Greg,
First off, thanks very much for the speedy and helpful response. I apologize
for not getting back and thanking you sooner. It was midterm time and I haven't
had much time for anything besides studying.
As for your suggestion, installing the rdkit-postgresql cartridge with conda
worked fine in a linux environment.
Thanks again,
Larson Danes
________________________________
From: Greg Landrum <greg.land...@gmail.com>
Sent: Friday, October 14, 2016 10:49:23 PM
To: Danes, Larson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Issues with rdkit and postgresql cartridge conda
installation
Hi Larson,
On Fri, Oct 14, 2016 at 6:17 PM, Danes, Larson
<larson.da...@und.edu<mailto:larson.da...@und.edu>> wrote:
>
> First and foremost, please excuse any inaccuracies as I am new to the world
> of Cheminformatics. I'll start with some background on my issue. I've got a
> MySQL database with chemical information such as CASRNs, Annotation Class,
> and SMILE strings. I have a web app currently in development that takes a
> list of CASRNs as input and performs an enrichment analysis on those
> chemicals. The goal is to now take a SMILE string as input, query the rdkit
> postgresql database (which will consist of a table with rows that have CASRNs
> and SMILE strings) to find any chemicals that match the input SMILE string
> over a set threshold. These chemicals CASRNs will then become the input for
> enrichment and the rest of the app will be agnostic toward how the CASRNs
> were obtained.
>
>
> I suppose I should say this: if the description above isn't something rdkit
> is suited for and I'm totally off base, please let me know! As I stated
> earlier, I'm new to this realm.
The basic flow you describe: search a database for molecules similar to a query
and retrieve the results is definitely right inline with what the RDKit
cartridge can do.
> Anyway, the issues I'm facing currently involve the installation of rdkit and
> the postgresql cartridge. I should say, I've tried this on both Windows 7 and
> Windows 10 (work desktop in 7 and laptop is 10). So, the first question I
> have is when running the command
>
This is the problem from which all the others stem: We don't currently provide
conda builds of the rdkit-postgresql cartridge for any systems other than 64bit
linux. There hasn't been a lot of demand for this and it's a non-zero amount of
work to set things up, so it hasn't happened.
Do you have access to linux? The cartridge should work fine on a VM running on
your windows machine (using virtual box) or using the new "Bash on Windows"
subsystem in Windows 10
(https://msdn.microsoft.com/en-us/commandline/wsl/about?f=255&MSPPError=-2147217396)
-greg
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