ZINC-22:3D Building

Revision as of 22:20, 15 March 2022 by Frodo (talk | contribs) (Frodo moved page ZINC 3D Building to ZINC-22:3D Building: rationalize naming)
Jump to navigation Jump to search


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:

  • build_3d_smiles.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.

Example Usage

export ZINC_PORT=5434
export EXPORT_DEST=/local2/3d/export

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

Example Usage

export SMILES_FILE=/local2/3d/export/H30P400_H30P400_5434.export
export TEMPDIR=/local2/3d/build/scratch

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)