Of course, if all you need is the raw 2D RMSD matrix, you can also get it
directly from the rms2d/2drms command in cpptraj, which has some more
formatting options (such as gnuplot output etc).
-Dan
On Tue, Dec 17, 2013 at 2:44 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The CpptrajPairDist file is binary; the exact format depends on what
> version of cpptraj generated the file (since earlier versions had no
> concept of 'sieve'). The CpptrajPairDist file starts with a 4 byte header
> containing the characters 'C' 'T' 'M' followed by the version number. A
> quick way to figure out the version is to use the linux 'od' command to
> output the first 4 bytes as hexadecimal, e.g.:
>
> $ od -t x1 -N 4 CpptrajPairDist
> 0000000 43 54 4d 02
>
> So the CpptrajPairDist file version in the above example is 2.
>
> The next few numbers describe the matrix size and depend on the version.
>
> Version 0: Two 4-byte integers: # of rows and # of elements.
> Version 1: Two 8-byte unsigned integers (equivalent to size_t on most
> systems): # of rows and # of elements.
> Version 2: Three 8 byte unsigned integers: original # of rows, actual # of
> rows, and sieve value.
>
> This is followed by the actual matrix data, stored as a single array of
> floats (4 bytes). For versions 1 and 2 the number of elements is explicitly
> stored. For version 2, to calculate the number of matrix elements you need
> to read:
>
> Elements = (actual_rows * (actual_rows - 1)) / 2
>
> The cluster pair-distance matrix is an upper-right triangle matrix without
> the diagonal (in row-major order), so the first element is the distance
> between elements 0 and 1, the second is between elements 0 and 2, etc.
>
> In version 2 files, if the sieve value is greater than 1 that means
> original_rows > actual_rows and there is an additional array of characters
> original_nrows long, with 'T' if the row is being ignored (i.e. it was
> sieved out) and 'F' if the row is active (i.e. is active in the actual
> pairwise-distance matrix).
>
> The code that cpptraj uses to read in CpptrajPairDist files is in
> ClusterMatrix::LoadFile() (ClusterMatrix.cpp). Let me know if you have more
> questions.
>
> -Dan
>
>
>
> On Tue, Dec 17, 2013 at 12:37 PM, JAIME RUBIO MARTINEZ <jaime.rubio.ub.edu
> > wrote:
>
>>
>> I want to use the CpptrajPairDist file from the cluster savepairdist
>> command of cpptraj
>> to analyse the RMSD distance matrix, but I do not know how to extract the
>> data.
>>
>> can anyone give me info on the format of this file?
>>
>> Thanks
>>
>> Jaime
>>
>>
>>
>>
>> Aquest correu electrònic i els annexos poden contenir informació
>> confidencial o protegida legalment i està adreçat exclusivament a la
>> persona o entitat destinatària. Si no sou el destinatari final o la persona
>> encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo,
>> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu
>> rebut aquest correu electrònic per error, us preguem que n’informeu al
>> remitent i que elimineu del sistema el missatge i el material annex que
>> pugui contenir. Gràcies per la vostra col·laboració.
>>
>> Este correo electrónico y sus anexos pueden contener información
>> confidencial o legalmente protegida y está exclusivamente dirigido a la
>> persona o entidad destinataria. Si usted no es el destinatario final o la
>> persona encargada de recibirlo, no está autorizado a leerlo, retenerlo,
>> modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha
>> recibido este mensaje electrónico por error, le rogamos que informe al
>> remitente y elimine del sistema el mensaje y el material anexo que pueda
>> contener. Gracias por su colaboración.
>>
>> This email message and any documents attached to it may contain
>> confidential or legally protected material and are intended solely for the
>> use of the individual or organization to whom they are addressed. We remind
>> you that if you are not the intended recipient of this email message or the
>> person responsible for processing it, then you are not authorized to read,
>> save, modify, send, copy or disclose any of its contents. If you have
>> received this email message by mistake, we kindly ask you to inform the
>> sender of this and to eliminate both the message and any attachments it
>> carries from your account. Thank you for your collaboration.
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 17 2013 - 14:00:04 PST
