From Peter.Lackner at sbg.ac.at Thu Sep 1 10:14:06 2005 From: Peter.Lackner at sbg.ac.at (Peter Lackner) Date: Thu Sep 1 16:51:25 2005 Subject: [Biopython-dev] Contribution Structure Comparison Message-ID: 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 From thamelry at binf.ku.dk Fri Sep 2 10:06:44 2005 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Fri Sep 2 20:27:23 2005 Subject: [Biopython-dev] Contribution Structure Comparison In-Reply-To: References: Message-ID: <200509021606.44404.thamelry@binf.ku.dk> > 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/ From bugzilla-daemon at portal.open-bio.org Sun Sep 4 15:11:39 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sun Sep 4 15:23:01 2005 Subject: [Biopython-dev] [Bug 1851] New: implicitly converted pointer Message-ID: <200509041911.j84JBcrL031921@portal.open-bio.org> 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@biopython.org ReportedBy: mail@philipp-benner.de Begin forwarded message: Date: Fri, 02 Sep 2005 15:51:43 -0600 From: dann frazier To: submit@bugs.debian.org Cc: David Mosberger 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 greater than the size of an integer, such as ia64. [1]http://people.debian.org/~dannf/check-implicit-pointer-functions [2]Function `mmcif_get_string' implicitly converted to pointer at Bio/PDB/mmCIF/MMCIFlexmodule.c:47 --- python-biopython-1.40b/Bio/PDB/mmCIF/MMCIFlexmodule.c~ 2003-10-10 05:23:38.000000000 -0600 +++ python-biopython-1.40b/Bio/PDB/mmCIF/MMCIFlexmodule.c 2005-09-02 15:47:44.000000000 -0600 @@ -1,5 +1,7 @@ #include +char *mmcif_get_string(void); + FILE *fp; static PyObject *MMCIFlex_open_file(PyObject *self, PyObject *args) ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Sep 5 02:32:13 2005 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Mon Sep 5 03:22:53 2005 Subject: [Biopython-dev] [Bug 1851] implicitly converted pointer Message-ID: <200509050632.j856WDSc010777@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1851 thamelry@binf.ku.dk changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From thamelry@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. From Peter.Lackner at sbg.ac.at Mon Sep 5 05:06:03 2005 From: Peter.Lackner at sbg.ac.at (Peter Lackner) Date: Mon Sep 5 13:25:31 2005 Subject: [Biopython-dev] Contribution Structure Comparison In-Reply-To: <200509021606.44404.thamelry@binf.ku.dk> References: <200509021606.44404.thamelry@binf.ku.dk> Message-ID: 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 University of Salzburg Hellbrunner-Str. 34 A-5020 Salzburg / Austria E-mail: Peter.Lackner@sbg.ac.at -------------- next part -------------- A non-text attachment was scrubbed... Name: SComPy1.0.tar.gz Type: application/x-gunzip Size: 26561 bytes Desc: Url : http://portal.open-bio.org/pipermail/biopython-dev/attachments/20050905/f712f273/SComPy1.0.tar-0001.bin -------------- next part -------------- SComPy provides python code for building protein structure comparison tools as well as two ready-to-use structure comparison approaches. INSTALLATION ============ SComPy is intended to be part future biopython releases. Meanwhile, SComPy is being installed as separate package but requires Biopython, release 1.40b or later (http://biopython.org/) and Numerical Python (http://numeric.scipy.org/). SComPy was tested on several 32 and 64 Bit Linux systems but also should work on any Unix like system. Unpack files: tar xvzf SComPy1.0.tar.gz and: cd SComPy1.0 As root run: python setup.py install That's it. USAGE ===== As input it uses structure files with PDB ATOM records, where every residue is represented by exactly 5 atoms, N,CA,C,O,CB. Other lines may not included. The scripts folder contains a python script to convert PDB files into the required format. PDB files are searched locally or they are downloaded from http://www.rcsb.org. E.g.: python get_backbones.py 2hhb creates the files 2hhb-A.bb, 2hhb-B.bb, 2hhb-C.bb, 2hhb-D.bb , one for each chain. Chains may be joined in single bb files, allowing for multi chain comparisons, e.g.: cat 2hhb-A.bb 2hhb-B.bb > 2hhb-AB.bb However, if you pack more than one chain into a bb file, different chain ids are required for each chain. python get_backbones.py 2bbm -c A extracts chain A from 2bbm, and creates file 2bbm-A.0.bb. The "0" indicates that 2bbm is an NMR file. 2bbm-A.0.bb contains model number 0 from 2bbm. After processing the pdb files for input, you may go ahead with the ready-to-use sample