How to use Arthor Command Line

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Revision as of 21:56, 22 February 2023 by Jgutierrez6 (talk | contribs) (Created page with "== Introduction == Here is an introduction on how to use the Arthor commands in the command line for substructure searching. == Important Information == *Arthor Databases are backed up in '''/nfs/exj/arthor_db_backup/'''. *Arthor version will differ as time goes on but the command line should be fairly the same. == Simple use of Arthor Commands == # Export the Arthor bin path to use executables #: <source> export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-3.4.7/arthor...")
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Introduction

Here is an introduction on how to use the Arthor commands in the command line for substructure searching.

Important Information

  • Arthor Databases are backed up in /nfs/exj/arthor_db_backup/.
  • Arthor version will differ as time goes on but the command line should be fairly the same.

Simple use of Arthor Commands

  1. Export the Arthor bin path to use executables 
    export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-3.4.7/arthor-3.4.7-centos7/
export PATH=$ARTHOR_DIR/bin/:$PATH
  2. Grep a database for a substructure search. This command will take a while to run 
    atdbgrep '<SMILES/SMARTS>' -s <path_to_.smi_file> <path_to_.atdb_file>
  3. Example: 
    atdbgrep 'Cn1cnc2c1c(=O)n(C)c(=O)n2C' -s /nfs/exj/arthor_db_backup/public_arthor/bb_10.smi /nfs/exj/arthor_db_backup/public_arthor/bb_10.smi.atdb
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