Re: 'cutting' colvars.traj file

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue May 03 2011 - 05:45:23 CDT

On Monday 02 May 2011 19:34:26 you wrote:
> Hi Bjoern,
>
> Unfortunately, same problem in Linux, I suppose that "header" line in
> colvars.traj file could be a problem, so I try to delete this line
> manually, but file is huge and could not be edited because I have no
> enough memory in computer (still configuration is OK). Please let me
> know which version of python you use in order to try to really be able
> to use script. Out the script problem, I simply try to obtain rgyr (that
> I use as one of colvars) for my simulations and very obviously that NAMD
> "write" this data (numerical values of rgyr) in different way comparing
> to tools that I am able to use for analysis (VMD with script, VegaZZ,
> PluMed). Because of that I was really satisfied when conclude that 2.8
> indeed write colvars.traj, you see the rest of story..
>
> Kind regards

Regarding your tries under Windows/Linux:
No matter what OS you use, start cattraj.py with python and not from within
the python shell. You approach is completely wrong. The same syntax applies to
Windows and Linux:

If Python is in the Windows/Linux executable path type:
python cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out

If Python is not in the Windows/Linux executable path, type:
/your/path/to/python cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out

The header has nothing to do with my script.
My script is "stupid", it simply counts lines and ignores commented (#) lines.
Thats it. You could basically run this script on any file, even on some lyrics
text, and it would print out something.

Memory shouldn't be a problem with my script, since I read a line and dump it
to the new file, I don't glob the entire file to memory. This might not be the
fastest way, but spares memory.

I am using Python 2.6 but it works with 2.7 and 3.1.
As you can see it works for me with all versions (for python 3 I had to change
the print syntax slightly, or simply use 2to3 to convert it).

I uploaded a newer version (v1.1) with cleaner indentation (Your error might
be related) and a default output file value of "cattraj.out.traj" so the "-o"
option is no longer mandatory.
http://olausson.de/downloads/view.download/6/13

Please keep in mind that Linux uses UNIX-Style line-breaks, just in case you
want to edit the file under Windows.

~~~~~Python 2.6.6~~~~~
#python2.6 cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out

Reading colvars.traj
Frames - r: 500
Frames - w: 250

-----------------------------------
-----------------------------------
Overall frames - r: 500
Overall frames - w: 250

~~~~~Python 2.7.1~~~~~
#python2.7 cattraj.py -f 1 -l 500 -s 2 -i test.traj -o test.out

Reading test.traj
Frames - r: 500
Frames - w: 250

-----------------------------------
-----------------------------------
Overall frames - r: 500
Overall frames - w: 250

~~~~~Python 3.1.3~~~~~
python3.1 cattraj3.py -f 1 -l 500 -s 2 -i test.traj -o test.out

Reading test.traj
Frames - r: 500
Frames - w: 250

-----------------------------------
-----------------------------------
Overall frames - r: 500
Overall frames - w: 250

Cheers,
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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