VMD-L Mailing List

From: JONATHAN BLACK (nihilique_at_hotmail.com)
Date: Wed Oct 22 2008 - 04:30:19 CDT

actually i have to write a perl script that can do that as part of a larger program. i've found a fortran script that can do that but it will take me a while to "decode" how it does what it does since i don't know fortran. however i would like to ask for the format with which a dcd is packed. i've found this :
 
#===DCD=FORMAT==============================================
#HDR NSET ISTRT NSAVC 5-ZEROS NATOM-NFREAT DELTA 9-ZEROS
#CORD files step1 step zeroes (zero) timestep zeroes
#C*4 INT INT INT 5INT INT DOUBLE 9INT
# [CHARACTER*20]
#===========================================================
#NTITLE TITLE
#INT C*MAXTITL
#C*2 C*80
#===========================================================
#NATOM
#INT
#===========================================================
#X(I), I=1,NATOM (DOUBLE)
#Y(I), I=1,NATOM
#Z(I), I=1,NATOM
#===========================================================
 
as part of another script but i don't know if it's true and accurate, and even if it is, i can't understand some parts of it (eg : character*20 at 5th line). Any guidelines would be appreciated. Thank you...
 
 
 
----------------------------------------
> From: gillescche_at_gmail.com
> Subject: Re: vmd-l:
> Date: Tue, 21 Oct 2008 08:22:01 -0400
> To: nihilique_at_hotmail.com
>
> Since you want the information contained in the dcd file I would use
> catdcd to write out the coordinates of a certain frame in some format
> you can use such as pdb or xyz.
>
> You can find catdcd here:
>
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> If you want to include the files in a script I know there are some
> fortran reads that are given on the mailing list.
>
> Best
> Chris
>
> On Oct 21, 2008, at 5:16 AM, JONATHAN BLACK wrote:
>
>>
>> hi guys. i am a biologist and i haven't been programming in perl
>> for a long time so my question may seem a little naive but i'm at a
>> total loss and any help would be appreciated. i need a perl script
>> to convert some binary files (.dcd if anyone knows what they are)
>> to ascii or just extract the ascii that they contain. i tried plain
>> read with no results. i searched the net and i only found this code :
>>
>> use warnings;
>> use strict;
>> @ARGV == 2 or die "usage: $0 in_filename out_filename\n";
>> # get first argument, i.e filename my $in_filename = shift;
>> print "You chose input \n";
>> my $out_filename = shift;
>> print "You chose output \n";
>> #set infile to binary mode open INFILE, '', $out_filename or die
>> "can't open $out_filename: $!";
>> # read 8 bytes at a time
>> $/ = \8;
>> while ( )
>> {
>> print OUTFILE join( ', ', map sprintf( '0x%04x', $_ ), unpack 'S*',
>> $_ + ), "\n";
>> }
>>
>> but when i run it it comes out with four columns of something
>> seeming like hexadecimal (0xe15d ...). The dcd files are about 700
>> mb so i can't upload it for you to see it, but i managed to cut the
>> first 80kb of it with hexedit and i upload it here: http://
>> www.gigasize.com/get.php?d=7qfs5f331bf Does anyone have any idea or
>> some plain guidelines because i really need get it done for my
>> work. Thanks anyway!
>> _________________________________________________________________
>> You live life beyond your PC. So now Windows goes beyond your PC.
>> http://clk.atdmt.com/MRT/go/115298556/direct/01/
>
 
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