I've attached a mol file from KEGG that has several disconnected components.
When I run this file using cxcalc:
./cxcalc -N hi majorms -H 7 -f mol C12505.mol
I get an output that only contains the sulfate molecule and not the magnesium or any of the water.
I can't seem to find any options that will allow me to keep the all of the components.
The major microspecies calculation is performend only on the largest fragment, all other fragments (magnesium, water) are removed by cxcalc. There is no option to change that.
At my last count, of the 15K or so mol files released by KEGG, there are about 330 of them that have these multiple components.
I would like to be able to apply the majorms plugin to each of these components within a mol file, automatically. Is there a way of using MarvinBeans to take these mol files, disconnect them into the respective components, run the majorms plugin on each component, and then re-connect the results?
It can be done using the Java API.
- convert the molecule to fragments,
- generate the microspecies of all fragment,
- fuse the microspecies of fragments.
It's been years, evidently, but I wanted to write and confirm something. I can be sure that I'm using this plugin in the Java API:
but I was trying to find some documentation on this class, and in particular how it matches the options available when using cxcalc on the command line, is there any examples that relate the command line options to the plugin class functions?
...and then re-connect the results?
I've wrote an example code for your question.
Input is "Test.sdf". There are four molecules in this test file and every molecule contains at least two fragments.
The major forms are calculated from molecule to molecule separately for fragments. The final major form of the molecule is created from the linking of fragments.
The output is after running the attached "MultimajorMs.java" code on the "Test.sdf " file:
I hope this example is help you in certain point view.
P.S. I am not programmer just a chemist, my code may be is not so nice