On Mar 4, 2014 9:19 PM, "João Henriques" <joao.henriques.32...@gmail.com> wrote: > > Hello everyone, > > Let me start by saying that I am unsure whether this is a question for the > gmx-users or gmx-developers mailing list, but here it goes: > > I have written a Python/NumPy script that parses the rmsd comparison matrix > dumped by g_rms in the .xpm format. However the "nlevels" are not > sufficient to give me the desired detail for posterior calculations. > Therefore I have decided to forget the .xpm and focus on the binary dump > produced by g_rms using the flag -bin. My sole purpose is to fetch the > binary rmsd data and pass it into an array, so that I can then do some > calculations over it. > > I am a total newbie in binary file parsing, but I know that I can, for > example, use something like "numpy.fromfile" for that purpose. The problem > is that I have absolutely no idea of what is the structure of the binary > rmsd comparison matrix file. I'm pretty sure that besides the actual data, > there are other stamps and stuff being written to the file, with > potentially different formats as well. I tried looking at gmx_rms.c but I > got lost very quickly.
No, g_rms -bin is very plain, see http://redmine.gromacs.org/projects/gromacs/repository/revisions/master/entry/src/gromacs/gmxana/gmx_rms.c#L1073 Do let us know how you go! Mark > Is there anyone out there that might be able to help me identify the > correct structure OR is there any Python or C++ routine capable of doing > similar things to what I need? I have no urge in "reinventing the wheel". > > P.S.: I know that there is the possibility of modifying g_rms itself, but > that is not what I'm looking for. > > Thank you in advance, > Best regards, > João Henriques > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.