DCD Module doesn't support Python 3

[richardjgowers]

The DCD module doesn't currently support Python 3

Master py3 issue: #260

There's a py3 compatible version based on our version here:
https://github.com/arose/simpletraj/tree/master/simpletraj/dcd

So hopefully this will be simple

[orbeckst]

See @arose 's comments on his work modifying the MDA DCD reader for simpetraj with Py3, in #260 (comment) .

Update: sorry, saw that you already linked #260 and simpletraj...

[tylerjereddy]

Ok, let me take a look.

[tylerjereddy]

Note that with biophysics and other talks coming up I'm a bit inundated so progress here is quite slow lately. Do feel free to reassign the task if desired, otherwise I'll just occasionally chip away it.

[tylerjereddy]

I've removed my assignment to this for now in case somebody else wants to step in. Otherwise, I will probably chip away at it slowly.

[dotsdl]

I'll take it, but it won't be until November. If anybody else feels moved by the spirit before then, I'm happy to let them work on it.

[kain88-de]

When I have some partially working cython up I'll push it to this repo instead of my fork. Then we can work together on it.

I'm strongly in favor of a clean cython port because it will increase the maintainability of the code dramatically.

[orbeckst]

On 20 Jul, 2016, at 13:06, Max Linke [email protected] wrote:

I'm strongly in favor of a clean cython port because it will increase the maintainability of the code dramatically.

Did you have a look at https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/dcdtimeseries.pyx ? This is has a lot of cython code that shows how to use the VMD C code from “readdcd.h”.

Of course, it is later patched into the DCD object https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/DCD.py#L600 which relies on the code in https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/coordinates/src/dcd.c – the very thing that needs to be rewritten.

Nevertheless, the reading of the trajectory in dcdtimeseries.pyx is independent from the reading in dcd.c so it should make for a useable starting point.

Oliver Beckstein * [email protected]
skype: orbeckst * [email protected]

[kain88-de]

I've looked into that module. It is pretty old cython (rather pyrex) code that is close to the C-API of python. It's helpful but not as much as you would imagine.