How to use command line to run metabolizer

Currently, I have 400 chemicals. I would like to know their major meatbolites.

I tried the command line under window prompt

metabolize
in.mol -x -lg 3 -g -f sdf -o out.sdf

the command line did nothing but to open the GUI interface.

Could you please instruct me how to run the metabolizer command line?

Moverover, is there any way to only output the 1st metabolite after ranking?

Thank you very much

I tried it and it seems working, the command line starts when parameters are given, GUI starts when the metabolize command is called without any parameters. Don't you have any preview versions on your computer as well accidentally calling it?

Metabolizer does not have a filter to limit the number of metabolites printed out, I am figuring out a solution.

Thank you ver much for help! I will try it once more.

One more thing, do you think it is possible to integrate the command line into a script and run it as a script or not?

Thank you very much for your answer!

 

Do you mean the bash script? As far as I know it is possible.

I have enhanced the command line functionalities providing better control for batch output. These new options (and a couple more) will appear in the 6.0.1 bugfix release shortly.

-m
write the metabolites of each substrate into a different output file, otherwise all metabolites go to a single output file

-gn 3
write the top 3 most likely metabolites only to the output file (based on global accumulation)

-ga 0.001
write metabolites having higher global accumulation than 0.1% to the output file

 

In the meantime, you can probably use the head command of bash to filter out the top N lines of the output. This can help if your metabolites are in a line notation format such as SMILES. You can certainly convert the filtered SMILES to MRV or SDF if you wish with the molconvert tool.

that is great improvement! Looking forward to the version!

Thanks a lot for your help!

I recently updated JChem to version 14.9.1.  After installing this new version, I'm no longer able to run Metabolizer from the command line.  When I type "metabolize InputFileName -o OutputFileName", the Metabolizer application window opens instead of executing in batch mode.

Thank you for reporting the issue. I will try to reproduce it and will get back to you soon.

I tested with the latest jchem version (14.9.29.0), and it works correctly. Does your path point to the correct version of the metabolize tool?