exj/Fe/


Using Chemspace Building Blocks (480K) the enumerations are in  
Using Chemspace Building Blocks (480K) the enumerations are in  


/mnt/nfs/exj/Fe/Chemspace0324/ChemspaceBB_enumerated
/mnt/nfs/exj/Fe/Chemspace0324/ChemspaceBB_enumerated


there are also some in /mnt/nfs/exj/Fe/Chemspace0324/170split
there are also some in /mnt/nfs/exj/Fe/Chemspace0324/170split


they are also available on Wynton
Some molecules are also available on Wynton
/wynton/group/bks/iron-24/
/wynton/group/bks/iron-24/
and /wynton/group/bks/Fe-stage




They are also available on AWS.  
They are also available on AWS.  
aws:///zinc3d/Fe/
aws:///zinc3d/Fe/
 
==Reaction Codes==
You can find the corresponding reaction to reaction id in:
commons.docking.org
 
==Organization in Fe Files==
1st item: Enumerated compound
2nd item: Generated enumerated compound ID consisting of reaction ID, library, and building block IDs used to make compound
3rd item: Tranch or HAC/logP of enumerated compound
4+ items: 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 +2 > 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.
 
 




[[Category:Databases]]
[[Category:Databases]]
[[Category:Chemical Space]]
[[Category:Chemical Space]]

Revision as of 19:19, 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

1st item: Enumerated compound 2nd item: Generated enumerated compound ID consisting of reaction ID, library, and building block IDs used to make compound 3rd item: Tranch or HAC/logP of enumerated compound 4+ items: 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 +2 > 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.