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 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).
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? Would you also know the copyright licence for this code? 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?
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. Maybe, if this is legally possible, starting with Jurgen's
original code rather than the CCPN code would be better?
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. 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
Re: BMRB NMR-STAR v3.1 file format or STAR format reader/writer (maybe using CCPN?).