marvinsketch fails on mozilla 3.6 on linux with kernel 2.6

I’ve downloaded Marvin-all, Marvin-use,
Instant JChem, JChem,  and the Webservices.

 I’ve installed the web services on a Linux
box and I can load up the home page.  I’ve tried accessing the “marvinSketch
quick example” on a few platforms.  It fails with mozilla 3.6 on linux with  kernel
2.6.31 optimized for PAE.  

What do I need to do next on my side?

We are hoping to find a software solution to the calculation of logD.  Currently our work flow is scripted in python.  We operate almost
exclusively on SDF files.  Does chemaxon offer a tool (preferable
sciptable) that we would be able to demo in our process for a few days.

Jon,

Meanwhile I have got the WebService
working.  I can log into my Macbook and go to:  http://deathstar/marvin and I’m immediately
welcomed to the Marvin Applets page.  From there I go to “MarvinSketch
Quick Example” and I’m able to draw and load molecules as well as
calculate various properties…including logD.

 However when I try and following the
instructions below I get errors.  I’m installed ZSI without issue I
believe.  I think ran ./wsdl2py –complexType –url http://localhost:8180/axis2/services/ChemicalTermsWS?wsdl

 This returns with two deprecation warnings
but appears to work.  I intentionally tried the above command with “axis”
in place of “axis2” and I did indeed get error messages.

 This is all still server side.  I
then go to the JChemWebServices/examples/python directory and I try to issue a
command similar to:

 ./ChemTermScript.py –e ringCount
molecule.sdf

 And my mouse cursor turns into a cross
hair…which results in a reboot because I’ve lost mouse control.  And
nothing but default param info is written to the terminal….I checked the
ChemTermScript.py file itself to determine this.

 I’m confused at this step about how
to proceed?  I can clearly calculate logD with the Marvin interface, but I
seem unable to connect to the vi ZSI.

 Any ideas?

 BTW if you post this on the forum and
shoot me a link to it I’ll monitor it there.

 BTW I like the logD curve plots in the
interface…very nice touch.

 Cheers

John

---

 

To demo this I would use Python and the Zolera Soap Interface (ZSI). 
[They can use any type of soap library for python, but this seems to be
the most widely used library and it would be harder to support for us]

1. Download the web services .zip installation
   (JChemWebServices-5_3_3.zip) from the page you listed below.  Is sounds
   like he may have already done this.  Unzip it.


2. Install Python and ZSI as directed on the Python
   Developers Guide. Generally this means download the ZSI package and
   run the installer(python
   setup.py install)


3. Startup the web services server. (<JChemWebServices_Dir>/bin/startup.sh)


4. Change directories to the python examples directory (cd
   <JChemWebServices_Dir>/examples/python)


5. Run the wsdl2py script for the Chemical Terms Web Service (python
   <Python_Dir>/scripts/wsdl2py --complexType
   http://localhost:8180/axis2/services/ChemicalTermsWS?wsdl)


6. Run the ChemTerms Python Script with appropriate parameters (ChemTermsScript.py -e
   "logd('7.4')" myMolFile.sdf) The preceding command will return
   the logD value at pH 7.4, for example, 1.9732458159999997. 

There are other functionalities and expressions available in the
Chemical Terms language.  For other logD methods, you may use logDKLOP,
logDPHYS, logDVG, logDWeighted as described in the Evaulator
Functions Description. The ChemTermsScript.py is a simple example
and creating their own custom script or editing the example may be
helpful in fitting their workflow constraints. 

I have resolved part of this issue.

To the top of the ChemTermsScript.py I added: #!/usr/bin/env python

This allows the script to be executable without doing a python ChemTermsScript.

 

After making this modification I get an error griping about not being able to find the ChemicalTermsWS_client file to import.  So I went back to the wsdl stage and reran this command: 

./wsdl --complexType --url http://localhost:8180/axis2/services/ChemicalTermsWS?wsdl

According to the documentation this should generate three files one of them being the _client file.  However this step only geneates two filles both like *_services*.

I think once this issue is resolved I should be able to demo your software.

 

Thanks in avance!

 

John

John,

Try removing the "--url" flag in your call to wsdl2py.  Just the wsdl file or the url to the wsdl file is needed.  Does this help?

What version of ZSI and Python are you using?

 

Jon

Jon.

 

I'm using ZSI version 2.0.  When I issue the command without the --url I get the following error message:

"/usr/lib/python2.6/site-packages/ZSI-2.0-py2.6.egg/ZSI/resolvers.py:7: DeprecationWarning: the multifile module has been deprecated since Python 2.5
Must specify either --file or --url option"

When I run it with the --url I get the following warnings:

"/usr/lib/python2.6/site-packages/ZSI-2.0-py2.6.egg/ZSI/resolvers.py:7: DeprecationWarning: the multifile module has been deprecated since Python 2.5
/usr/lib/python2.6/site-packages/ZSI-2.0-py2.6.egg/ZSI/wstools/XMLSchema.py:3072: DeprecationWarning: object.__init__() takes no parameters"

But the command seems to complete as two files are written in the director:  ChemicalTermsWS_services.py   and ChemicalTermsWS_services_types.py

Any other ideas?

 

Cheers

-John

 

 

 

John,

Try using the latest 2.1 version of ZSI (I believe 2.1a1).  I believe I tried the 2.0 version earlier, but was unable to get it working before I found the 2.1 version. 

When using the 2.1 version of ZSI, I also get the two warnings you mention. 

 

Also, there are other Python WebService libraries discussed on the python wiki: http://wiki.python.org/moin/WebServices

Jon

Jon,

 

Thanks the ZSI upgrade fixed the problem. 

 

For anyone else reading, I also had to install the license in /root/.chemaxon because I started the tomcat server like:  sudo ./startup.sh.

 

Cheers

John

Glad to know it helped.

Let us know if there is any other questions we can answer.

Jon