[Biojava-l] Find hydrogen bond angle

[Andreas Prlic]

Hi Avid,

The Calc class uses the atom object to represent vectors. You will
need to identify the vectors between which you want to measure the
angle and represent them as "atoms" as well. For example to get the
vector NH you can do

AminoAcid aa1 ...

Atom N = aa1.getN();
Atom H = aa1.getH();

Atom nh = Calc.subtract(N,H);

Andreas

On Tue, Jun 21, 2011 at 4:49 AM, MOHAMMAD (AVID) AFZAL
<1000947A at student.gla.ac.uk> wrote:
> Dear Dr.PRLIC ,
> I want to calculate NHO and COH angle in a pdb file, using bioJava. However the angle method only takes two atoms as parameter and in your weblog you only mentioned how to calculate hydrogen bond energy by using distance method. I wonder how can I find the angle of hydrogen bond by using bioJava. Thank you kindly in advance for your time and concern.
> Yours sincerely,
> Avid Afzal.