[cctbxbb] Question about HHpred parser

[Louis Dumas]

Dear CCTBX developers,

 

I am a postdoc at EPFL working with HHpred for homology modeling of membrane proteins.

 

I have been trying to write my own HHpred alignment parser until I found the python script under “cctbx_fork/iotbx/bioinformatics/__init__.py/” that contains an HHpred parser.

 

My goal is to correctly parse the raw HHpred output file (.hhr), which involves unwrapping every alignment, parsing out a lot of text to finally obtain something like this:

 

>pdb_name

query-sequence

column score

 

Example:

 

>4U15

VYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWS

+........+..+..++|+++|++++.++.+.++++ +..+.++.+|+++|++.++...+........     +...|..

 

 

Being somewhat new to python, I was wondering whether the people who wrote this script are still around and could help me figure out whether the parser could be implemented in such a way.

 

Thanks for any help you can provide!

 

Best,

 

Louis D

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