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Peter Lackner | 1 Sep 2005 16:14
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Contribution Structure Comparison


Dear Biopython developers,

I'd like to contribute code (Module SComPy) for protein structure
comparison to biopython. This expands the PDB and SVDSuperimposer
module. The code consists of (i) a library of classes and functions
for performing different steps in standard structure comparison
approaches, (ii) a C extension implementing some time-critical
procedures and (iii) examples application performing structure
alignments. The code is documented in epydoc conform style.

There is one supplementary script which preprocess PDB files to
be usable for for SComPy a two scripts which demonstrate some
low level functionality.

Please let me know if you are interested to integrate SComPy 
into Biopython.

-Peter

-----------------------------------------------

 Peter Lackner
 Department of Molecular Biology
 University of Salzburg , Austria
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Thomas Hamelryck | 2 Sep 2005 16:06
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Re: Contribution Structure Comparison


> I'd like to contribute code (Module SComPy) for protein structure
> comparison to biopython. 

Hi Peter,

Sounds great. Can you send the code so we can take a look at it?

Cheers,

--

-- 
Thomas Hamelryck, Postdoctoral researcher
Bioinformatics center
Institute of Molecular Biology and Physiology
University of Copenhagen      
Universitetsparken 15 Bygning 10                 
2100 Copenhagen, Denmark
---
http://www.binf.ku.dk/users/thamelry/
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bugzilla-daemon | 4 Sep 2005 21:11

[Bug 1851] New: implicitly converted pointer

http://bugzilla.open-bio.org/show_bug.cgi?id=1851

           Summary: implicitly converted pointer
           Product: Biopython
           Version: Not Applicable
          Platform: Other
               URL: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=326403
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: mail <at> philipp-benner.de

Begin forwarded message:

Date: Fri, 02 Sep 2005 15:51:43 -0600
From: dann frazier <dannf <at> hp.com>
To: submit <at> bugs.debian.org
Cc: David Mosberger <David.Mosberger <at> acm.org>
Subject: Bug#326403: python-biopython: implicitly converted pointer

Package: python-biopython
Version: 1.40b-1
Severity: important
Tags: patch

Our automated buildd log filter[1] detected a problem[2] that will cause
your package to segfault on architectures where the size of a pointer is
(Continue reading)

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bugzilla-daemon | 5 Sep 2005 08:32

[Bug 1851] implicitly converted pointer

http://bugzilla.open-bio.org/show_bug.cgi?id=1851

thamelry <at> binf.ku.dk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Additional Comments From thamelry <at> binf.ku.dk  2005-09-05 02:32 -------
Fixed in CVS.

------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
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Peter Lackner | 5 Sep 2005 11:06
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Re: Contribution Structure Comparison


Here is the code and a README file. The setup.py installs SComPy 
as separate module, at the moment.

On Fri, 2 Sep 2005, Thomas Hamelryck wrote:

> 
> > I'd like to contribute code (Module SComPy) for protein structure
> > comparison to biopython. 
> 
> Hi Peter,
> 
> Sounds great. Can you send the code so we can take a look at it?
> 
> Cheers,
> 
> -- 
> Thomas Hamelryck, Postdoctoral researcher
> Bioinformatics center
> Institute of Molecular Biology and Physiology
> University of Copenhagen      
> Universitetsparken 15 Bygning 10                 
> 2100 Copenhagen, Denmark
> ---
> http://www.binf.ku.dk/users/thamelry/
> 
> 
-----------------------------------------------
 Assoc.Prof. Peter Lackner
 Department of Molecular Biology
(Continue reading)

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Dr. Christoph Gille | 6 Sep 2005 17:50
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Contribution Structure Comparison

Dear Peter,

I think it is good idea.
Would you also like to add SComPy to STRAP ?

It usually takes to evenings to add a module to STRAP.
CE/CL  and a superposition program by A Goede are already included but
it is nice to have the choice between several methods when remote homologs
are compared.

People could use it either in BATCH mode, for scripting and inside the GUI.
I  also consider to bring STRAP and Biopython together.

There is a button which displays both models in Pymol.

