[BioPython] DSSP parser in Biopython
Robert Campbell
rlc1 at post.queensu.ca
Wed Feb 18 12:31:28 EST 2004
Catherine,
On 2004-02-16 10:43 you wrote:
>
> Is there any biopython module under development for DSSP?
> Does someone have a DSSP parser in python (or biopython)?
I guess that would depend on how much of the DSSP output you need to
parse. Kristian Rother has a DSSP parser as part of his rTools for
PyMOL:
http://www.rubor.de/bioinf/pymol_rubor.html
I'm not sure if it does all that you need, but if you look at the
function calcDSSP in the file rtools/rModel.py in that distribution
you'll have one. It simply steps over the output file of DSSP and
appends the secondary structure information to an array.
inl=inf.readlines()
residues=0
sec=[]
# parse all the lines and collect secondary structures in sec[]
for l in inl:
if residues and len(l)>50:
resno=l[6:10]
chain=l[11]
sstype=l[16]
sec.append((resno,chain,sstype))
if re.search("\A # RESIDUE AA STRUCTURE BP1 BP2",l):
residues=1
I wouldn't be too difficult to add to the same loop the necessary code
for extracting the other information in the DSSP output file.
Cheers,
Rob
--
Robert L. Campbell, Ph.D. <rlc1 at post.queensu.ca>
Senior Research Associate phone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
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