Proxy issue with java tool MetFrag CL

[UlliMasse]

Hi,

I use the java tool MetFrag CL and have an issue with the connection to the website.
Probable an issue with the proxy server. the tool worked on a comuter where the internet connection doesnt pass an proxy server.
The error message I get is:

• INFO de.ipbhalle.metfraglib.databases.OnlinePubChemDatabase - Fetching candidates from PubChem
• Error: Could not upen URL connection!
• https://pubchem.ncbi.nlm.

Does the tool need here the connection to an adress from the Uni Halle or to pubChem?
May I have an list of adress that the tool is connecting to? In this case, we can configure the proxy server to let pass connection to these adresses.

Best

Ulli

[schymane]

It should be https://pubchem.ncbi.nlm.nih.gov/

[UlliMasse]

Hi,
thank you for your answer.
Unfortunately, it didnt worked.
Does someone have a solution to pass the proxy server?
Or is it possible to update the software to pass proxys? E.g. authentication of the system (Password username) will be send together with the request.

thanks

Ulli

[schymane]

There are plenty of alternative options but it depends what you are trying to achieve.
You could try a local copy of PubChem instead, or try a smaller local database like PubChemLite (or others), which is a subset of PubChem with all the scoring terms and more:
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00489-0
You can download the CSV needed from here:
https://zenodo.org/record/4183801

Otherwise the code/instructions are all here:
https://github.com/ipb-halle/MetFragRelaunched

[UlliMasse]

Thank you for the information.
I think our work around will be to receive a list of candidates from the web interface and process it on the local computers.

Best

Ulli