[Biopython-dev] Notification: incoming/50

[biopython-bugs at bioperl.org]

JitterBug notification

jchang moved PR#50 from incoming to fixed-bugs
Message summary for PR#50
	From: "Gavin E. Crooks" <gec at compbio.berkeley.edu>
	Subject: Re: [Biopython-dev] Notification: incoming/49
	Date: Wed, 24 Oct 2001 17:40:52 -0700
	0 replies 	0 followups
	Notes: Gavin reports this as fixed.
- jchang


====> ORIGINAL MESSAGE FOLLOWS <====

>From gec at sienna.berkeley.edu Wed Oct 24 20:49:43 2001
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From: "Gavin E. Crooks" <gec at compbio.berkeley.edu>
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Subject: Re: [Biopython-dev] Notification: incoming/49
Date: Wed, 24 Oct 2001 17:40:52 -0700
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How about  "A:-1-126", direct from SCOP...
16118	px	a.4.5.8	d1b9ma1	1b9m A:-1-126

I am in the middle of updating the SCOP module, and I have already
refactored that code, and fixed this bug. And I've written a nice shiny
unit test.  But I was concerned that this same bug could crop up elsewhere.
Its the kind of obscure boundary case that could trip up any code working 
with PDB sequence numbers.

Gavin

gec at compbio.berkeley.edu
http://threeplusone.com

> Hi Gavin,
> 
> Could you send me a sample of this?  It'll be helpful to have a test 
> case to test fixes.
> 
> Thanks,
> Jeff
>
> >Full_Name: Gavin Crooks
> >Module: SCOP/Location.py
> >Version:
> >OS:
> >Submission from: sienna.berkeley.edu (128.32.236.51)
> >
> >PDB residue sequence numbers can, on occasion, be
> >negative. e.g. 1B9N. SCOP domains sometimes start
> >on negative sequence numbers. This breaks the
> >location parser in Bio.SCOP.Location.py
>