FastROCS: Difference between revisions
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===Install FastROCS=== | ===Install FastROCS=== | ||
See [[Openeye python libraries]] | See [[Openeye python libraries]]. | ||
There is also an installation guide on OpenEye website for alternatives. [http://docs.eyesopen.com/toolkits/python/quickstart-python/install.html Click here] | There is also an installation guide on OpenEye website for alternatives. [http://docs.eyesopen.com/toolkits/python/quickstart-python/install.html Click here] | ||
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Any computer | Any computer | ||
====1. Set up virtual environment==== | ====1. Set up virtual environment==== | ||
On bash shell | |||
$ source /nfs/ex9/work/khtang/openeye/FastROCS/source_venv | |||
To deactivate conda environment | |||
$ conda deactivate | |||
====2. Run search==== | ====2. Run search==== | ||
$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_Shape | |||
Convert smiles into sdf molecules. I wrote a script that converts each smiles into individual sdf files | |||
$ python /nfs/ex9/work/khtang/openeye/FastROCS/scripts/smi2sdf.py [smiles] | |||
$ ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly] | $ ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly] | ||
[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}] | [--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}] | ||
server:port query results [nHits] | server:port query results [nHits] | ||
example: ShapeDatabaseClient.py | example: ShapeDatabaseClient.py epyc-a40.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000 | ||
Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules | Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules | ||
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$ ShapeDatabaseClientHistogram.py <server:port> <query> <results> [num_hits = 100] | $ ShapeDatabaseClientHistogram.py <server:port> <query> <results> [num_hits = 100] | ||
===Running FastROCS on command line on a small database=== | |||
[[Category:Tutorials]] | [[Category:Tutorials]][[Category:Khanh]] | ||
Latest revision as of 20:23, 7 October 2022
Overview
FastROCS is an virtual screening tool using shape comparison for potential actives discovery. It is vastly improved of ROCS in term of speed. It could automatically split the search into many parallel searches depending on how many GPU are there.
Tutorials
Install FastROCS
See Openeye python libraries. There is also an installation guide on OpenEye website for alternatives. Click here
(Admin-only) Setting up FastROCS server
This needs to take place in a GPU-enabled computer
View FastROCS Server
Running query on FastROCS server
Any computer
1. Set up virtual environment
On bash shell
$ source /nfs/ex9/work/khtang/openeye/FastROCS/source_venv
To deactivate conda environment
$ conda deactivate
2. Run search
$ source /nfs/home/khtang/ex9/openeye/FastROCS/source_Shape
Convert smiles into sdf molecules. I wrote a script that converts each smiles into individual sdf files
$ python /nfs/ex9/work/khtang/openeye/FastROCS/scripts/smi2sdf.py [smiles]
$ ShapeDatabaseClient.py [-h] [--tversky] [--shapeOnly]
[--alternativeStarts {random,subrocs,inertialAtHeavyAtoms,inertialAtColorAtoms}]
server:port query results [nHits]
example: ShapeDatabaseClient.py epyc-a40.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf 3000
Send a query to a specified ShapeDatabaseServer and print the histogram of scores for the entire database of molecules
$ ShapeDatabaseClientHistogram.py <server:port> <query> <results> [num_hits = 100]