License Installed - No Valid License Found

I am having trouble using JChem Web Services tools (in specific generatemd called from command line).

     Some details: I'm running Redhat Enterprise Linux, and have installed a Freeweb License (according to the License Manager software - the license is installed correctly). I have also placed the license at /root/.chemaxon/license.cxl

    However, when I try to run most of the functions, I get licensing errors. For example, generatemd called from Bash. I took this command from an example in the documentation (here: http://www.chemaxon.com/jchem/doc/user/GenerateMD.html). I have confirmed that the files referenced in this statement actually exist in those locations.

   The command: generatemd c molecules/nci1000.smiles -k PF -c config/pharma-frag.xml -o nci1000.pf

 

    The error message:

No valid license has been found.

Product name: Pharmacophore Recognition

License path: /root/.chemaxon/license.cxl

Please contact sales _at_ chemaxon.com to obtain the corresponding license.

Students and academic researchers are entitled of free use

through our Academic Package, for more information

please visit: http://www.chemaxon.com/acpack_conditions.html

chemaxon.license.LicenseException: No valid license has been found.

Product name: Pharmacophore Recognition

License path: /root/.chemaxon/license.cxl

Please contact sales _at_ chemaxon.com to obtain the corresponding license.

Students and academic researchers are entitled of free use

through our Academic Package, for more information

please visit: http://www.chemaxon.com/acpack_conditions.html

at chemaxon.license.LicenseHandler.checkLicense(LicenseHandler.java:513)

at chemaxon.pharmacophore.PMapper.checkLicense(PMapper.java:533)

at chemaxon.pharmacophore.PMapper.createFeatureMap(PMapper.java:438)

at chemaxon.descriptors.PFGenerator.generate(PFGenerator.java:156)

at chemaxon.descriptors.PFParameters.generate(PFParameters.java:444)

at chemaxon.descriptors.PharmacophoreFingerprint.generate(PharmacophoreFingerprint.java:441)

at chemaxon.descriptors.MDSet.generate(MDSet.java:379)

at chemaxon.descriptors.MDFileWriter.put(MDFileWriter.java:378)

at chemaxon.descriptors.GenerateMD.step(GenerateMD.java:690)

 

 

Thank you,

I found the following post: https://www.chemaxon.com/forum/ftopic8147.html&highlight=valid+licence+license

and following it's advice, I found that generatemd will run with  'CF' (Chemical Fingerprint) but not 'PF' pharmacophore fingerprints. I have no idea why this might be.

 

Has anyone else encountered this problem?

 

 

HI,

The FreeWeb license does not include all products and is aimed to support structure storage and search within a content for the freely available site.

Can you comment on the web services use, is this a preference for architectural reasons - notice the freweb license will not let you serve services to other sites/aplications because you are unable to confirm that these are not frely available and they may even be commercial.

Cheers/Alex

The site is intended to be a freely available web archive of compounds which might be of interest to researchers. The website will be large (more than 20 million compounds), and it is intended to be searchable by a user-input SMILES string -- with the website finding, and ranking, compounds based on their similarity to the query string.

For 20+ million compounds to be searchable in a reasonable amount of time, obviously a direct substructure search would be far too slow. Hence, I was hoping to use JChem's fingerprint- matching / screening capabilities.

EDIT: For context - the compounds are held in a MySQL database constructed via 'jcman', and I am currently attempting to call screenmd() from the command-line, so I can avoid having to use the Java API (if possible).

Will this be possible under the Freeweb License?

 

 

alexa wrote:

Can you comment on the web services use, is this a preference for architectural reasons - notice the freweb license will not let you serve services to other sites/aplications because you are unable to confirm that these are not frely available and they may even be commercial. Cheers/Alex

Thanks I understand better.

I am interested in the use of web services however, can you comment on why you use this - you can use the same functionality through java or .NET or command line and this is included in the FreeWeb license.

Regarding the speed issue - I am not sure how your speed tests are set up but our clients tell us speed is excellent we have benchmarks against 19.5m rows. Speed is based on numbers of hits and in the case of large numbers of hits our users normally use cache or serve results as they become available - so the users sees results almost immediately. Does this change anything?

Notice also that the FreeWeb license includes marvin chemical editor so your users can also draw structure queries (more chemist friendly than SMILES). If you look at these tryout examples of drawing queries and seeing results (JChem) we provide the code examples of these to let you put the system up quickly

Cheers/Alex

(1) We are using your software to allow users to draw structure queries (which are then translated into SMILES). This is a good tool!

(2) We are using web services, because it was somewhat unclear how the various JChem functional components are packaged. For developing a website, the Web Services seemed the natural option.

We are using the command line approach for speed in prototyping, since using the java or .NET API's would add an additional layer of complexity and development time (since we have only one developer, and he is not an expert on either of those).

(3) The benchmarks convince me that the fingerprint comparison speed will be more than sufficient. Am I correct in concluding that using fingerprints will be necessary for a database of this size? In other words, a more direct query-to-target-molecule sub-structure or similarity search would be far too slow?

 

(4) A question: I cannot find an example in the documentation of the use of screenmd, where the targets themselves are drawn from a SQL database (rather than an SDF file). The documentation seems to say this is possible. Could you provide a brief example (or link to one)?

 

Thank you,

Oakland

alexa wrote:

Thanks I understand better. I am interested in the use of web services however, can you comment on why you use this - you can use the same functionality through java or .NET or command line and this is included in the FreeWeb license. Regarding the speed issue - I am not sure how your speed tests are set up but our clients tell us speed is excellent we have benchmarks against 19.5m rows. Speed is based on numbers of hits and in the case of large numbers of hits our users normally use cache or serve results as they become available - so the users sees results almost immediately. Does this change anything? Notice also that the FreeWeb license includes marvin chemical editor so your users can also draw structure queries (more chemist friendly than SMILES). If you look at these tryout examples of drawing queries and seeing results (JChem) we provide the code examples of these to let you put the system up quickly Cheers/Alex

HI,

Good I think I almost have it. Can you confirm that

1.  You will not make any web services available to external websites or applications (where they may be commercial vendors) and


2. There is no login to access all the functionality we provide (ie additional services hidden behind a log in)

Cheers
Alex

Yes, I can confirm both points.

alexa wrote:

HI, Good I think I almost have it. Can you confirm that  You will not make any web services available to external websites or applications (where they may be commercial vendors) and There is no login to access all the functionality we provide (ie additional services hidden behind a log in) Cheers Alex

Hi,

I am also getting the same error

The error message:

No valid license has been found.

Product name: Markush Enumeration Product

License path: /root/.chemaxon/license.cxl

Please contact sales _at_ chemaxon.com to obtain the corresponding license.

Students and academic researchers are entitled of free use

through our Academic Package, for more information

please visit: http://www.chemaxon.com/acpack_conditions.html

 

HI Serat,

This is not the same problem - academic package does include Markush enumeration.

If you are trying to run on a server this is correct as acpack licensing is personal and so not relevant for running on a server. Alternatively you may have an old license and to refresh your academic license see this forum post.

Cheers/Alex