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

[<sri...@th...>]

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

 

From: Kuntamukkula, Sridhar (Hlthcr&Science) 
Sent: Tuesday, October 19, 2010 4:45 PM
To: 'nik...@no...'
Subject: RE: [Rdkit-devel] How to build the RDKit?

 

Hi Nik,

You and Eddie  (thanks to both of you) pointed to the same link which is
what I used to download the RDKit. But haven't any idea whether that was
source or binary. Now I know I downloaded the binary install for
Windows.

And am trying to follow the "install" file's instructions from the
RDBASE folder.

In this process I happened to install the other required
software/utilities such as python, numpy, scipy, PIL, Boost, etc..

But my RDKIT download referred to python2.5, so I had to downgrade to
python2.5 (originally install2.6 and 2.6 utilities)

I have set the ENV vars. For,

PYTHONPATH,

RDBASE,

PATH,

BOOSTHOME (although this is boost 1.44, not 1.36 as the install doc
referred to)

BOOST_BUILD_PATH 

 

But the "install" doc (from the RDBASE) referes to a folder called,
%RDBASE%\Code which is not there in the package I downloaded.

 

In the end, when I follow the test guidelines, with the following
command,

python C:\RDkit\RDKit_Q22009_1\rdkit\testrunner.py test_list.py

 I get the following errors reported.

!-!-!-!-!-!-!-!-!-!-!

        Script: test_list.py.  Failed 3 (of 32) tests in 71.61 seconds

                (.): python UnitTestChem.py

                (.): python UnitTestCatalog.py

                (Pharm3D): python test_list.py

 

It is a bit confusing, to say the least. And now, after the re-install
of python2.5 and removal of python2.6 (in this order), the *.py files
are not opening with python.

Dbl click flashes a command window and disappears. Right click and
choose "Open with IDLE" does nothing.

 

Appreciate any insights (to get me started with RDkit).

-Sridhar

 

From: nik...@no... [mailto:nik...@no...]

Sent: Tuesday, October 19, 2010 3:59 PM
To: Kuntamukkula, Sridhar (Hlthcr&Science)
Cc: rdk...@li...
Subject: Re: [Rdkit-devel] How to build the RDKit?

 


Hi Sridhar, 

are you using the windows binaries or is that a Linux system? Did you
follow the installation instructions on
http://code.google.com/p/rdkit/wiki/GettingStarted ? I guess some more
details is needed to help you out here ... most likely you have not set
any of the important environment variables such as RDBASE etc. 

Cheers 
Nik 



<sri...@th...> 

10/19/2010 05:19 PM 

To

<rdk...@li...> 

cc

	
Subject

[Rdkit-devel] How to build the RDKit?

 

		




Hi, 
I am new to the RDKIT. Just got introduced. The command, "from rdkit
import chem. Gives me an error as below 
Traceback (most recent call last): 
  File "<pyshell#9>", line 1, in <module> 
    from rdkit import chem 
ImportError: No module named rdkit 
  
I have python installed in C:\python26 folder. 
I also have the RDKit unzipped into the same folder. 
  
What else do I need to do? 
Are there step by step instructions online or in the docs somewhere that
could get me going with RDKit? 
  
Many thanks 
  
Sridhar Kuntamukkula
Chemical Prog Analyst Sr 
Healthcare & Science 

Thomson Reuters 
  
Phone: +1-215-823-5657
sri...@th...
<mailto:sri...@th...> 
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