openmolecules.org

 
Home » DataWarrior » Cheminformatics » chembl server (chembl server)
chembl server [message #671] Sun, 13 October 2019 19:30 Go to next message
pc419714@ohio.edu is currently offline  pc419714@ohio.edu
Messages: 20
Registered: February 2019
Junior Member
I'm building a QSAR creator in python. https://www.aidrugdiscovery.net

We are trying to figure out how you communicated with the Chembl server to download compounds from the target name. Are you aware of any python clients that allow you to do this with Chembl? We're looking at your source code-- ChemblCommunicator.java, ChemblServerConstants.java, DETaskChemblQuery.java

There's pugrest for pubchem. I don't see any easy way of communicating with either pubchem or chembl to download the compounds based on their target. We might just tell our clients to download Data Warrior in order to get the compounds.... (or maybe create a Data Warrior plugin that allows you to communicate with our toolkit). Maybe a data warrior plugin that piped the compounds to our QSAR creator. If you had any thoughts on our concept, I'd love to hear.

Loving Data Warrior, defending my masters thesis using it. Thanks so much for your great software and answering all my questions!

Patrick Chirdon

Report message to a moderator

Re: chembl server [message #678 is a reply to message #671] Mon, 21 October 2019 21:13 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 715
Registered: June 2014
Senior Member
DataWarrior is accessing a copy of the Chembl database on openmolecules.org.
This server is optimized for fast structure search and result retrieval and is accessible via http.

For your purpose the fastest approach would probably be to download the Chembl database in MySQL,
install it on your server and access it via SQL language. From python this should be possible.

Alternatively, as you suggest, you may, of course, use DataWarrior for target specific downloads.
DataWarrior plugins are meant for getting data into DataWarrior, not for export.

Thomas

Report message to a moderator

Re: chembl server [message #701 is a reply to message #678] Sat, 02 November 2019 17:07 Go to previous message
pc419714@ohio.edu is currently offline  pc419714@ohio.edu
Messages: 20
Registered: February 2019
Junior Member
I think what we will probably do is launch Data Warrior from our application. I think this should be possible.

Report message to a moderator

Previous Topic: Computational Chemistry
Next Topic: MD/ab initio for polymer solubility?
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Sun Nov 24 17:19:58 CET 2024

Total time taken to generate the page: 0.03833 seconds
openmolecules.org