[ghemical-devel] MM calculations in Bioclipse port of libghemical

[Rob Schellhorn]

Hi all,

I'am working on a Bioclipse plug-in which allows for using libghemical 
and making good progress. Now I have some questions however:

1) My first goal is to get MM calculations working. This is how I call 
libghemical:
   
    JNI_Wrapper *wrapper = ...;
    model *m = new model();
    // ...
    ParseModel(wrapper, m, in); // See description below
    m->AddHydrogens();
    m->DoEnergy();
    // ...  
    return;

The wrapper objects reads from my Java model, which provides an array of 
atoms and bonds. The idea is that the plug-in must handle all CDK 
(http://almost.cubic.uni-koeln.de/cdk/cdk_top) supported formats. Those 
formats might contains Hydrogen atoms and bonds containing Hydrogen 
atoms, so my first assumption is to skip them, because they are handled 
by the AddHydrogens method. Is this assumption correct or do I need to 
process them otherwise?

Second, the atom coordinates routine I took from the winlibghemical demo 
application, which scales the coordinates. I think is is specific for 
that input format, so what is the unit those coordinates must be?

As I run a computation for 2-methylpropan-1-ol
==>
http://svn.sourceforge.net/viewvc/bioclipse/branches/b1/bc_blueobelisk_data/data/chemical-structures/alcohols/2-methylpropan-1-ol.cml?view=markup

The output is:
    PrintToLog: Using default rules in AddHydrogens().
    creating bt1-terms: 14 terms, 0 errors.
    creating bt2-terms: 25 terms, 0 errors.
    creating bt3-terms: 30 terms, 0 errors.
    creating nbt1-terms: PrintToLog: Calculating Energy (setup = allmm, 
engine
    = tripos5.2 implementation ported from ghemical-1.00).
    PrintToLog: Energy = 1932265.41311765 kJ/mol

Which seems to be ok, but I like to verify the output (which has a 
positive value?). Is it correct the energy of MM calculations is 
positive or is there something going wrong?

2) I like to read those calculated values from the model, but can't 
figure out how I can access that data. Perhaps someone can point me in 
the right direction?

With kind regards,

Rob Schellhorn