"Environment variable not set" error

Dear all,

I have installed the ChemAxon components for PP according to the povided Readme of the installer.

However, the components do not work properly. The reason seems to be that the licese file can not be found. When I run the "Show ChemAxon Environment" component within PP I get the message

CHEMAXON_LICENSE_URL environment variable NOT SET.

But the variable is set and running the command "echo %CHEMAXON_LICENSE_URL" shows the correct path to the installed license file.

Does anyone have an idea how to solve this?

Thanks a lot!

Frank

 

PS:

Here is the complete output of the PP script:

 

ChemAxon For Pipeline Pilot System Information
  JChem version : 6.0.3
Component collection version : 2.6.4_j60
JVM: Oracle Corporation  Java HotSpot(TM) 64-Bit Server VM  1.7.0_15
Memory:  368.0 MB maximum  368.0 MB total  350.0 MB free
OS: amd64 Windows 7 6.1
User: BRLNDT0366$
User home: C:\
OSRA environment variable NOT SET.

License information:
---------------------

CHEMAXON_LICENSE_URL environment variable NOT SET.

Valid licenses:
---------------


Licenses not found or invalid:
------------------------------

Marvin Applets
Marvin Beans
Instant JChem
Instant JChem VIZ
JChem Base
JChem Cartridge
Standardizer
Screen
Reactor
Fragmenter
JKlustor
Metabolizer
Markush Search
Name to Structure
Chinese Name to Structure
Document to Structure
JChem for Excel
Calculations Pack
Web Services Server
JChem for SharePoint
JChem for SharePoint Search
Structure Checker
3D Alignment
3D Screen
Molecular Descriptors
ECFP/FCFP
Registration System
Plexus
Protonation Plugin Group
Partitioning Plugin Group
Charge Plugin Group
NMR Predictor
Isomers Plugin Group
Conformation Plugin Group
3D Alignment
Geometry Plugin Group
Huckel Analysis Plugin
Refractivity Plugin
HBDA Plugin
Markush Enumeration Plugin
Structure to Name Plugin
Structural Frameworks Plugin
Predictor Plugin

------------------------------------------------------------------

Hi Frank,

1. Please make sure the environment variable is set for the same user as the one who runs the PP server process.

On a Windows server please pay attention that you should set a System environment variable (lower section, valid for all users), not a User one  (upper section, valid only for the administrator account currently used).

2. Please  make sure to restart the PP server process after changing an environment variable, so the process can see the new values.

After these the output should show the variable as set, and the licenses recognized. 

Please let me know if this helps.

Best regards,

Szilard

Hi Szilard,

Thanks for the quick reply. The problem was indeed that the environment variable was only set for the current user and not system wide.

However, when I now run the "Show ChemAxonEnvironment" script it seems that I my license is only valid vor Instant  JChem (VIZ).

Does this meen that I cannot access all the other components? What kind of license would be required for that?

Thanks

Frank

 

PS: Here is the PP output

ChemAxon For Pipeline Pilot System Information
  JChem version : 6.0.3
Component collection version : 2.6.4_j60
JVM: Oracle Corporation  Java HotSpot(TM) 64-Bit Server VM  1.7.0_15
Memory:  368.0 MB maximum  368.0 MB total  350.0 MB free
OS: amd64 Windows 7 6.1
User: BRLNDT0366$
User home: C:\
OSRA environment variable NOT SET.

License information:
---------------------

CHEMAXON_LICENSE_URL environment variable SET: C:\Users\a0361447\chemaxon\license.cxl

Valid licenses:
---------------

Instant JChem
Instant JChem VIZ

Licenses not found or invalid:
------------------------------

Marvin Applets
Marvin Beans
JChem Base
JChem Cartridge
Standardizer
Screen
Reactor
Fragmenter
JKlustor
Metabolizer
Markush Search
Name to Structure
Chinese Name to Structure
Document to Structure
JChem for Excel
Calculations Pack
Web Services Server
JChem for SharePoint
JChem for SharePoint Search
Structure Checker
3D Alignment
3D Screen
Molecular Descriptors
ECFP/FCFP
Registration System
Plexus
Protonation Plugin Group
Partitioning Plugin Group
Charge Plugin Group
NMR Predictor
Isomers Plugin Group
Conformation Plugin Group
3D Alignment
Geometry Plugin Group
Huckel Analysis Plugin
Refractivity Plugin
HBDA Plugin
Markush Enumeration Plugin
Structure to Name Plugin
Structural Frameworks Plugin
Predictor Plugin

------------------------------------------------------------------

Hi Frank,

The component collection (the integration bit) itself does not require a license.

