From btiwari at ceh.ac.uk Fri Nov 4 04:39:00 2005 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri Nov 4 09:04:38 2005 Subject: [BioPython] biosql problem - AttributeError: 'Cursor' object has no attribute 'insert_id' Message-ID: Hello, I am new to using biopython and biosql. I have been following the information in the document Basic BioSQL with Biopython to try and get familiar with using biopython to work with mysql databases and specifically I have tried to load a Genbank file containing a small bacterial genome into a database. I believe I have carried out all the instructions correctly (i.e. interpreted to fit the system I am working on - Debian Sarge). The code and traceback call that results is: ############################# >>> from BioSQL import BioSeqDatabase >>> from Bio import GenBank >>> server = BioSeqDatabase.open_database(driver="MySQLdb", user="root", host="localhost", db="bioseqdb") >>> db = server.new_database("testorama7") >>> parser = GenBank.FeatureParser() >>> iterator = GenBank.Iterator(open("CP000010.gbk"), parser) >>> db.load(iterator) Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.3/site-packages/BioSQL/BioSeqDatabase.py", line 414, in load db_loader.load_seqrecord(cur_record) File "/usr/lib/python2.3/site-packages/BioSQL/Loader.py", line 37, in load_seqrecord bioentry_id = self._load_bioentry_table(record) File "/usr/lib/python2.3/site-packages/BioSQL/Loader.py", line 225, in _load_bioentry_table taxon_id = self._get_taxon_id(record) File "/usr/lib/python2.3/site-packages/BioSQL/Loader.py", line 198, in _get_taxon_id taxon_id = self.adaptor.last_id("taxon") File "/usr/lib/python2.3/site-packages/BioSQL/BioSeqDatabase.py", line 148, in last_id return self.dbutils.last_id(self.cursor, table) File "/usr/lib/python2.3/site-packages/BioSQL/DBUtils.py", line 34, in last_id return cursor.insert_id() AttributeError: 'Cursor' object has no attribute 'insert_id' ################################ I have seen information on the web suggesting that MySQLdb has undergone an API change such that the insert_id() function has moved from the cursor to the database object. Is it possible that such a change is at the core of my problem? Or have I just done something wrong? I am working on Debian Sarge, using biopython version 1.40b (though I have checked the code for the latest release and nothing under BioSQL has changed). Any advice anyone has about how to sort out this error would be greatly appreciated. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. -------------- next part -------------- A non-text attachment was scrubbed... Name: Header Type: application/octet-stream Size: 1533 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20051104/a05f586a/Header-0001.obj From tozim at gmx.de Fri Nov 4 10:21:17 2005 From: tozim at gmx.de (kaoskrew.de) Date: Fri Nov 4 11:42:27 2005 Subject: [BioPython] Sequence Numbering in PDB-Files Message-ID: <38df62ca8df4ffe87620cd7396de5c81@gmx.de> Hi Everyone! I'm pretty new in terms of biopython, so it might be, that I just didn't get into the right parts of the manual yet. So first I'd like to refer to this email from the archive: http://portal.open-bio.org/pipermail/biopython/2004-November/002452.html I have the same problem. Because I need a list of all positions in a pdb-structure including the position and the icode, I'd need to find out the start- and end- position. Additionally I didn't found out yet how it's possible for me to iterate over all positions or how I even could get all of the positions. Yet the way I chose looks like that: from Bio.PDB.PDBParser import PDBParser p = PDBParser(PERMISSIVE=1) structure_id="1nrn" filename="PDBs/1nrn.pdb" s=p.get_structure(structure_id,filename) print s model=s[0] chain_L=model["L"] res=chain_L[10] test=res.get_id() print test[1] That would lead to an output of just the position. But it's not really working out yet. I had to submit the chain, which should be found automatically, iterating over the positions stopped somewhere in between the