calling the calculator from Java

User e94ae98ec6

06-08-2010 17:54:25

I am trying to call the chemaxon calculator from java

The following code works perfectly:

String[] args = {inputName, "logp"};

However i can't find the correct arguments to make it save the output to a file. The following fails:
        String[] args = {"-o "+ outputName, inputName, "logp"};

Although the following shell command works fine:

cxcalc -o results.sdf molecules.sdf logp

Any idea about how to pass the -o argument to the chemaxon.marvin.Calculator.main or at least how can i capture the output of the calculator?


User e94ae98ec6

06-08-2010 17:59:40

I forgot to mention that when i try to execute the aforementioned        String[] args = {"-o "+ outputName, inputName, "logp"};

I get the following errors: -o /Users/path/to/my/output/results.sdf (No such file or directory)

It seams that the class doesn't undestand the -o argument and just treats it as a part of a filename

User e94ae98ec6

10-08-2010 10:43:58

In case anyone else is following the thread without posting, i was able to find the correct arguments:

String[] args = {"-o", outputName, inputName, "logp"};

ChemAxon e08c317633

23-08-2010 10:12:56


Sorry, this topic escaped our notice.

FYI: calculator plugins have their own Java API, see e.g. the logP plugin API: