[BioPython] HETATM records retrieval
Peter
biopython at maubp.freeserve.co.uk
Sat Jul 14 18:23:07 UTC 2007
Orlando Döhring wrote:
> Dear community,
>
> how should HETATM records be retrieved via Biopython? I assume it should be
> somewhere on the chain or residue level
In the PDB file you used, 1DHR, all the HETATM records are for solvents
(NAD = NICOTINAMIDE ADENINE DINUCLEOTIDE and HOH = water) so they don't
appear as part of the protein chains. I haven't looked at this recently
so its not fresh in my mind.chain.
When there are HETATM entries within a protein (e.g. alternative amino
acids) then they should be part of the chain.
> Using the following basic sample code :
>
> for model in self.structure.get_iterator():
> for chain in model.get_iterator():
> print chain.__repr__()
> for residue in chain.get_iterator():
> print residue.__repr__()
You don't need to explicitly call the get_iterator() method, so I much
prefer this style myself:
structure = ...
for model in structure:
for chain in model:
print repr(chain)
for residue in chain:
print repr(residue)
I've also used the repr() function rather than the hidden __repr__ of
the object; its the same end result but I find this clearer.
Have you read the example on this page? In particular the use of the
PPBuilder or CaPPBuilder classes:
http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/ramachandran/calculate/#BioPython
I also urge you to look at the author's (Thomas Hamelryck) documentation
here:
http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
This is much more useful than the automatic API documentation you linked to.
Peter
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