sequence without concrete reason and the icode was totally ignored. So, if anyone has worked with this problem already, help would be greatly appreciated! If I just didn't find the right page in the manual, please give me a hint. Thanks, Tobias Zimmer -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1423 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20051104/8f429024/attachment.bin From thamelry at binf.ku.dk Fri Nov 4 11:57:43 2005 From: thamelry at binf.ku.dk (thamelry@binf.ku.dk) Date: Fri Nov 4 11:56:15 2005 Subject: [BioPython] Sequence Numbering in PDB-Files In-Reply-To: <38df62ca8df4ffe87620cd7396de5c81@gmx.de> References: <38df62ca8df4ffe87620cd7396de5c81@gmx.de> Message-ID: <40392.83.92.39.206.1131123463.squirrel@www.binf.ku.dk> > Hi Everyone! > > I'm pretty new in terms of biopython, so it might be, that I just didn't > get into the right parts of the manual yet. It shows :-) The Bio.PDB FAQ is at http://www.biopython.org/docs/cookbook/biopdb_faq.pdf You probably need something like: for model in structure: for chain in model: for residue in chain: hetatm_flag, resseq, icode=residue.get_id() print resseq, icode The hetatm_flag is blank (' ') for ordinary residues, 'W' for waters and 'H' for other hetero-residues. The resseq and icode have the usual PDB meaning. Cheers, -Thomas From boris.steipe at utoronto.ca Fri Nov 4 17:15:58 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Fri Nov 4 17:21:43 2005 Subject: [BioPython] Fwd: Software Carpentry workshop at AAAS Annual Meeting in February 06 References: Message-ID: <18C41F90-1D63-467A-82E1-909F254A775C@utoronto.ca> Life-science pythonistas (and their labmates) may be interested in Greg Wilson's Software-Carpentry course that emphasizes best- practices for many of the development tasks we all constantly face. It is geared towards the small-group scientific developer, very practice-oriented, taught in python, open, and free. I am forwarding a request for suggestions, below. best regards, Boris (The course lives at http://www.third-bit.com/swc/ ) Begin forwarded message: > From: Greg Wilson > Date: 4 November 2005 15:06:26 GMT-05:00 > To: Software Carpentry Students <2005fall@third-bit.com> > Subject: [2005fall] Software Carpentry workshop at AAAS Annual > Meeting in February 06 > > > I'm going to be running a workshop on "Essential Software Skills for > Research Scientists" at the Annual Meeting of the AAAS in St Louis in > February. The aim of the workshop is to persuade scientists > (particularly > senior scientists and administrators) that basic software engineering > skills are essential to doing computational science well. If you > have any > thoughts on particular topics the workshop ought to emphasize, war > stories > you'd like to share, or how to get word out about it, I'd be very > grateful. (And yes, feel free to circulate this notice to message > boards, > mailing lists, and your supervisors ;-) > > http://www.aaas.org/meetings/Annual_Meeting/02_PE/ > PE_06_Career_Workshops.shtml#EssentialSoftware > > Thanks, > Greg > > _______________________________________________ > 2005fall mailing list > 2005fall@pyre.third-bit.com > http://pyre.third-bit.com/cgi-bin/mailman/listinfo/2005fall > From yu.wang at gsf.de Fri Nov 11 05:24:21 2005 From: yu.wang at gsf.de (Yu Wang) Date: Fri Nov 11 05:21:17 2005 Subject: [BioPython] installation error Message-ID: <43747155.5030800@gsf.de> Hello, I got the following error message when I tried to install biopython-1.41 on Red Hat Fedora core 3. My python is 2.4.2. Python: Python 2.4.2 (#1, Nov 10 2005, 14:43:54) [GCC 3.4.4 20050721 (Red Hat 3.4.4-2)] on linux2 Error message: running build_ext building 'Bio.PDB.mmCIF.MMCIFlex' extension gcc -pthread -shared build/temp.linux-i686-2.4/Bio/PDB/mmCIF/lex.yy.o build/temp.linux-i686-2.4/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o build/lib.linux-i686-2.4/Bio/PDB/mmCIF/MMCIFlex.so /usr/bin/ld: cannot find -lfl collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1 Does anyone know how to solve this problem? With many thanks, Yu -- Yu Wang Institute for Bioinformatics Building 56, Room 158 GSF - German Research Center for Environment and Health Ingolstaedter Landstr. 