Wilke:ParseDSSP

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Line 10: Line 10:
Load the script in python:
Load the script in python:
-
   import dsspData as dd
+
   import DSSPData as dd
Instantiate an object instance:
Instantiate an object instance:
-
   dd_ob = dd.dsspData()
+
   dd_ob = dd.DSSPData()
Input a dssp data file:
Input a dssp data file:

Revision as of 03:21, 21 February 2012

Image:DSSPData.txt

Above 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.

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