ZINC-22:3D Building: Difference between revisions

Latest revision as of 18:06, 9 March 2023

Redirect to:

@@ Line 1: / Line 1: @@
-= 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.
-= 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
-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.