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

Oliver Stueker ostueker at gmail.com
Tue Jun 5 00:40:32 CEST 2012

As far as I know there is no field at the beginning of the file that would
give a parser hints how many frames are in it.
(probably because that makes it easier/more performant to append to the
file while reducing the risk of corrupting it in case a write goes bad)

On the other hand that makes it hard to implement random-access to frames
in XTC/TRR files.

Interestingly there is just a discussion on the mailing list of MDAnalysis
(a python framework that can deal with XTC and other trajectories) on how
libxdr might be extended to generate a checksum-protected index for XTC
files, so that a given trajectory has to be read only once from beginning
to end.

a different Oliver

On Mon, Jun 4, 2012 at 3:24 PM, Paolo Franz <paolo.franz at gmail.com> wrote:

> 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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