Wilke:ParseDSSP

From OpenWetWare

Revision as of 12:41, 21 February 2012

Here is a python script created to allow easy parsing of DSSP files.

For some reason, openwetware does not like the '.py' extension. Thus, you will have to download the txt file and change the extension from '.txt' to '.py'

To use it:

Load the script in python:

 import DSSPData as dd

Instantiate an object instance:

 dd_ob = dd.DSSPData()

Input a dssp data file:

 dd_ob.parseDSSP( dssp_file_name )

To get data for example:

 accesibilities = dd_ob.getACC()

Will return all of the solvent accesibilties. Each column in the dssp output file has its own getter. Here are all the getters:

 getResnums()
 getChainType()
 getAAs()
 getSecStruc()
 getBP1()
 getBP2()
 getACC()
 getH_NHO1()
 getH_NHO2()
 getH_OHN1()
 getH_OHN2()
 getTCO()
 getKAPPA()
 getALPHA()
 getPHI()
 getPSI()
 getX()
 getY()
 getZ()

The secondary structure method does not strip white space because it is necessary for decoding the output.