Wuxi make-on-demand: Difference between revisions

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To search the WuXi make on demand library before it has been loaded into ZINC, please proceed as follows.
To search the WuXi make on demand library before it has been loaded into ZINC, please proceed as follows.


use the script in ~xyz/wuxi/searchwuxiparallel.csh


1. set up environment
* first argument is your filename
* second argument is TC e.g. 0.6
* results will be in results-xa?.txt where a is a-f and represents the 52M split into 6 files of max 10M mols each.


2. set up your list of query molecules
Thus for example
~xyz/wuxi/searchwuxiparallel.csh  myfile.ism  0.5


3. run molgrep.py
It runs 6 jobs in parallel, so please only run one of these at a time. If you prefer, there is a non-parallel version searchwuxi.csh.  
 
it should take 10 minutes to search 1 molecule against the 52 M WuXi make-on-demand library.
4. profit.
Searching 100 molecules in myfile.ism takes only a slightly longer.
This is fine to run on gimel or gimel2.  


[[Category:Internal]]
[[Category:Internal]]

Latest revision as of 20:30, 4 June 2018

To search the WuXi make on demand library before it has been loaded into ZINC, please proceed as follows.

use the script in ~xyz/wuxi/searchwuxiparallel.csh

  • first argument is your filename
  • second argument is TC e.g. 0.6
  • results will be in results-xa?.txt where a is a-f and represents the 52M split into 6 files of max 10M mols each.

Thus for example

~xyz/wuxi/searchwuxiparallel.csh  myfile.ism  0.5

It runs 6 jobs in parallel, so please only run one of these at a time. If you prefer, there is a non-parallel version searchwuxi.csh. it should take 10 minutes to search 1 molecule against the 52 M WuXi make-on-demand library. Searching 100 molecules in myfile.ism takes only a slightly longer. This is fine to run on gimel or gimel2.