[Biopython-dev] PDB module

[Iddo Friedberg]

Hi,

I have played a bit more with the PDB module, and I really like it.
Thomas: any chance of added functionalities? I was thinking of:

Methods:

Residue:
* psi, phi, omega, chi1 and chi2 angles
* centroid "atom" position (in order to calculate residue distances).
* neighbors: returns neighboring residues by centroid

Atom:
neighbors: returns neighboring atoms. can be limited to a chain, or not.

Functions:
hbond(residue1, residue2) returns true if residue1 and residue2 are
hbonded.

ramachandran_plot(chain) (can be a method)

contact_map(chain)  (ditto)

I think these are basic functions (some of which you have probably written
already), which will look nice in the PDB module.

Yours,

Iddo

--

Iddo Friedberg                                  | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/