ZINC 3D Building

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Introduction

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

export ZINC_PORT=[PORT]
export EXPORT_DEST=[DIR]
./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.

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

export SMILES_FILE=/local2/3d/export/[SMILES].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.