Difference between revisions of "Querying All Arthor Databases With Python"

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Excerpt from email:
 
Excerpt from email:
  

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 mentioned​previously, 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