Re: Read DCD file in Java

From: Kejun (Kevin) Dong (kevin_at_cnic.ac.cn)
Date: Mon Jun 08 2009 - 12:33:58 CDT

Hi Axel,

Thanks you for advice.  It's really helpful to me.
Now I'm working on the VMD molfile plugin...

Cheers!

-Kevin


-----Original Message-----
From: Axel Kohlmeyer
Sent: 2009-6-7 0:23
On Sat, 2009-06-06 at 13:39 +0800, Kejun (Kevin) Dong wrote:
  
Hi All,

I want to stream the dcd data from one server to another by frames and
it is the first step to parse the dcd files in Java.
Does anyone have the source code to read dcd files in Java?
    

kevin,

i don't have any java code, but i can give you some 
unsolicited advice. parsing .dcd files cleanly and
reliably is a painful exercise. dcd is fortran unformatted
binary output. as such the exact number and order of bytes
in it changes due to endianness and other characteristics
of the machine or the compiler (and compiler flags) that 
were used when compiling the original code.

the VMD molfile library contains a plugin that can handle
a very large variety of these different incarnations of
dcd files. it is written in c, so you can consider either
interfacing or translating it to your code. 

http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html

cheers,
   axel.

  
I would really appreciate your help!


-Kevin Dong



    

  

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