Amber-MD
Add support for new trajectory formats
Add support for the following trajectory formats:
- [x] TNG format
- [ ] MMTF format http://mmtf.rcsb.org/
- [x] Desmond DTR format
See also
- https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-May/008300.html
- https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/xtc/src
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-May/008300.html
The xdrfile package seems like a good option, esp. since it's available with major Linux distros. It can be an optional package for people who want xtc support (and the trr support via xdrfile is probably better than what I currently have in cpptraj).
https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/xtc/src
These seem really cool - unfortunately I don't think the BSD license is compatible with GPL so cpptraj can't use these.
I think GPL can use BSD, but not vice-versa, so cpptraj should be able to use them
p.s. +1 on supporting xtc however it is done :)
- xrd is the lower layer that handles getting floats/ints/bytes out of the file in an endian-independent way, but you still need to gromacs xtc code to decompress the coordinates.
- the 2-clause bsd is compatible with the gpl http://www.gnu.org/licenses/license-list.en.html#ModifiedBSD
the 2-clause bsd is compatible with the gpl http://www.gnu.org/licenses/license-list.en.html#ModifiedBSD
Cool, good to know. Thanks for the info!
so should we close this issue? or change to TNG?
No. It's just to remind me. It will probably make sense to open a separate issue for TrajNG eventually, but it's probably still higher priority to get XTC supported at the moment.
What is TrajNG? Traj-Next-Gen?
I think that's exactly it. See: http://redmine.gromacs.org/issues/1926#note-6
I really hate when "next-gen" makes it into the name of a product. It's an accurate descriptor for like 2 minutes.
@hainm So they can have both good compression and good reading afterwards...
I'm happy to help get xtc and tng supported.
@mabraham That would be great! I've started playing around with using libxdrfile under the hood for this but I think it would be good to have someone who is more familiar with the formats take a look at this.