[gmx-developers] How to get the number of frames contained by an .xtc trajectory file??

[Justin A. Lemkul]

If all you need is the number of frames contained in an .xtc file, is there some 
reason why running gmxcheck on the .xtc file is insufficient?

-Justin

On 6/4/12 4:56 PM, Paolo Franz wrote:
> Hi Tsjerk,
> Thanks, but I don't really want to use a python script, I am doing this from
> some c/c++ code. I think I figured out a way to do it, but I haven't tested it yet:
>
> i)    open the file
> ii)   do a read_first_xtc
> iii)  then get the file pointer positon from ftellg, which should be the length
> of the frame in bytes;
> iv)  place the file pointer at the end of the file with an fseek, then get the
> length with an ftellg
> v)   Divide the total length by the length of a frame and obtain the number of
> written frames.
>
> I am only wondering what to do when the length in bytes of the file is too large
> for a long int!
>
> On 4 June 2012 16:11, Tsjerk Wassenaar <tsjerkw at gmail.com
> <mailto:tsjerkw at gmail.com>> wrote:
>
>     Hey Paolo,
>
>     I think I posted a script for extracting a last frame before, but if I
>     can't even find it myself... Here it is:
>
>     #!/usr/bin/env python
>
>     from struct import unpack
>     import sys
>
>     def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])
>
>     f = open(sys.argv[1])
>     tag = f.read(8)                   # Tag: magic number and number of atoms
>     n = 92 + i(f.read(84)[-4:])       # Size of frame in bytes
>
>     f.seek(-5*n/4, 2)                 # This should contain a complete frame
>     frame = f.read()                  # Read the remaining part in
>     frame = frame[frame.index(tag):]  # Find the tag
>
>     # Open the output file
>     if len(sys.argv) > 2:
>         o = sys.argv[2]
>     else:
>         o = sys.argv[1][:-4]+"-last.xtc"
>     open(o,"w").write(frame)
>
>     ###
>
>     Hope it helps. Cheers,
>
>     Tsjerk
>     On Mon, Jun 4, 2012 at 12:59 PM, Paolo Franz <paolo.franz at gmail.com
>     <mailto:paolo.franz at gmail.com>> wrote:
>      > Hello everybody!
>      >
>      > I am wondering how I can figure out the number of frames contained in an
>      > .xtc file. Indeed, I need to read a particular frame of a trajectory and I
>      > thought that the function
>      > xtc_seek_frame(FILE * , int *, int *)
>      > would return 0 if the frame was there and 1 when it was not. Instead, if I
>      > call it with a frame outside the boundaries it seems to go into an infinite
>      > loop. What I am doing wrong? Is there a way to read the last frame of an
>      > .xtc file?
>      >
>      > Sincerely
>      > Paolo
>      >
>      >
>      >
>      >
>      > --
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>
>
>
>     --
>     Tsjerk A. Wassenaar, Ph.D.
>
>     post-doctoral researcher
>     Molecular Dynamics Group
>     * Groningen Institute for Biomolecular Research and Biotechnology
>     * Zernike Institute for Advanced Materials
>     University of Groningen
>     The Netherlands
>     --
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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