Change Java heap size when using metabolizer in command line

Dear all,

first of all i wish you a happy new year.

Recently, i started using metabolizer as command line tool but i have the problem that the java heap size seems to be too low when running the tool in the exhaustive mode with 3 generations of predicted metabolites.

Is it somehow possible to change the heap size with an additional parameter (similar to mview: https://docs.chemaxon.com/display/marvinsketch/Java+VM+options ) when using the metabolizer as command line tool?

Best regards,

MG

I have checked the script files and it seems, that -Xmx512m setting is hardcoded in the metabolize script which overwrites your custom setting. This is not good, but as a workaround, you can modify the last two entries of the metabolize script manually to set your preferred memory size. They are in the bin folder of your jchem installation directory.

Thanks for your fast reply to both of my questions.

Regarding the Java heap size, do you think it is possible to add this in the future also as a parameter to the command line? It might be more obvious for the user when this possibility is already described in the documentation of the metabolizer command line tool.