[Biopython] DSSP python version

[Andrew Dalke]

On Jan 21, 2011, at 5:09 AM, Rojan Shrestha wrote:
> I am very much interested on python libraries available for bioinformatics.
> Currently, I need python version of DSSP or any other programs that can
> evaluate secondary structure of protein from coordinate data.

Another option is STRIDE, which is what VMD uses for its
secondary structure calculation code. That's all available
though the scripting interface, and VMD supports Python.

(Some history now; or should I say reminiscing?)

I chose STRIDE instead of DSSP for VMD because 15 years ago
there were only three secondary structure programs I could
find. DSSP didn't allow redistribution and its output format
was nasty to parse. The DSSP implementation in RasMol was
completely undocumented. While STRIDE allowed redistribution
and was easy to parse.

I have no idea on the current state of the art.


				Andrew
				dalke at dalkescientific.com