1 D-85764 Neuherberg, GERMANY _______________________________________________________ http://mips.gsf.de Email:yu.wang@gsf.de Tel: (+49) 89/3187-3586 Fax: (+49) 89/3187-3585 _______________________________________________________ From thamelry at binf.ku.dk Fri Nov 11 05:26:29 2005 From: thamelry at binf.ku.dk (thamelry@binf.ku.dk) Date: Fri Nov 11 05:24:51 2005 Subject: [BioPython] installation error In-Reply-To: <43747155.5030800@gsf.de> References: <43747155.5030800@gsf.de> Message-ID: <33910.83.92.39.206.1131704789.squirrel@www.binf.ku.dk> > Hello, I got the following error message when I tried to install > biopython-1.41 on Red Hat Fedora core 3. My python is 2.4.2. > > Python: > Python 2.4.2 (#1, Nov 10 2005, 14:43:54) > [GCC 3.4.4 20050721 (Red Hat 3.4.4-2)] on linux2 > > Error message: > > running build_ext > building 'Bio.PDB.mmCIF.MMCIFlex' extension > gcc -pthread -shared build/temp.linux-i686-2.4/Bio/PDB/mmCIF/lex.yy.o > build/temp.linux-i686-2.4/Bio/PDB/mmCIF/MMCIFlexmodule.o -lfl -o > build/lib.linux-i686-2.4/Bio/PDB/mmCIF/MMCIFlex.so > /usr/bin/ld: cannot find -lfl > collect2: ld returned 1 exit status > error: command 'gcc' failed with exit status 1 > > Does anyone know how to solve this problem? Install flex (GNU's lex). Cheers, -Thomas From chrisf at fagmed.uit.no Fri Nov 11 05:20:32 2005 From: chrisf at fagmed.uit.no (Chris) Date: Fri Nov 11 10:07:13 2005 Subject: [BioPython] Does biopython have a 'WORKING' blastparser and where ? Message-ID: <43747070.1080109@fagmed.uit.no> *output for blast out.html and out.xml attached NCBIWWW.BlastParser(): * /usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py:1070: UserWarning: qblast works only with blastn and blastp for now. warnings.warn("qblast works only with blastn and blastp for now.") Traceback (most recent call last): File "/usr/bin/npw_blast2tab", line 93, in ? blast() File "/usr/bin/npw_blast2tab", line 14, in __init__ self.parse_blast(opts) File "/usr/bin/npw_blast2tab", line 51, in parse_blast b_record = blast_parser.parse(b_results) File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py", line 47, in parse self._scanner.feed(handle, self._consumer) File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py", line 98, in feed has_re=re.compile(r'.?BLAST')) File "/usr/local/lib/python2.4/site-packages/Bio/ParserSupport.py", line 335, in read_and_call_until line = safe_readline(uhandle) File "/usr/local/lib/python2.4/site-packages/Bio/ParserSupport.py", line 411, in safe_readline raise SyntaxError, "Unexpected end of stream." SyntaxError: Unexpected end of stream. * NCBIXML.BlastParser():* /usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py:1070: UserWarning: qblast works only with blastn and blastp for now. warnings.warn("qblast works only with blastn and blastp for now.") Traceback (most recent call last): File "/usr/bin/npw_blast2tab", line 93, in ? blast() File "/usr/bin/npw_blast2tab", line 14, in __init__ self.parse_blast(opts) File "/usr/bin/npw_blast2tab", line 51, in parse_blast b_record = blast_parser.parse(b_results) File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIXML.py", line 112, in parse self._parser.parse(handler) File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 107, in parse xmlreader.IncrementalParser.parse(self, source) File "/usr/local/lib/python2.4/xml/sax/xmlreader.py", line 125, in parse self.close() File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 217, in close self.feed("", isFinal = 1) File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 211, in feed self._err_handler.fatalError(exc) File "/usr/local/lib/python2.4/xml/sax/handler.py", line 38, in fatalError raise exception xml.sax._exceptions.SAXParseException: :1:0: no element found -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biopython/attachments/20051111/5c03d8e2/out-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: