How to use Arthor Command Line: Difference between revisions

Revision as of 22:20, 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

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

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>
```

@@ Line 7: / Line 7: @@
 == Substructure Search ==
-=== Simple ===
+=== Simple Version ===
 # Export the Arthor bin path to use executables
 #: <source>
@@ Line 23: / Line 23: @@
 === Useful Options For Searching ===
+:{| class="wikitable"
+|-
+! 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 ===
+=== Advanced Version ===
+# Export the Arthor bin path to use executables
+#: <source>
+export ARTHOR_DIR=/nfs/soft2/arthor_configs/arthor-3.4.7/arthor-3.4.7-centos7/
+export PATH=$ARTHOR_DIR/bin/:$PATH
+</source>
+# Grep a database for a substructure search. '''This command will take a while to run'''
+#: <source>
+atdbgrep '<SMILES/SMARTS>' -s <path_to_.smi_file> <path_to_.atdb_file>
+</source>
 == Similarity Search ==