I'm trying to calculate BCUT descriptors on an SD file (JChem 6.2.2, Windows 7) using the following command:
generatemd c input.sdf -k BCUT -c config.xml -o output.txt
The config .xml file looks like this, taken straight from your web site:
<BCUT Type="Charge" Lowest="1" Highest="1" />
<BCUT Type="Polarizability" Lowest="1" Highest="1" />
<BCUT Type="HBond" Lowest="1" Highest="1" />
If I run the command, nothing happens, I just get 'Check configuration fil config.xml'.
It works with this bcut-example.xml file, sort of, but I first get an error message:
Too many arguments after -k, ignored
The calculation runs to its end, and 4 BCUT values rather than 6 are calculated for each compound.
Sorry for the late answer. The behaviour of the BCUT calculation you reported is a real issue, and we are investigating it further.
We will come back to you soon with a solution.
We have fixed this issue. The fix will be available in the next major release.