[Bioperl-l] [Q] distance calculation between residues in PDB

[Kris Boulez]

Quoting Vlad P (reason@postmark.net):
> Hello,
> I am trying to find out how to calculate distances between protein residues
> using PDB files,
> wanted to know if there is some support in bioperl for that ( I did look at
> the PDB class
> but did not find an explicit support for it).
> 

In the bioperl source tree there is an example code in
examples/structure/struct_example2.pl . It calculates the distances
between all Cysteine SG atoms to see which can form a disulfide bridge.

There is no explicit method in bioperl to do distance calculations, but
the subroutine in the example is pretty trivial.

The example does calculations between atoms, not residues. So, you'll
have to calculate the center of the residue for now.

Which brings me to my question: which helper methods would you find
usefull to have to do structure based work in Bioperl ?

Kris,