[Biopython-dev] [Biopython - Bug #3441] (New) DSSP parser fails for some DSSP 2.1.0 output files

[redmine at redmine.open-bio.org]

Issue #3441 has been reported by Ahmet Sinan Yavuz.

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Bug #3441: DSSP parser fails for some DSSP 2.1.0 output files
https://redmine.open-bio.org/issues/3441

Author: Ahmet Sinan Yavuz
Status: New
Priority: High
Assignee: 
Category: 
Target version: 
URL: 


Some of the DSSP files created by mkdssp 2.1.0 starts with following header:
<pre>
==== Secondary Structure Definition by the program DSSP, CMBI version by M.L. Hekkelman/2010-10-21 ==== DATE=2013-07-15        .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
                                                                                                                               .
  336  1  0  0  0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
</pre>

and following parsing code (make_dssp_dict function, line 121, @sl[1]@ part) fails for the 3rd line in the example given above with "IndexError: list index out of range" as expected.
<pre>
try:
        start = 0
        keys = []
        for l in handle.readlines():
            sl = l.split()
            if sl[1] == "RESIDUE":
            # Start parsing from here
                start = 1
                continue
...

</pre>

Potential temp. solution:
<pre>
    try:
        start = 0
        keys = []
        for l in handle.readlines():
            sl = l.split()
            if len(sl) > 1:
                if sl[1] == "RESIDUE":
                    # Start parsing from here
                    start = 1
                    continue
...
</pre>



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