How to use Arthor Command Line: Difference between revisions
Jump to navigation
Jump to search
Jgutierrez6 (talk | contribs) (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...") |
Jgutierrez6 (talk | contribs) mNo edit summary |
||
(2 intermediate revisions by the same user not shown) | |||
Line 6: | Line 6: | ||
*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 | == Substructure Search == | ||
=== Simple Version === | |||
# Export the Arthor bin path to use executables | # Export the Arthor bin path to use executables | ||
#: <source> | #: <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 | 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
- 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
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
- 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>' -j <how_cores_you_want> -n <how_many_results_you_want> -s <path_to_.smi_file> <path_to_.atdb_file>
- 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