How to use Arthor Command Line
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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.
Substructure Search
Simple
- 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
- 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>
- 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