approaches. Please note that we only did a rough optimization of the parameters. Thus in some intricate cases of remote structural similarity you may need to change some parameters. Additionally, the refinement step applies only 4 iterations to save execution time. It may be useful to increase the parameter maxiter. An example: Prepare bb files for 2bbm and 4cln, open a python shell and type: >>> from SComPy import * >>> p=Parameter() # creates new set of parameters >>> approach2(p,"2bbm-A.0.bb","4cln.bb") This generates an number of output files: 2bbm-A.0_4cln.eqs ... a list of equivalent residues for the best superimposable solution 2bbm-A.0_4cln.ali ... the corresponding alignment 2bbm-A.0_4cln.pml ... a pymol script for visualizing the result. Additionally you get: 2bbm-A.0_4cln.joined.eqs 2bbm-A.0_4cln.joined1.pml 2bbm-A.0_4cln.joined2.pml 2bbm/4cln contain two similar domains which are not superimposable at the same time. Approach1 produces several alternative alignments, where two of them represent the superimpositions of the corresponding domains. As the two alternative solutions are non-overlapping, we may join them. *.joined1.pml and *joined2.pml contain the two corresponding superimpositions. If you prefer rasmol scripts instead of pymol scripts, after creating the parameter object, type: p.mf_format = "rasmol" Approach2 also detects circular permutations, as long as the permutated parts are superimposable. You might try this with 2bqp-A and 1nls. The spheres in the rasmol/pymol images represent the point of permutation (or the point where alternative alignments are joined). From christoph.gille at charite.de Tue Sep 6 11:50:07 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Tue Sep 6 11:49:44 2005 Subject: [Biopython-dev] Contribution Structure Comparison Message-ID: <63597.84.190.13.94.1126021807.squirrel@webmail.charite.de> 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 From wxuncheng at yahoo.com.cn Fri Sep 16 03:49:37 2005 From: wxuncheng at yahoo.com.cn (xuncheng wang) Date: Fri Sep 16 03:56:29 2005 Subject: [Biopython-dev] AlignAce help Message-ID: <20050916074938.41045.qmail@web15004.mail.cnb.yahoo.com> 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 "", 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! --------------------------------- DO YOU YAHOO!? 雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱 From bartek at rezolwenta.eu.org Fri Sep 16 04:43:32 2005 From: bartek at rezolwenta.eu.org (bartek wilczynski) Date: Fri Sep 16 05:18:32 2005 Subject: [Biopython-dev] AlignAce help In-Reply-To: <20050916074938.41045.qmail@web15004.mail.cnb.yahoo.com> References: <20050916074938.41045.qmail@web15004.mail.cnb.yahoo.com> Message-ID: <1126860212.432a85b439579@imp.rezolwenta.eu.org> Cytowanie xuncheng wang : > 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 "", 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. If you have AlignACE in your system, then make sure that it is either in your path or that you supply its location by using cmd parameter (like cmd="/opt/AlignAce/AlignACE"). -- regards Bartek Wilczynski From Biopython-dev at maubp.freeserve.co.uk Fri Sep 16 04:58:51 2005 From: Biopython-dev at maubp.freeserve.co.uk (Peter) Date: Fri Sep 16 05:33:31 2005 Subject: [Biopython-dev] AlignAce help In-Reply-To: <20050916074938.41045.qmail@web15004.mail.cnb.yahoo.com> References: <20050916074938.41045.qmail@web15004.mail.cnb.yahoo.com> Message-ID: <432A894B.5040901@maubp.freeserve.co.uk> 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 "", 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/ Note that they do warn that the Windows version is "out of date". (2) Is the AlignACE program on the path? i.e. If you type AlignACE at the command prompt, what happens? The program might be called AlignACE.exe or AlignACE.com, but in any case, just AlignACE should work. (Note that linux is case sensitive, I'm not sure what the proper capitalisation should be. It doesn't matter on Windows) If this fails (something like "command not found" or "'alignace' is not recognized as an internal or external command, operable program or batch file." etc depending on the version of windows) then... (3) Try adding the program's directory to the path. (4) In python, try modifying the cmd='AlignACE' to include a full path to the program executable file. Good luck Peter From rjw500 at cs.york.ac.uk Fri Sep 16 11:19:48 2005 From: rjw500 at cs.york.ac.uk (rjw500@cs.york.ac.uk) Date: