Hello All,
Over the past few months I have been working on a project I have
dubbed cpptraj, since it is trajectory analysis software in the spirit
of ptraj but written in C++. I initially started writing it because I
wanted to be able to analyze structures with different topologies in
the same analysis run, and modifying ptraj to do that would have been
quite difficult to do based on the way ptraj is currently set up. It
has since developed into a full-fledged trajectory analysis program.
For the most part it should run just like ptraj (and usually a bit
faster, especially when processing Netcdf trajectories). Here are some
notable differences:
1. File compression is handled internally rather than external calls
to gzip, bzip2, etc, which makes reading and writing compressed files
more efficient.
2. Any file read or written by Cpptraj can be compressed (with the
exception of Netcdf trajectories). So e.g. topology files could be
read in as .gz files, and data files could be written as .bz2 files.
Compression is detected automatically when reading, and is determined
by the filename extension when writing.
3. If two actions specify the same file with the 'out' keyword, data
from both actions will be written to that file in separate columns.
4. Data files specified by the 'out' keyword can be written in xmgrace
format if the filename given has a '.agr' extension.
5. Multiple output trajectories can be specified. In addition, output
files can be directed to write only specific frames from the input
trajectories.
6. Multiple reference structures can be specified. Specific frames
from trajectories may be used as a reference structure.
7. The rmsd action allows specification of a separate mask for the
reference structure. In addition, per-residue RMSD can be calculated
easily.
8. When stripping coordinates with the strip action, a stripped
topology file can be written out. Currently this topology is good for
visualization only, not simulation (although this support is planned
for future releases).
The ptraj commands currently implemented are: trajin, trajout,
reference, angle, center, dihedral, distance, hbond, image, rmsd,
secstruct, and strip.
Since I have had several requests to get the code out there I have
uploaded it to the master branch of the amber GIT repository. The code
is located in the directory:
amber/AmberTools/src/cpptraj
and is completely self-contained. It will not be built by the overall
Amber Makefile. The code is still very much in an Alpha state and I am
still making modifications and enhancements, but as it is it should
function just fine. There is a manual located in the doc/ directory
(along with a very incomplete developers guide), and test cases
located in the test/ directory. The README file in the cpptraj/
directory contains info on how to build it:
./configure gnu
make install
make check
should work on most systems. This will place the cpptraj binary in the
amber/AmberTools/src/cpptraj/bin directory, then run all test cases.
The configure script by default sets everything up to link
dynamically. If you encounter linking errors you may need to specify
library locations using the '--with-LIB=' options. For example, to use
Netcdf compiled with Amber use the option:
--with-netcdf=$AMBERHOME/AmberTools/src/netcdf
Alternatively you could disable the library with the 'no-LIB' options.
Feedback on this will be hugely appreciated. Likes, dislikes, bugs,
desired features - send it all my way. Thanks!
-Dan
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Nov 19 2010 - 13:00:03 PST
