Difference between revisions of "ZINC 3D Building"

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(Usage)
(Example Usage)
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== Example Usage ==
 
== Example Usage ==
 
  <nowiki>
 
  <nowiki>
export SMILES_FILE=/local2/3d/export/[SMILES]
+
export SMILES_FILE=/local2/3d/export/H30P400_H30P400_5434.export
 
export TEMPDIR=/local2/3d/build/scratch
 
export TEMPDIR=/local2/3d/build/scratch
 
./build_3d_smiles.bash</nowiki>
 
./build_3d_smiles.bash</nowiki>

Revision as of 11:24, 30 June 2020

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.

The name of the output file is formatted as follows:

$EXPORT_DEST/[PARTITION_RANGE]_[PORT].export

build_3d_smiles.bash

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
./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.