out.xml Type: text/xml Size: 104522 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20051111/5c03d8e2/out-0001.xml From mdehoon at c2b2.columbia.edu Fri Nov 11 10:18:53 2005 From: mdehoon at c2b2.columbia.edu (Michiel Jan Laurens de Hoon) Date: Fri Nov 11 10:26:12 2005 Subject: [BioPython] Does biopython have a 'WORKING' blastparser and where ? In-Reply-To: <43747070.1080109@fagmed.uit.no> References: <43747070.1080109@fagmed.uit.no> Message-ID: <4374B65D.8070103@c2b2.columbia.edu> Chris wrote: > *output for blast out.html and out.xml attached > Works for me: >>> blast_out = open('out.xml') >>> from Bio.Blast import NCBIXML >>> parser = NCBIXML.BlastParser() >>> record = parser.parse(blast_out) >>> # no error --Michiel. -- Michiel de Hoon Center for Computational Biology and Bioinformatics Columbia University 1150 St Nicholas Avenue New York, NY 10032 From arareko at campus.iztacala.unam.mx Fri Nov 11 10:43:19 2005 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Fri Nov 11 10:51:58 2005 Subject: [BioPython] FreeBSD port Message-ID: <4374BC17.9000504@campus.iztacala.unam.mx> Hi, Just to inform you that the FreeBSD port for Biopython has been upgraded from 1.30 to 1.41. Unfortunately, Johann Visagie hasn't been able to maintain it for a while, so now I'll be taking care of it. Thanks to Johann for creating and maintaining the port for so long. If you run into any issues with the new version please let me know. Regards, Mauricio. -- MAURICIO HERRERA CUADRA arareko@campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From fkauff at duke.edu Fri Nov 11 16:46:22 2005 From: fkauff at duke.edu (Frank Kauff) Date: Fri Nov 11 17:45:52 2005 Subject: [BioPython] blastx works fine? Message-ID: <1131745582.4368.22.camel@osiris.biology.duke.edu> Hi all, qblast currently says it works only for blastp and blastn. Actually it seems to work fine with blastx as well - xml output parses well with NCBIXML. Or am I missing something? Frank -- Frank Kauff Dept. of Biology Duke University From fdu.xiaojf at gmail.com Sun Nov 13 09:01:24 2005 From: fdu.xiaojf at gmail.com (Xiao Jianfeng) Date: Sun Nov 13 09:23:23 2005 Subject: [BioPython] How is frowns going on ? Message-ID: <43774734.80405@gmail.com> Hello, Does anybody know how is frowns(frowns is a chemoinformatics toolkit written in python,http://frowns.sourceforge.net/) going on ? Is it still active ? I have tried to contact Brian Kelley at bkelley@wi.mit.edu but got no reply. Regards, xiaojf From dalke at dalkescientific.com Sun Nov 13 17:41:38 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Sun Nov 13 17:52:56 2005 Subject: [BioPython] How is frowns going on ? In-Reply-To: <43774734.80405@gmail.com> References: <43774734.80405@gmail.com> Message-ID: <633b983c1f78de0251c29c8ed2fd588f@dalkescientific.com> On Nov 13, 2005, at 3:01 PM, Xiao Jianfeng wrote: > Does anybody know how is frowns(frowns is a chemoinformatics toolkit > written in python,http://frowns.sourceforge.net/) going on ? Is it > still > active ? > > I have tried to contact Brian Kelley at bkelley@wi.mit.edu but got no > reply. Frowns is no longer under development. Brian currently works for OpenEye, a chemical informatics software development company. See http://www.eyesopen.com/about/staff/bios.html?print=yes Andrew dalke@dalkescientific.com From omid9dr18 at hotmail.com Sun Nov 13 21:03:23 2005 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Sun Nov 13 21:18:37 2005 Subject: [BioPython] Structural alignment In-Reply-To: <633b983c1f78de0251c29c8ed2fd588f@dalkescientific.com> Message-ID: Hello, I was wondering what's the current common practice to align two different structures belong to the same protein. In particular I want to align two HIV-1 protease structures obtained from PDB and get the RMSD. I know how to do this with Swiss-PdbViewer, using the "majic fit". In a paper they have done this with the program MOLMOL but I am having difficulty installing it on my Windows computer