The licenses you will need greatly depends on the type of components and calculations you want to use.

(Unfortunately the IJC and IJC VIZ licenses do not really enable any functionality here.)

Just a few examples:

If you want to  enumerate Markush structures with the component "ChemAxon Markush Enumeration" then you will need a Markush Enumeration license for that.

If you use the ChemAxon Calculator, you need to have license for those specific calculations, that you have selected to calculate. (so it can vary for some components, depending on parameters)

Some things might be  also be free, for example Standardizer requires a license in general but:

http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#notes

Some Standardizer actions ("aromatize", "aromatize:b", "dearomatize", "addexplicitH", "removeexplicitH", "wedgeclean","convertwedgeinterpretation") do not require a license key: standardization composed of these actions only can be run unlimited even without license.

The good news is that any time you attempt to use something without the correct license, the first part of the error message should clearly state what kind of license is missing (usually followed by several lines of mambo-jumbo).

If you get or generate some evaluation licenses, it is best  to replace the license file where your environment variable already points to, in this case there is no need to restart the PP server process.

Best regards,

Szilard

Hi Szilard,

Sorry to bother you again. I have tried to run several of the components. What I observe is that all test scripts finish without error message - in particular there is no failure due to a missing license. But the data does not seem to be processed either.

For instance, if I understood you correctly, the Standardizer should work without any license if the task is something like addExplicitH should work in my case as well. However, my data goes through an no hydrogens are added to the structure.

Also other simple tasks like "Molecule to IUPAC Name (ChemAxon)" just pass the pipeline without error but no property IUPAC Name is added to the data.

Any ideas?

Thanks again!

Frank

Hi Frank,

Also other simple tasks like "Molecule to IUPAC Name (ChemAxon)" just pass the pipeline without error but no property IUPAC Name is added to the data.

Please note that this component has a "Continue on Error" parameter, which is True by default.

So due to licensing all structures may produce an error, which is stored in the "Error Property" (if specified).

In this case they should also be directed to the Fail port.

If you set  "Continue on Error" to false, the protocol should stop at the first error.

Regarding Standardizer, it adds explicit H atoms properly, and complains if a license is needed, so I could not reproduce the problem.

I have tested all with the same version, also with PP 9, used the first few Asinex structures.

Please see a simple protocol attached.

Could you attach yours maybe ?

(confidential things can be sent to the "pp-support" e-mail address on our server, chemaxon.com)

Best regards,

Szilard

 

.

Hi Szilard,

Thanks for your script. That works fine for me and runs as expected. It adds the hydrogens and gives me a license error message if I want to do a Cean 3D for example.

The difference to my script is that I was using the "Materials Reader" from Accelrys Materials Studio to read the structures. With that all the ChemAxon compontents don't get processed in the pipeline - and there is no error message due to a missing license (even if "Continue on Error" parameter is set to False).

Best

Frank

 

 

Hi Frank,

I do not have that component,  but I'm guessing that if it reads structural information, it reads structures to a different data record property, than the usual PP molecule.

Out of curiosity:

Do the structures appear with "HTML Molecular Table Viewer".

And how about "ChemAxon HTML Molecular Table Viewer"  ? Also with ChemAxon type rendering ? 

In any case if you can create CTAB from these structures and then transform them back to regular PP molecules again using the standard PP components for this, all of our components should be fine downstream.

 

Best,

Szilard

Hi Szilard,

with the Materials Reader component do not appear in any of these viewers. Seems that it does use another property than the usual PP molecule.

Thanks for your help!

Frank