How to use Arthor Command Line: Difference between revisions

Revision as of 21:59, 22 February 2023

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

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.

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

@@ Line 6: / Line 6: @@
 *Arthor version will differ as time goes on but the command line should be fairly the same.
-== Simple use of Arthor Commands ==
+== Substructure Search ==
+=== Simple ===
 # Export the Arthor bin path to use executables
 #: <source>
@@ Line 20: / Line 21: @@
 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
 </source>
+=== Useful Options For Searching ===
+=== Advanced ===
+== Similarity Search ==