VMD-L Mailing List

From: Adam Goler (adamgoler_at_gmail.com)
Date: Sat Mar 22 2014 - 14:08:10 CDT

Hello again,

I would like to call functions from dcdplugin.c (found
here<http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c.html>)
but this file does not seem to be within the VMD directory on my machine
(v. 1.9.1). How can I import this file (or the whole API) to a C program in
order to call the functions within? It seems like there are header files
vmdplugin.h, vmdconio.h, etc. but none of them are complete. I suppose I
could try to copy+paste the source into a .c file on my machine, but I
wonder if there is a cleaner way to go about this?

Also, John, can I just write a .c program that takes my data as input and
calls VMD's dcd-writing commands to output a dcd file, or do I need to
write a plugin and run it through VMD?

Thanks,
Adam

On Fri, Mar 21, 2014 at 4:08 PM, Adam Goler <adamgoler_at_gmail.com> wrote:

>
>
> I found the dcdplugin.c source code and file reference on (what appears to
> be) the VMD plugin API
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/dcdplugin_8c.html
>
> I will see if I can make any progress using this.
>
>
>
>
> On Fri, Mar 21, 2014 at 11:14 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> 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, Jérôme Hénin 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. März 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!
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>> > > >>
>> > > >>
>> > > >
>> > >
>>
>> --
>> 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/
>>
>
>
>
> --
> Adam Goler
> Graduate Student
> Fulmer 126
> Dept. of Physics and Astronomy
> Washington State University
> PO Box 642814
> Pullman, WA 99164-2814
> Office Phone: (509) 335 7050
>
> adamgoler.com
> 

-- 
Adam Goler
Graduate Student
Fulmer 126
Dept. of Physics and Astronomy
Washington State University
PO Box 642814
Pullman, WA 99164-2814
Office Phone: (509) 335 7050
adamgoler.com