since the program is meant to be used by Linux/Unix machines. Are there any other efficient publicly available tools for this purpose? Thanks for your help, Omid K. From idoerg at burnham.org Mon Nov 14 01:41:01 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon Nov 14 01:49:31 2005 Subject: [BioPython] Structural alignment In-Reply-To: Message-ID: I think your question is better directed to the pdb-l list. pdb-l@sdsc.edu The unlike sequence alignemnt, structure alignment is not such a well-defined quesiton, and the answer you get depends a lot on your prerequisites. There are quite a few publically available structure alignment programs. Surprisingly, Wikipedia has a nice list. (OK, I wrote in a few of the table entries. Guilty!). http://en.wikipedia.org/wiki/Structural_alignment Cheers, Iddo -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo On Mon, 14 Nov 2005, Omid Khalouei wrote: > Hello, > > I was wondering what's the current common practice to align two different > structures belong to the same protein. In particular I want to align two > HIV-1 protease structures obtained from PDB and get the RMSD. I know how to > do this with Swiss-PdbViewer, using the "majic fit". In a paper they have > done this with the program MOLMOL but I am having difficulty installing it > on my Windows computer since the program is meant to be used by Linux/Unix > machines. > Are there any other efficient publicly available tools for this purpose? > > Thanks for your help, > Omid K. > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From omid9dr18 at hotmail.com Mon Nov 14 15:17:58 2005 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Mon Nov 14 15:33:27 2005 Subject: [BioPython] Structural alignment In-Reply-To: Message-ID: Thanks alot, the wikipedia site links are indeed a good collection put together. It's interesting that sometimes what you get from these sites is more informative than hours of searching on scientific search engines. I also realized that it's better if I use the keywords structural "superposition" rather than "alignment" for my purpose. Thanks again, Omid K. >From: Iddo Friedberg >To: Omid Khalouei >CC: biopython@biopython.org >Subject: Re: [BioPython] Structural alignment >Date: Sun, 13 Nov 2005 22:41:01 -0800 > >I think your question is better directed to the pdb-l list. > >pdb-l@sdsc.edu > >The unlike sequence alignemnt, structure alignment is not such a >well-defined quesiton, and the answer you get depends a lot on your >prerequisites. > >There are quite a few publically available structure alignment programs. >Surprisingly, Wikipedia has a nice list. (OK, I wrote in a few of the >table entries. Guilty!). > >http://en.wikipedia.org/wiki/Structural_alignment > >Cheers, > > >Iddo > > >-- >Iddo Friedberg, Ph.D. >Burnham Institute for Medical Research >10901 N. Torrey Pines Rd. >La Jolla, CA 92037, USA >Tel: +1 (858) 646 3100 x3516 >Fax: +1 (858) 646 3171 >http://ffas.ljcrf.edu/~iddo > >On Mon, 14 Nov 2005, Omid Khalouei wrote: > > > Hello, > > > > I was wondering what's the current common practice to align two >different > > structures belong to the same protein. In particular I want to align two > > HIV-1 protease structures obtained from PDB and get the RMSD. I know how >to > > do this with Swiss-PdbViewer, using the "majic fit". In a paper they >have > > done this with the program MOLMOL but I am having difficulty installing >it > > on my Windows computer since the program is meant to be used by >Linux/Unix > > machines. > > Are there any other efficient publicly available tools for this purpose? > > > > Thanks for your help, > > Omid K. > > > > > > _______________________________________________ > > BioPython mailing list - BioPython@biopython.org > > http://biopython.org/mailman/listinfo/biopython > > > From dalke at dalkescientific.com Mon Nov 14 17:42:50 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Mon Nov 14 17:54:23 2005 Subject: [BioPython] Structural alignment In-Reply-To: References: Message-ID: <577c84e1842394d10b5c4879e21ebba3@dalkescientific.com> Iddo Friedberg wrote: > The unlike sequence alignemnt, structure alignment is not such a > well-defined quesiton, and the answer you get depends a lot on your > prerequisites. > > There are quite a few publically available structure alignment > programs. > Surprisingly, Wikipedia has a nice list. (OK, I wrote in a few of the > table entries. Guilty!). > > http://en.wikipedia.org/wiki/Structural_alignment Though it's perhaps a bit easier problem since the original poster, Omid, wants >> to align two different structures belong to the same protein. >> In particular I want to align two >> HIV-1 protease structures obtained from PDB and get the RMSD. If it's two conformations of the same structure and the goal is to minimize overall RMSD through a single global alignment matrix then the usual reference I know is Kabsch [Kabsch, 1976] Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta. Crystal, 32A:922-923. [Kabsch, 1978] Kabsch, W. (1978). A discussion of the solution for the best rotation to related two sets of vectors. Acta. Crystal, 34A:827-828. (The first had an ambiguity that could cause a sign error; fixed in the second.) Several structure program implement that including: O - http://xray.bmc.uu.se/usf/factory_4.html VMD - http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node183.html PyMol - http://www.pymolwiki.org/index.php/Kabsch This algorithm is not mentioned on the Wiki page and is 11 years older than the oldest mentioned reference. It isn't NP-hard as alluded to in the Wiki, since it's solving a much simpler problem. The date for ProFit is strange on the Wiki. I knew about ProFit before the claimed 1996. The web site says http://www.bioinf.org.uk/software/profit/faq.html > No paper has been published describing ProFit itself since it is > simply a convenient program (I hope) to let you use a standard fitting > algorithm; consequently, it is a little difficult to reference. The > exact wording is up to you and dependent on the context, but I suggest > something similar to: > > Fitting was performed using the McLachlan algorithm (McLachlan, A.D., > 1982 ``Rapid Comparison of Protein Structres'', Acta Cryst A38, > 871-873) as implemented in the program ProFit (Martin, A.C.R., > http://www.bioinf.org.uk/software/profit/). The McLachlan algorithm is also not mentioned in the Wiki. I found a usenet announcement about ProFit at http://groups.google.com/group/bionet.software/msg/f219c5163bbadbdc? dmode=source&hl=en > From: mar...@bsm.bioc.ucl.ac.uk (Andrew Martin) > Subject: ANNOUNCE: Protein Fitting Software > Date: 1995/07/20 > Message-ID: <1995Jul20.101545.37119@ucl.ac.uk>#1/1 > X-Deja-AN: 106640715 > organization: University College London > newsgroups: bionet.software > > I've finally (after about 2 years) got around to fixing the last (?) > remaining bugs in my ProFit protein least-squares fitting software and > decided to make it generally available. so the date should be 1995 or 1993 or earlier. I suspect the 1996 date came from the "first written" date for the documentation, at http://www.bioinf.org.uk/software/profit/doc/ Well, that was entirely too much information about a minor nit! I cc'ed as it were this email to the wiki page, but I don't like learning wiki formatting rules so put it on the talk page. Andrew dalke@dalkescientific.com From thamelry at binf.ku.dk Tue Nov 15 00:56:43 2005 From: thamelry at binf.ku.dk (Thomas Hamelryck) Date: Tue Nov 15 00:55:04 2005 Subject: [BioPython] Structural alignment In-Reply-To: <577c84e1842394d10b5c4879e21ebba3@dalkescientific.com> References: <577c84e1842394d10b5c4879e21ebba3@dalkescientific.com> Message-ID: <32781.83.92.39.206.1132034203.squirrel@www.binf.ku.dk> Andrew Dalke wrote: > If it's two conformations of the same structure and the goal is > to minimize overall RMSD through a single global alignment matrix > then the usual reference I know is Kabsch > > [Kabsch, 1976] Kabsch, W. (1976). A solution for the best rotation > to relate two sets