---------- Forwarded message ---------- From: gary thompson <[EMAIL PROTECTED]> Date: Thu, Jul 31, 2008 at 2:29 PM Subject: Re: BMRB NMR-STAR v3.1 file format or STAR format reader/writer (maybe using CCPN?). To: Edward d'Auvergne <[EMAIL PROTECTED]>
On Thu, Jul 31, 2008 at 1:42 PM, Edward d'Auvergne <[EMAIL PROTECTED]>wrote: > Hi, > > Thanks for the pointers. I have a few questions about these below. > > > > Hi Ed > > > > some alternatives > > > > 1. stardom (gpl; ignore what it says on the first web page and just look > at > > the license) converts start files to an xml format > > http://www.pasteur.fr/recherche/unites/Binfs/stardom > I think producing the files is not too hard (essentially the modelfree input is a cif file which is a star file (mmcif and nmrstar are both implementations of the start format) > > I was aware of StarDOM and it's compatible licence, but I'm not sure > if it would be the best tool. I couldn't find on their website > whether this will create STAR formatted files, or simply convert from > STAR to XML. For BMRB submission by everyone doing a model-free > analysis, we need to have the capacity to create STAR formatted files > containing all the data from the analysis. Even if relax is used as a > wrapper for Modelfree4 and Dasha, it can still be used to produce a > 100% complete NMR-STAR v3.1 file from these program's results for > submission. Do you know if StarDOM will create STAR files? Reading > the BMRB files is only half of the relax-BMRB integration (and the > less important half). so no stardom won't create star files but it does do the heavy lifting of converting a start file to an xml file which can then be transformed by xslt... > > > > 2. ccpn format converters come in two parts (I have helped write one for > > import of data from xplor-marvin) I would have a look at > > ccpnmr1.0/python/ccp/format/nmrStar which is a basic star file reader > > framework... > > Ah, I was looking in the wrong directory. This appears to be > originating from Jurgen Doreleijers' original code. Hmmm, it has > quite a mix of Windows and Unix line termination characters. It looks > like Jurgen wrote the code in Windows and then afterwards Wim Vranken > did some CCPN integration on a Unix or Linux machine. Do you know how > this code could be used? Is it a STAR format reader, a writer or > both? from my short reading both > Would you also know the copyright licence for this code? LGPL all the way this is data-model code not analysis code ======================COPYRIGHT/LICENSE START========================== generalIO.py: General I/O information and code for nmrStar files. Copyright (C) 2005-2007 Wim Vranken (European Bioinformatics Institute) ======================================================================= This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. A copy of this license can be found in ../../../../license/LGPL.license This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ======================COPYRIGHT/LICENSE END============================ > And > do you know if it could it be incorporated into relax or, if it is a > generic STAR format parser/writer, be incorporated into Python itself? I don't think that anyone other than the bio people are interested in star files so it won't have a general audience in python ;-) > > Maybe this code has been made specific to NMR-STAR or CCPN already. > I should have a closer look at this, but it would probably be > preferable to not have CCPN as an essential relax dependency right > now. as it is LGPL'd we steall it an distribute it I guess... The in the code that uses it we just look for the ccpn files first and then fall back to ours if they can't be found... > Maybe, if this is legally possible, starting with Jurgen's > original code rather than the CCPN code would be better? I would actually go with the ccpn code it will be much more activley supported and used... > > > > 3. I can assist here (my structure calculation stuff is now done [mostly > so > > I am heading back to dynamics]) ;-) > > You are most welcome to help in any way you wish. I would however > consider BMRB and CCPN integration as two separate projects (for two > branches from the 1.3 development line), and not having one depend on > the other would be better. indeed they would be anyway I think there are 3 things here 1. import and export of relax files into analysis via format converter 2. loading the datamodel into relax and sucking data out of it and pushing data into it 3. bmrb inter operation > Once a good STAR reader/writer is > accessible in relax, then reading and writing BMRB files will be > relatively quick. It only took me a few days to implement XML results > files in relax (both reading and writing) thanks to the Python built > in XML reader/writer. > > Cheers, > > Edward > regards gary
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