[Biopython-dev] PDB module

[Thomas Hamelryck]

Hi Iddo,

> I have played a bit more with the PDB module, and I really like it.

Glad you like it. 

> Thomas: any chance of added functionalities? 

Yep. I am (still!) working on the C++ code to do lookup in space (eg. find 
all atom pairs within 3 A, find all residues within a certain radius etc.). 
Many of the items in your list (neighboring residues and atoms, contact maps, 
H-bonds) can then be easily (and efficiently!) implemented in python. 

I have some code to calculate angles, dihedral angles etc. I'll add that one 
of these days.

Before I add things like Ramachandran plots etc. I want to add code to locate 
the various polymers in crystal structures (polypeptides, RNA, DNA, 
glycosidic bonds etc.). Polymer objects would be built by a PolymerBuilder 
object, which in turn relies on a PolymerDefinition object that specifies how 
to build the polymer (e.g. whhich atoms are involved etc.). 

Something like:

p=PolymerBuilder(PolypeptideDefinition)
model=structure[0]
list_of_polymers=p.build(model)
 
Cheers,

---
Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
Intitute for Molecular Biology           ULTR Department
Paardenstraat 65   1640 Sint-Gensius-Rode    Belgium
              http://ultr.vub.ac.be/~thomas