How to use Arthor Command Line

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.

Substructure Search

Simple Version

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

Useful Options For Searching

Options	Type	Description
-c		Count, only report the number of records matched
-v		Invert match, report records that did not match
-j	Integer	Jobs, Use multiple processors (default: 1)
-b	Integer	Begin reporting only after <num> hits have been found (default: 0)
-n	Integer	Number of hits (default: 0)
--stat		Report stats on the search time of each query

Advanced Version

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>' -j <how_cores_you_want> -n <how_many_results_you_want> -s <path_to_.smi_file> <path_to_.atdb_file>

3. Example:

   atdbgrep '[NX3,NX4+][CX3](=[OX1])[OX2,OX1-]' -j 16 -n 1000 -s /nfs/exj/arthor_db_backup/public_arthor/all-zinc.smi /nfs/exj/arthor_db_backup/public_arthor/all-zinc.smi.atdb