How to use Arthor Command Line: Difference between revisions

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(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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*Arthor version will differ as time goes on but the command line should be fairly the same.
*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 Version ===
# Export the Arthor bin path to use executables
# Export the Arthor bin path to use executables
#: <source>
#: <source>
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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
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>
</source>
=== 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 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>' -j <how_cores_you_want> -n <how_many_results_you_want> -s <path_to_.smi_file> <path_to_.atdb_file>
</source>
# Example:
#: <source>
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
</source>
== Similarity Search ==

Latest revision as of 22:31, 22 February 2023

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

Similarity Search