Re: NAMD trajectory format

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 30 2008 - 09:24:17 CDT

(But either way, this certainly would do a lot more than just wrapping
the molfile plugins -- thanks for reminding me :-)

Peter Freddolino wrote:
> Good point (and yes, you're correct... I'd forgotten). I know that's
> under current development/testing; not sure if it'll be shipping with
> 1.8.7 or not, I'll have to ask John.
> Peter
>
> Axel Kohlmeyer wrote:
>> On Fri, 30 May 2008, Peter Freddolino wrote:
>>
>> PF> On a related note, I know that someone had wrapped the catdcd 3.0
>> readers
>> PF> for python (http://code.google.com/p/mdanalysis/); a similar
>> python wrapper
>> PF> for the molfile plugins would probably be the ideal solution to
>> this and
>> PF> many other problems.
>>
>> if i'm not totally mistaken, the next version of VMD should be
>> importable as a python module. that would give that
>> feature in pythong for free and a ton of others...
>>
>> axel.
>>
>>
>> PF> Best,
>> PF> Peter
>> PF> PF> Axel Kohlmeyer wrote:
>> PF> > On Thu, 29 May 2008, Konrad Hinsen wrote:
>> PF> >
>> PF> > KH> On May 28, 2008, at 16:05, Axel Kohlmeyer wrote:
>> PF> > KH> PF> > KH> >it is not that difficult and you could use the
>> fortran wrapper code
>> PF> > KH> >that i contributed as a starting point. OTOH, you can also
>> just link
>> PF> > KH> >the individual subroutines as a static library. see:
>> PF> > KH> >
>> PF> > KH> >http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
>> PF> > KH> >
>> PF> > KH> >and particularly:
>> PF> > KH> >
>> PF> > KH>
>> >http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/callmolfileplugins.html#callmolfileplugins
>>
>> PF> > KH> PF> > KH> Thanks, I will look at that for use in the
>> future. For my current
>> PF> > KH> needs, I
>> PF> > KH> am quite happy with my DCD parser written in Python, which
>> seems to
>> PF> > KH> work
>> PF> > KH> fine, at least for the one trajectory that I have for testing.
>> PF> >
>> PF> > dcd trajectories are nasty to parse in general because they are
>> fortran
>> PF> > unformatted. depending on whether the file was written on a
>> machine
>> PF> > with the same or different endianness and a (64-bit) compiler
>> that uses
>> PF> > either 32-bit (most) or 64-bit (some versions of gfortran and g95,
>> PF> > depending on flags) record markers and 64bit default integers
>> PF> > you get a different file. john has put a lot of effort into making
>> PF> > the dcd reader in molfile particularly flexible and efficient.
>> PF> >
>> PF> > there is a lot of convenience in writing your own stuff, but it
>> also
>> PF> > adds inconsistencies (just look at how many
>> broken/non-compliant .pdb
>> PF> > format writers and readers there are). with computational tools
>> becoming
>> PF> > increasingly ubiquitous in our research it is high time to
>> consolidate on
>> PF> > a few tools/libraries and use and improve those instead of
>> re-inventing
>> PF> > the same old wheels over and over again.
>> PF> >
>> PF> > that is why, for instance, i wrote those fortran wrappers to
>> molfile.
>> PF> > instead of adding just one more file formats to the (fortran
>> based)
>> PF> > analysis code of a colleague, i added _all_ the formats that
>> molfile
>> PF> > supports and any future file format work from me can focus on
>> improving
>> PF> > the molfile library. this in turn
>> PF> > will also help every other project that uses it at the same time.
>> PF> >
>> PF> > cheers,
>> PF> > axel.
>> PF> >
>> PF> > KH> Thanks again for your help,
>> PF> > KH> Konrad.
>> PF> > KH> PF> > KH> PS: If anyone wants a copy of my DCD parser in
>> Python, just ask!
>> PF> > KH> --
>> PF> > KH>
>> ---------------------------------------------------------------------
>> PF> > KH> Konrad Hinsen
>> PF> > KH> Centre de Biophysique Moléculaire, CNRS Orléans
>> PF> > KH> Synchrotron Soleil - Division Expériences
>> PF> > KH> Saint Aubin - BP 48
>> PF> > KH> 91192 Gif sur Yvette Cedex, France
>> PF> > KH> Tel. +33-1 69 35 97 15
>> PF> > KH> E-Mail: hinsen_at_cnrs-orleans.fr
>> PF> > KH> Web: http://dirac.cnrs-orleans.fr/~hinsen/
>> PF> > KH>
>> ---------------------------------------------------------------------
>> PF> > KH> PF> > KH> PF> > KH> PF> >
>> PF> > PF>
>>

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