Cheers Christoph
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xuncheng wang | 16 Sep 2005 09:49
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AlignAce help

Hello everyone,
  T'm newer for Biopython.I run it in windows.I have no programming 
experience.Now I use AlignAce module in Bio. My programming process is:
>>> from Bio.AlignAce.AlignAceStandalone import AlignAce
>>> from Bio.AlignAce.Parser import AlignAceParser
>>> AlignAce("test.seq", cmd='AlignACE', gcback=0.38)

the error is:

Traceback (most recent call last):
  File "<pyshell#27>", line 1, in -toplevel-
    AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
  File 
"D:\Python24\Lib\site-packages\Bio\AlignAce\AlignAceStandalone.py", line 63, in AlignAce
    raise IOError, "Executable does not exist at %s" % cmd
IOError: Executable does not exist at AlignACE

What can i do with this error. How can I programme this modules 
exactly. thanks!

		
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bartek wilczynski | 16 Sep 2005 10:43
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Re: AlignAce help


Cytowanie xuncheng wang <wxuncheng <at> yahoo.com.cn>:

> Hello everyone,
>   T'm newer for Biopython.I run it in windows.I have no programming 
> experience.Now I use AlignAce module in Bio. My programming process is:
> >>> from Bio.AlignAce.AlignAceStandalone import AlignAce
> >>> from Bio.AlignAce.Parser import AlignAceParser
> >>> AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
>  
> the error is:
> 
> Traceback (most recent call last):
>   File "<pyshell#27>", line 1, in -toplevel-
>     AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
>   File 
> "D:\Python24\Lib\site-packages\Bio\AlignAce\AlignAceStandalone.py", line 63,
> in AlignAce
>     raise IOError, "Executable does not exist at %s" % cmd
> IOError: Executable does not exist at AlignACE
> 
>  
> 
> What can i do with this error. How can I programme this modules 
> exactly. thanks!
> 

In order to use AlignAce, you have to have AlignACE executable present in your
system. It seems that your script cannot find AlignACE executable. you can
download it from here: http://atlas.med.harvard.edu/download/index.html.
(Continue reading)

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Peter | 16 Sep 2005 10:58
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Re: AlignAce help

xuncheng wang wrote:
> Hello everyone,
>   T'm newer for Biopython.I run it in windows.I have no programming 
> experience.Now I use AlignAce module in Bio. My programming process is:
> 
>>>>from Bio.AlignAce.AlignAceStandalone import AlignAce
>>>>from Bio.AlignAce.Parser import AlignAceParser
>>>>AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
> 
>  
> the error is:
> 
> Traceback (most recent call last):
>   File "<pyshell#27>", line 1, in -toplevel-
>     AlignAce("test.seq", cmd='AlignACE', gcback=0.38)
>   File 
> "D:\Python24\Lib\site-packages\Bio\AlignAce\AlignAceStandalone.py", line 63, in AlignAce
>     raise IOError, "Executable does not exist at %s" % cmd
> IOError: Executable does not exist at AlignACE
> 
> What can i do with this error. How can I programme this modules 
> exactly. thanks!

I've not used the module myself, but there are a few things I suggest
you check.

(1) Have you installed the standalone AlignAce program?

http://atlas.med.harvard.edu/
(Continue reading)

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rjw500 | 16 Sep 2005 17:19
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Re: [BioPython] Fwd: An interface to the maximum-likelihood programs ofPHYLIP

Dear Peter,

I have now put up a link to my interface to the maximum-likelihood
programs of PHYLIP:

http://www-student.cs.york.ac.uk/~rjw500/phylip/index.php

My MSc course finishes soon, so I am afraid the page will only be
available for one week. I will post another address as soon as I have
found a new home.

I have really enjoyed the project and will be interested to hear what you
think. I developed the interface on an Apple iMac, and thanks to Gemma
Atkinson have also tested it under Windows. However, it would be nice to
know how it performs in the outside world.

All the best,

Robert.

PS. If you would like to contact me after the 22/9 write to r77a21 <at> gmx.de

> Robert Wilson <rjw500 <at> cs.york.ac.uk> wrote:
>  > I am studying for an MSc in Information Processing at York  University
>  > in the UK. As part of the course I am carrying out a  short research
>  > project with Dr. James Cussens. I chose to develop  an interface in
>  > Python to the maximum-likelihood programs of the  phylogenetic
>  > analysis package PHYLIP. The code is based on the  modules available
>  > in Biopython and I was wondering if you would be  interested in
>  > incorporating it into the next release of Biopython.
(Continue reading)

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