of vectors. Acta. Crystal, 32A:922-923. > [Kabsch, 1978] Kabsch, W. (1978). A discussion of the solution > for the best rotation to related two sets of vectors. Acta. Crystal, > 34A:827-828. > > (The first had an ambiguity that could cause a sign error; fixed > in the second.) > > Several structure program implement that including: > O - http://xray.bmc.uu.se/usf/factory_4.html > VMD - http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node183.html > PyMol - http://www.pymolwiki.org/index.php/Kabsch Maybe more relevant in the context of this newsgroup is that it's implemented in Biopython's Bio.PDB.Superimposer. The Kabsch algorithm mentioned sometimes returns a rotation+a reflection, but that can easily be avoided, see: Umeyama S: Least squares estimation of transformation parameters between two point patterns. IEEE Trans Pattern Anal Mach Intell 1991, 13:376-80. There's an automated structure superposition method (which finds the alignment itself) on its way to Biopython, BTW. -Thomas From aloraine at gmail.com Wed Nov 23 22:49:01 2005 From: aloraine at gmail.com (Ann Loraine) Date: Thu Nov 24 02:31:29 2005 Subject: [BioPython] saving pickled objects in MySQL database Message-ID: <83722dde0511231949l238db852m1c995dc3156c413d@mail.gmail.com> Hi, This may be a bit off topic - my apologies if so. Can anybody point me to some good references or recipes on the best way to save pickled Python objects in a MySQL database? I'm using MySQLdb to talk to the database. Ideally, I'd like to find a way to stream object data directly into the database without an intermediate step of writing data to a file on disk. Thanks in advance for your help! -Ann -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org From dtomso at athenixcorp.com Mon Nov 28 08:26:41 2005 From: dtomso at athenixcorp.com (Daniel Tomso) Date: Mon Nov 28 08:49:34 2005 Subject: [BioPython] saving pickled objects in MySQL database Message-ID: Hi-- There's probably a better way to do this - - - But - - - You could use StringIO (or cStringIO) to create a file handle in memory, write to it w/ Pickle (or cPickle), read the contents from it with readlines(), then drop the result into a memo field in MySQL using MySQLdb. Seems like it would work . . . I've also done similar semi-workaround solutions using a ramdisk, which is straightforward and relatively fast. Dan T. Daniel J. Tomso Senior Scientist, Bioinformatics Athenix Corporation 2202 Ellis Road Suite B Durham, NC 27703 919.281.0920 dtomso@athenixcorp.com www.athenixcorp.com Disclaimer: This message (including any attachments) may contain confidential or privileged information and is intended only for the use of the addressee named above. If you are not the intended recipient of this message, you are hereby notified that you must not use, copy, disclose or take any action based on this message or information herein. If you have received this message in error, please advise the sender immediately and erase all copies of this message and any related attachments. Thank you. -----Original Message----- From: biopython-bounces@portal.open-bio.org [mailto:biopython-bounces@portal.open-bio.org] On Behalf Of Ann Loraine Sent: Wednesday, November 23, 2005 10:49 PM To: biopython@biopython.org Cc: Ann Loraine Subject: [BioPython] saving pickled objects in MySQL database Hi, This may be a bit off topic - my apologies if so. Can anybody point me to some good references or recipes on the best way to save pickled Python objects in a MySQL database? I'm using MySQLdb to talk to the database. Ideally, I'd like to find a way to stream object data directly into the database without an intermediate step of writing data to a file on disk. Thanks in advance for your help! -Ann -- Ann Loraine Assistant Professor Section on Statistical Genetics University of Alabama at Birmingham http://www.ssg.uab.edu http://www.transvar.org _______________________________________________ BioPython mailing list - BioPython@biopython.org http://biopython.org/mailman/listinfo/biopython