From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 21 2014 - 13:14:55 CDT

Hi,
  It is pretty easy to call the VMD plugins from your own software,
so rather than hacking the DCD code, I would suggest the use
of the VMD plugin API, and then you can also write various
other trajectory formats as well. Various other tool such as
PyMol, the Gromacs analysis tols, and others make use of
the VMD plugin API, so there are also many examples of how to do this
in various ways out in the field.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 21, 2014 at 07:04:58PM +0100, Jrme Hnin wrote:
> Hi Adam,
>
> The DCD format is quite straightforward (small global header, then a series of tiny frame headers followed by coordinate arrays, IIRC), so you could reuse some code from the DCD plugin to do the conversion within your program - either interfacing the C++ with python, or possibly just reimplementing a subset of it in pure python.
>
> Cheers,
> Jerome
>
>
> ----- Original Message -----
> > Hi Ivan,
> >
> > I am looking into biopython, but I am not sure this is going to help. My
> > coordinates are literally a TxNx3 array (T = number of frames in
> > trajectory, N = number of alpha carbons, 3 for xyz coordinates). I suppose
> > you are right that going from coordinates to PDB as a first step is the way
> > to go. Can biopython (or any other tool) do this?
> >
> > Its looking like I will have to write a script to translate my coordinates
> > frame-by-frame into PDB files and then compile them into a DCD (perhaps
> > using VMD).
> >
> > Thanks,
> > Adam
> > On Mar 21, 2014 5:31 AM, "Ivan Gregoretti" <ivangreg_at_gmail.com> wrote:
> >
> > > Hi Adam,
> > >
> > > If I understand your goal correctly, you want to go from an arbitrary
> > > object instance to DCD. So, you want
> > >
> > > adamformat -> DCD
> > >
> > > I think that you can tackle the problem by doing it in two steps
> > >
> > > 1) adamformat -> PDB
> > >
> > > 2) PDB -> DCD
> > >
> > > For step 1, your best friend is Biopython's Bio.PDB module.
> > > http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
> > >
> > > For step 2, PDB to DCD, let us hear what the community is currently using.
> > > It sounds like a routine task to me.
> > >
> > > Ivan
> > >
> > >
> > >
> > >
> > > Ivan Gregoretti, PhD
> > > Bioinformatics
> > >
> > >
> > >
> > > On Fri, Mar 21, 2014 at 3:51 AM, Norman Geist <
> > > norman.geist_at_uni-greifswald.de> wrote:
> > >
> > >> VMD Main->File->Save Coordinates and choose DCD as file type. Otherwise
> > >> have a look at "catdcd".
> > >>
> > >>
> > >>
> > >> Norman Geist.
> > >>
> > >>
> > >>
> > >> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> > >> Auftrag von *Adam Goler
> > >> *Gesendet:* Freitag, 21. Mrz 2014 06:00
> > >> *An:* Vmd l
> > >> *Betreff:* vmd-l: Writing DCD from modified coordinates
> > >>
> > >>
> > >>
> > >> Hello,
> > >>
> > >> I have sets of modified xyz coordinate data (one set for each time step)
> > >> from some python output that I would like to convert back into a DCD
> > >> trajectory for further analysis in VMD.
> > >>
> > >> Can anyone offer suggestions on how to go about this?
> > >>
> > >> Thanks,
> > >> Adam
> > >>
> > >>
> > >> ------------------------------
> > >> <http://www.avast.com/>
> > >>
> > >> Diese E-Mail ist frei von Viren und Malware, denn der avast!
> > >> Antivirus<http://www.avast.com/>Schutz ist aktiv.
> > >>
> > >>
> > >
> >

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/