Re: NAMD trajectory format

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 30 2008 - 09:15:48 CDT

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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