Dihedral angle calculator

In the near future a GeometryAnalizer class will be provided as part of ChemAxon's calculator plugins. Among many other functions it will be capable of calculating dihedral (torsional) angles.





In the meantime (in response to user request, see http://www.chemaxon.hu/forum/viewtopic.php?p=1638#1638) we give away the source code. Please note, that this code comes with no guarantee and it is intended for demonstration purposes.

Thank you! But make sure you spell "Analyzer" correctly when you add the class. ;-)

miklos wrote:

In the near future a GeometryAnalizer class will be provided as part of ChemAxon's calculator plugins. Among many other functions it will be capable of calculating dihedral (torsional) angles. In the meantime (in response to user request, see http://www.chemaxon.hu/forum/viewtopic.php?p=1638#1638) we give away the source code. Please note, that this code comes with no guarantee and it is intended for demonstration purposes.

I updated the sample code. The directionality of the dihedral angle was not considered by the original code, now this is fixed. Only one source line is changed, and this is the return statement in the calcDihedral() method. It must be





return n1.dotProd( v4 ) < 0 ? -da : da;





instead of





return da;








Please update your copies of the source code to get correct dihedral angle values.





Regards,


Miklos

There is a bug in the dihedral angle calculator. When the angle is exactly


180 degrees, it sometimes returns NaN (that means "not a number"), indicating an attempt to take a sqrt of a negative or some such.

Ooopps that's bad news indeed. Thanks Bob, we'll fix it and post a message here when it's done.


Regards,


Miklos

GeometryPlugin.getDihedral(int,int,int,int) method is already available in GeomertyPlugin API. It can calculate dihedral angles.





Regards,


Zsolt