Querying All Arthor Databases With Python: Difference between revisions
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Latest revision as of 02:03, 17 April 2020
Excerpt from email:
Alternatively, I have a python script that will perform a SMARTS query on all compatible arthor databases. This script is located on the lab NFS at: /mnt/nfs/exa/work/btingle/query_all_smarts.py. Here's how you would use that:
instructions
- cd to my home directory on exa and activate the python environment there
cd /mnt/nfs/exa/work/btingle source py3/bin/activate
- if that doesn't work try
source py3/bin/activate.csh
- now copy the "query_all_smarts.py" script to wherever you want to store the results
cp query_all_smarts.py /path/where/you/want/results cd /path/where/you/want/results
- run the script, query_all_smarts.py
python query_all_smarts.py <Your SMARTS query> python query_all_smarts.py "[OX2]C(=O)c1[cH]nc([CH3])nc1[CH]2[CH2][CH2]2"
As I mentionedpreviously, this query may take a while. You may want to open a detached screen prior to running the script prior to running query_all_smarts.py run this command
screen -S query_all_smarts
You can detach from this screen by entering CTRL-A + CTRL-D You can re-attach later with
screen -r query_all_smarts
If everything goes right, your results should show up in the directory after some time
Let me know if you need anything else answered! -Ben