Re: [Rdkit-devel] How to build the RDKit?

[<nik...@no...>]

Hi Sridhar,

congrats on getting things working. One more comment - maybe you want to 
post these kind of questions rather in the discuss than the devel list. It 
is much more populated and you will for sure get replies quicker.

Cheers
Nik




Eddie Cao <cao...@gm...> 
10/19/2010 11:49 PM

To
sri...@th...
cc
rdk...@li...
Subject
Re: [Rdkit-devel] How to build the RDKit?






Hi Sridhar,

Congratulations! If from rdkit import Chem gives you >>>, then it is very 
good sign that things are all in place.

To load molecules from Oracle database, you need a database connector 
called cx_Oracle. After installing this module, you will be able to send 
SQL statement to Oracle to retrieve molecule SMILES or SDF, depending on 
how molecules are stored in your database. You might need to consult your 
database administrator.

To download cx_Oracle: http://cx-oracle.sourceforge.net/
For a simple example about how to use it: 
http://wiki.oracle.com/page/Python

Check Section 14 of the Getting Started in Python Guide for  a complete 
list of descriptors you can calculate using RDKit:

http://rdkit.org/GettingStartedInPython.pdf

Regards,
Eddie

On Oct 19, 2010, at 2:31 PM, sri...@th... 
wrote:

Hi Nik,
Looks like I had a version issue with the RDkit I downloaded. I needed 
Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was looking 
for Python2.5 (hardcoded path from one of the libs, looked like) when I 
ran the test command (hence I downloaded and installed Python2.5 and 
removed 2.6).
Now that I have a clean install of Py2.5 and fresh download of RDkit 
Q22010_1 for Py2.5, the test command ran well and passed the test.
 
I just have to go to the next step.
I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a 
given molecule.
My molecules are actually stored in an Oracle DB.
So, Where do I begin?
 
I just got your other mail. The install is set and OK now as it seems.
I ran the command ?from rdkit import Chem? from the command-line and it 
put me back to the >>> prompt, no add?l msgs.
As for sending to the whole group, it was an honest mistake. I just 
clicked ?Reply?. Some other lists that I subscribed to, send to the list 
automagically. I realized my mistake when I didn?t receive the mail back 
to me and fixed it in this one.
 
Regards,
Sridhar
 
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