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

[Paolo Franz]

I am trying to avoid doing it by brute force, that is reading all frames
until the last is found. In the origin, what I really need to do is to test
if a frame exists in the trajectory. I tried with xtc_seek_frame, but that
does not work. Of course, if I know how many frames are they the test
becomes trivial.

That said, I definitely know what is in the trajectory, how many frames are
there: I ran the md myself and I have the output file! What I want to do is
to write a code that figure out by itself what to expect and if, by any
chance I forget what is inside, it does not go into an infinite loop if I
ask to analyse the wrong frame.

Cheers
Paolo

On 4 June 2012 22:59, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> 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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>> >
>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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