Hi,
Sort of - if you put 'debug analysis 2' prior to your clustering command
then CPPTRAJ will write out the initial pairwise distance matrix to STDOUT
preceded by 'INITIAL FRAME DISTANCES', e.g.
INITIAL FRAME DISTANCES:
1 2 4.065107
1 3 6.155344
Otherwise, currently the only other option would be to write a separate
program that can convert to pairwise distance file to text. On my to-do
list is to enable users to manipulate the cluster pairwise distance matrix
data set just like any other data set.
Hope this helps,
-Dan
On Tue, Jul 21, 2015 at 8:50 PM, bharat lakhani <lakhbharat.gmail.com>
wrote:
> Dear Dan
>
> Is there a way to convert CpptrajPairDist into text file or is there any
> utilities which can automatically convert into text file?
> Thanks
>
> On Sat, Dec 28, 2013 at 2:58 PM, JAIME RUBIO MARTINEZ <jaime.rubio.ub.edu>
> wrote:
>
> > Thanks,
> > I think 2srms is the best option for my goal.
> > Jaime
> > ________________________________________
> > De: Daniel Roe [daniel.r.roe.gmail.com]
> > Enviado: martes, 17 de diciembre de 2013 22:52
> > Para: AMBER Mailing List
> > Asunto: Re: [AMBER] CpptrajPairDist
> >
> > 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
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> > >> 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
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> la
> > >> persona o entidad destinataria. Si usted no es el destinatario final o
> > la
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> > >> remitente y elimine del sistema el mensaje y el material anexo que
> pueda
> > >> contener. Gracias por su colaboración.
> > >>
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> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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
> >
> >
> > 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
> >
>
>
>
> --
> regards
>
> Bharat Lakhani
> _______________________________________________
> 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 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 23 2015 - 09:00:05 PDT
