Re: [Rdkit-discuss] Issues with rdkit and postgresql cartridge conda installation

[Greg L. <gre...@gm...>]

Hi Larson,

On Fri, Oct 14, 2016 at 6:17 PM, Danes, Larson <lar...@un...> 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