[OpenBabel-Devel] forcefield classes

[Tim V. <tim...@gm...>]

 Yesterday I commited some code to update the force field classes, this mail
contains some details about the changes.

LineSearch(OBAtom *atom, vector3 &direction),
SteepestDescent(int steps, int method),
ConjugateGradients(int steps, int method):

The algorithm for LineSearch is explained in forcefield.cpp
The method argument for SteepestDescent and ConjugateGradients can be
OBFF_ANALYTICAL_GRADIENT or OBFF_NUMERICAL_GRADIENT.
There are still some problems with the analytical gradients. The gradient
for the torsional term is not always correct, but I'm not really sure why.
The analytical gradients were calculated using mathematica and almost
copy/pasted to the source code. With the use of ValidateGradients() I hope
to solve this problem soon, but if you should see the problem please point
it out. (At the moment I think it has something to do with the derivative of
cos(n*tor) wich is zero where it should be zero, but also exactly between
these points. Need to look into this...)

More advenced optimization methods (Newton-Raphson) will be added later...


ValidateLineSearch(), ValidateSteepestDescent(),
ValidateConjugateGradients():
Used to validate the implementation of these optimization functions using a
simple example function x^2 + 2*y^2. The minimum of this function is (0,0)
as you can see directly. The ValidateSteepestDescent functions finds this
minimum (by approximation) in 3 steps as expected. The
ValidateConjugateGradients functions finds this minimum (by approximation)
in 2 steps as would be expected since this is a function of 2 variables.
(This example is taken from "Molecular Modelling, Principles and
Applications, Andrew R. Leach, 2nd ed.)



MMFF atom typing:
This is done using SMARTS rules in mmffsymb.prm. In the future this may
change since the rules become rather complex. There are alot of atom types
in mmff and atoms in a ring that OB perceives as aromatic isn't always
aromatic in mmff. Suggestions are welcome here.

The first 45% of the test suite works (excluding some molecules) producing
good results. The errors are in the range 0.00-1.00% and due differences in
calulated bond lengths etc.

While doing this I noticed that I sometimes got errors from openbabel's atom
type translation. In types.txt there are entries wich are case sensitive
such as Cl, Br, ... The mol2 files use CL, BR, ... Is this a bug, or should
the mol files use Cl, Br.?

Structure generation:
I started implementing a distance geometry algorithm. This requires some
complex matrix operations (eigenvalues, eigenvectors, ...) OB currently
doesn't support. What would be the best way to solve this problem? Linking
against a library may be might be unwanted for users only interested in
conversion. Making a new implementation is possible, but time consuming.
Integrating GPL parts from libraries is an option. Suggestions are
welcome...
These matrix operations would alse be usefull in other parts such as
newton-raphson optimization (determinant of 3Nx3N hessian needed, N = #
atoms)

Regards,
 Tim