You can email me to request access to the zinc 3d build repository here:
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:
This script exports the SMILES for all substances from a chosen TIN database and annotates them with unique ZINC codes.
export ZINC_PORT=5434 export EXPORT_DEST=/local2/3d/export ./export_zinc_ids.bash
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:
This script submits jobs on the cluster to build the 3d data for the output of export_zinc_ids.bash
export SMILES_FILE=/local2/3d/export/H30P400_H30P400_5434.export export TEMPDIR=/local2/3d/build/scratch ./build_3d_smiles.bash
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.
building on Wynton
I have previously built db2 on Wynton, and recently tested with the new script (/build_database_ligand_strain_noH_s.sh). Thought it might be useful to you. The only thing that might not be accessible to you is the python environment I previously installed under my HOME. (Guess Wynton sys admin does not want us to peek other people’s home directory).
Here’s the path to my script on Wynton: /wynton/group/bks/work/yingyang/prep_db2/5A_lig/prep_db2.csh
building on LBL
(space for info for building using docker containers on LBL)
building on AWS
(space for info about building on aws)