ZINC-22:3D Building: Difference between revisions

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= Introduction =
#REDIRECT [[Building The 3D Pipeline ZINC22]]
 
You can request access to the zinc 3d build repository here:
 
https://github.com/btingle/zinc-3d-build
 
The contents of this github can be found on /nfs/home/xyz/btingle/zinc_deploy/zinc-3d-build. There are two top-level bash scripts in this repository that should be used for the 3d building process:
 
* build_3d_smiles.bash
* export_zinc_ids.bash
 
= export_zinc_ids.bash =
 
This script exports the SMILES for all substances from a chosen TIN database and annotates them with unique ZINC codes.
 
== Usage ==
<nowiki>
export ZINC_PORT=[PORT]
export EXPORT_DEST=[DIR]
./export_zinc_ids.bash</nowiki>
 
ZINC_PORT is the port number of the database on this machine that should be exported from.
 
EXPORT_DEST is where the annotated smiles/ZINC ID file should be saved.
 
The name of the output file is formatted as follows:
 
<nowiki>
$EXPORT_DEST/[PARTITION_RANGE]_[PORT].export</nowiki>
 
= build_3d_smiles.bash =
 
This script submits jobs on the cluster to build the 3d data for the output of export_zinc_ids.bash
 
== Usage ==
<nowiki>
export SMILES_FILE=/local2/3d/export/[SMILES]
export TEMPDIR=/local2/3d/build/scratch
./build_3d_smiles.bash</nowiki>
 
The nodes allocated for these jobs are defined in nodelist.txt.
 
The output of this script will be in $TEMPDIR/[SMILES].out split into a number of batches. Each batch .tar file contains the output of 5000 jobs. Each job outputs a .tar.gz file containing the results of 3d building for 20 substances.

Latest revision as of 18:06, 9 March 2023

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