Fri Sep 16 11:48:03 2005 Subject: [Biopython-dev] Re: [BioPython] Fwd: An interface to the maximum-likelihood programs ofPHYLIP In-Reply-To: <43186003.90006@maubp.freeserve.co.uk> References: <43184DEC.60600@student.cs.york.ac.uk> <43186003.90006@maubp.freeserve.co.uk> Message-ID: <56286.172.16.8.66.1126883988.squirrel@www.cs.york.ac.uk> 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@gmx.de > Robert Wilson 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. > > I did have a look at scripting PHYLIP some time ago, but the lack of > command line arguments made this less than straight forward. > > Your work sounds very interesting, and should make a useful addition to > BioPython. We will have to see what the maintainers make of it. > > Do you have a link to the code? > > Good documentation/examples would really be a bonus. > > Thanks > > Peter > From rjw500 at cs.york.ac.uk Mon Sep 19 13:57:35 2005 From: rjw500 at cs.york.ac.uk (rjw500@cs.york.ac.uk) Date: Mon Sep 19 13:58:59 2005 Subject: [Biopython-dev] Re: An interface to the maximum-likelihood programs of PHYLIP In-Reply-To: <43186003.90006@maubp.freeserve.co.uk> References: <43184DEC.60600@student.cs.york.ac.uk> <43186003.90006@maubp.freeserve.co.uk> Message-ID: <55253.172.16.8.66.1127152655.squirrel@www.cs.york.ac.uk> Dear Peter, I thought I should explain an important point that I failed to emphasise in the user manual on the interface. The methods that invoke the PHYLIP programs (dnaml etc) should not be called from the interactive prompt. The reason is that the information written to the phylip.results file about the command used to invoke the program is obtained from the stack. I hope has not caused any problems. All the best, Robert Wilson From wxuncheng at yahoo.com.cn Sun Sep 25 04:23:15 2005 From: wxuncheng at yahoo.com.cn (xuncheng wang) Date: Sun Sep 25 04:35:45 2005 Subject: [Biopython-dev] TAMO help Message-ID: <20050925082315.39976.qmail@web15003.mail.cnb.yahoo.com> Everyone, I want to use your TAMO in cygwin but I can't install it freely. I have preinstalled with c compiler python ,Numeric, AlignACE. After the install process reach to data file download step, the error will be : No module named localpaths. what can i do to install it completely. Thank you! --------------------------------- DO YOU YAHOO!? 雅虎邮箱超强增值服务－2G超大空间、pop3收信、无限量邮件提醒 From mdehoon at c2b2.columbia.edu Thu Sep 29 13:46:21 2005 From: mdehoon at c2b2.columbia.edu (Michiel De Hoon) Date: Thu Sep 29 13:53:06 2005 Subject: [Biopython-dev] Blast Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AE9ECCFF@cgcmail.cgc.cpmc.columbia.edu> Hi everybody, Recently there have been some problems with the Blast parser in Biopython, to the degree that the example in 3.1.2 in the tutorial does not work as advertised. The problem, of course, is that the NCBI file format as returned by a www blast run keeps changing, so we are condemned to keep fixing our parser to keep up with NCBI. To my surprise, the parser in Blast.NCBIWWW tries to parse HTML output instead of text output. My guess is that the HTML output changes more often and is more difficult to parse than text output. So isn't it possible to make NCBIWWW.qblast return text output instead of HTML and parse that instead? So my question is, why was the choice made to parse HTML instead of text? Is it simply because blast-on-the-web couldn't return text output in the past? --Michiel. Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1150 St Nicholas Avenue New York, NY 10032 From fkauff at duke.edu Thu Sep 29 14:17:06 2005 From: fkauff at duke.edu (Frank Kauff) Date: Thu Sep 29 15:19:16 2005 Subject: [Biopython-dev] Blast In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AE9ECCFF@cgcmail.cgc.cpmc.columbia.edu> References: <6CA15ADD82E5724F88CB53D50E61C9AE9ECCFF@cgcmail.cgc.cpmc.columbia.edu> Message-ID: <1128017826.4373.40.camel@osiris.biology.duke.edu> Hi all, On Thu, 2005-09-29 at 13:46 -0400, Michiel De Hoon wrote: > Hi everybody, > > Recently there have been some problems with the Blast parser in Biopython, to > the degree that the example in 3.1.2 in the tutorial does not work as > advertised. The problem, of course, is that the NCBI file format as returned > by a www blast run keeps changing, so we are condemned to keep fixing our > parser to keep up with NCBI. > To my surprise, the parser in Blast.NCBIWWW tries to parse HTML output > instead of text output. My guess is that the HTML output changes more often > and is more difficult to parse than text output. So isn't it possible to make > NCBIWWW.qblast return text output instead of HTML and parse that instead? > So my question is, why was the choice made to parse HTML instead of text? Is > it simply because blast-on-the-web couldn't return text output in the past? > I'd guess many people still want to really *look* at the output in their browser, which is just more comfortable with html, not to mention the possibility of clicking on the links, etc. I was just looking at the parser a minute ago because I wanted to see if I can get it to work with blastx output as well. I think one reason that the parser often chokes is that it is very strictly looking for specific tags, e.g.

, or blank lines, which are often added/removed/changed between versions, or just change from lowercase to uppercase. Parser stability might improve if these tags are handled more flexibly (or ignored as much as possible), and we concentrate more on "stable" parts of the output? Frank > --Michiel. > > > Michiel de Hoon > Center for Computational Biology and Bioinformatics > Columbia University > 1150 St Nicholas Avenue > New York, NY 10032 > > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- Frank Kauff Dept. of Biology Duke University Box 90338 Durham, NC 27708 USA Phone 919-660-7382 Fax 919-660-7293 Web http://www.lutzonilab.net/members/page225.shtml From mdehoon at c2b2.columbia.edu Thu Sep 29 18:43:41 2005 From: mdehoon at c2b2.columbia.edu (Michiel De Hoon) Date: Thu Sep 29 18:47:40 2005 Subject: [Biopython-dev] Blast Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AE9ECD03@cgcmail.cgc.cpmc.columbia.edu> > On Thu, 2005-09-29 at 13:46 -0400, Michiel De Hoon wrote: > > Hi everybody, > > > > Recently there have been some problems with the Blast parser in Biopython, to > > the degree that the example in 3.1.2 in the tutorial does not work as > > advertised. The problem, of course, is that the NCBI file format as returned > > by a www blast run keeps changing, so we are condemned to keep fixing our > > parser to keep up with NCBI. > > To my surprise, the parser in Blast.NCBIWWW tries to parse HTML output > > instead of text output. My guess is that the HTML output changes more often > > and is more difficult to parse than text output. So isn't it possible to make > > NCBIWWW.qblast return text output instead of HTML and parse that instead? > > So my question is, why was the choice made to parse HTML instead of text? Is > > it simply because blast-on-the-web couldn't return text output in the past? > > > > I'd guess many people still want to really *look* at the output in their > browser, which is just more comfortable with html, not to mention the > possibility of clicking on the links, etc. Then, the easiest solution might be to add a keyword argument to qblast to specify if HTML or text output is desired (default is text output), and use the text parser in NCBIStandalone. Then we only need to maintain the text-based parser (which is easier to maintain anyway), and users who want HTML output can still get it. --Michiel. From jeffrey.chang at duke.edu Thu Sep 29 22:16:04 2005 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Thu Sep 29 23:46:49 2005 Subject: [Biopython-dev] Blast In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AE9ECCFF@cgcmail.cgc.cpmc.columbia.edu> References: <6CA15ADD82E5724F88CB53D50E61C9AE9ECCFF@cgcmail.cgc.cpmc.columbia.edu> Message-ID: <6C84D88B-F56C-446B-A249-D86765260B00@duke.edu> On Sep 29, 2005, at 1:46 PM, Michiel De Hoon wrote: > To my surprise, the parser in Blast.NCBIWWW tries to parse HTML output > instead of text output. My guess is that the HTML output changes > more often > and is more difficult to parse than text output. So isn't it > possible to make > NCBIWWW.qblast return text output instead of HTML and parse that > instead? > So my question is, why was the choice made to parse HTML instead of > text? Is > it simply because blast-on-the-web couldn't return text output in > the past? You are right. It was done that way in the past when the only way to use NCBI's BLAST was to use the HTML output. (Actually, there was a version that you could access through a proprietary non-HTTP protocol, but the databases were not updated as frequently.) Now that we can get text, perhaps it is time to encourage users to use the text one. I believe the HTML parser is a few versions behind now, and unable to parse current BLAST output anymore. Jeff