Hi Tsjerk It's very useful in my problem also. thanks again.
regards anupam > Hi Anupam, > > I recently wrote a small python script to convert gromacs .xpm files > to numbers. Maybe it'll be of some use to you: > > Cheers, > > Tsjerk > > ### > > #!/usr/bin/env python > > import sys > > def unquote(s): > return s[1+s.find('"'):s.rfind('"')] > > def uncomment(s): > return s[2+s.find('/*'):s.rfind('*/')] > > def col(c): > color = c.split('/*') > value = unquote(color[1]) > color = unquote(color[0]).split() > sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1], value)) > return color[0], value > > # Open the xpm file for reading > xpm = open(sys.argv[1]) > > # Read in lines until we fidn the start of the array > meta = [xpm.readline()] > while not meta[-1].startswith("static char *gromacs_xpm[]"): > meta.append(xpm.readline()) > > # The next line will contain the dimensions of the array > dim = xpm.readline() > # There are four integers surrounded by quotes > nx, ny, nc, nb = [int(i) for i in unquote(dim).split()] > > # The next dim[2] lines contain the color definitions > # Each pixel is encoded by dim[3] bytes, and a comment > # at the end of the line contains the corresponding value > colors = dict([col(xpm.readline()) for i in range(nc)]) > > for i in xpm: > if i.startswith("/*"): > continue > j = unquote(i) > z = [colors[j[k:k+nb]] for k in range(0,nx,nb)] > sys.stdout.write(" ".join(z)+"\n") > > ### > > On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha > <anu...@mbu.iisc.ernet.in> wrote: >> >> right. I also came to see one of them but with no result. >> and since it was done some time back so I thought if some one has come up >> with >> some method to get that. >> >> right now I wanted the matrix information obtained from command g_mdmat..... >> can you suggest some way to get that. >> >> thanks >> anupam >> >> >>> No, there's no ability to do this. I think there should be, though, and seem >>> to >>> recall discussion of it on one or other mailing list or the web page. >>> >>> Mark >>> >>> ----- Original Message ----- >>> From: Anupam Nath Jha <anu...@mbu.iisc.ernet.in> >>> Date: Saturday, October 2, 2010 21:32 >>> Subject: [gmx-users] numerical matrix from xpm file >>> To: gmx-users@gromacs.org >>> >>>> >>>> Hi all >>>> >>>> Is it possible to obtain the matrix in numeric form from xpm >>>> (obtained from >>>> gromacs analysis) files. >>>> >>>> because it's not coming in options for ourput files. >>>> >>>> thanks with regards >>>> anupam >>>> >>>> -- >>>> >>>> >>>> -- >>>> This message has been scanned for viruses and >>>> dangerous content by MailScanner, and is >>>> believed to be clean. >>>> >>>> -- >>>> gmx-users mailing list gmx-us...@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> -- >>> This message has been scanned for viruses and >>> dangerous content by MailScanner, and is >>> believed to be clean. >>> >>> -- >>> gmx-users mailing list gmx-us...@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search >>> before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> Science is facts; just as houses are made of stone, so is science is made of >> facts; but a pile of stones is not a house, and a collection of facts is not >> necessarily science. >> >> Anupam Nath Jha >> Ph. D. Student >> Saraswathi Vishveshwara Lab >> Molecular Biophysics Unit >> IISc,Bangalore-560012 >> Karnataka >> Ph. no.-22932611 >> >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > 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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists