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====
  cd /nfs/home/khtang/ex9/openeye/FastROCS
On bash shell
  $ source /nfs/ex9/work/khtang/openeye/FastROCS/source_venv


  source ./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 n-9-34.cluster.ucsf.bkslab.org:8080 ZINC000000002837.sdf result.sdf
  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]

Running FastROCS on command line on a small database