Hi,
As to the bug, would it be ok if I include the three Sparky *.list
peak list files into the test suite as well? This will help in fixing
the problem. If there is any unpublished data which you would prefer
to keep private, the numbers can be randomised while still being
useful for the test suite. The cNTnC_noe0_2.list could also be
significantly shortened for the test.
The problem is how relax handles the Sparky assignment strings. The
parsing of the assignment is not yet flexible enough to handle all the
different Sparky variants of missing 'groups', atom names, etc. And
it's currently only designed to handle the format of the group being a
residue name followed by number, and then two atom names with no
numbers. For example 'LEU3N-HN' is residue LEU 3 for the atoms N and
HN. I wonder how Sparky knows where the group finishes and were the
first atom starts? This could be a problem if the group doesn't end
in a number. Would you have any idea? For this, relax could simply
give a RelaxWarning that the 'group' format must end with the residue
number. Although this is problematic if you are working on a small
organic molecule. It might be worth me creating a list of all
possible variants to add to the test suite.
In the *.list files, there are a number of different assignment string
patters:
1) '?-?'
2) '15N-HN'
3) '15'
Number 1 relax will have to throw a RelaxWarning that that spin cannot
be identified. In Number 2 I can see where this causes a bug, as
relax is expecting text before the 15. This is an easy fix. I'm not
sure how to handle Number 3 though. relax now handles multiple spins
per residue, so this is confusing. I could just assume that this is
the residue number, try to find that residue, and check that only a
single spin exists for it within relax. All of this needs to be able
to handle proteins (with multiple spins per residue), RNA (again with
multiple spins per residue), small molecules with no residues but lots
of spins, etc. Would anyone have any ideas as to how to handle this
problem?
Regards,
Edward
On Sat, Jun 28, 2008 at 1:10 AM, Ryan MB Hoffman
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/bugs/?11913>
Summary: Problems with reading Sparky formatted file
Project: relax
Submitted by: rydog
Submitted on: Friday 06/27/2008 at 23:10
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: 1.2.13
Operating System: GNU/Linux
_______________________________________________________
Details:
Hello,
First of all, I would like to request that relax support NMRView peak lists.
I appreciate this is not the right location to request this, but the
community is still small, and I'm submitting a bug anyways. I have attached
an example of this type of file (debug.xpk), and a Perl script that can
extract the volume lines (xpk2list.pl). They are attached as the tarball
"convert.tgz"
For the meantime, I have been converting the NMRView peaklists to Sparky
with
a script.
The actual session I/O looks like:
noe.read(name,file='cNTnC_noe0_3.list',spectrum_type='ref',format='sparky')
Reference spectrum.
Sparky formatted data file.
Opening the file 'cNTnC_noe0_3.list' for reading.
Number of header lines found: 2
RelaxError: Improperly formatted Sparky file.
I get the same error with a handful of .list files, generated either by my
conversion scripts or from Sparky itself. Three files are attached. The one
ending in '_2' was directly outputted from Sparky.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10 Name: cNTnC_noe0_2.list Size: 8kB By:
rydog
<http://gna.org/bugs/download.php?file_id=4485>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10 Name: cNTnC_noe0_3.list Size: 157B By:
rydog
<http://gna.org/bugs/download.php?file_id=4486>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10 Name: cNTnC_noe0-2.list Size: 153B By:
rydog
<http://gna.org/bugs/download.php?file_id=4487>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10 Name: convert.tgz Size: 776B By: rydog
<http://gna.org/bugs/download.php?file_id=4488>
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?11913>
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Re: [bug #11913] Problems with reading Sparky formatted file