Is it possible to store in data or somewhere else files or paths to them?

[sperezconesa]

Hello,
I am considering using MDSynthesis in my projects but I was wondering a couple of things:
-Is it possible to store in simulations files (or maybe only their paths) like you do dataframes, for example a dssp.pdf file that I make from a trajectory.
-Can you store any arbitrary object in a sim, like a dictionary, a list or even a function?
Best regards and thank you,
Sergio

[orbeckst]

@sperezconesa development on MDSynthesis has largely halted – @dotsdl is not really maintaining it anymore. Instead we suggest to used datreant directly.

MDSynthesis was a good idea but it turned out to be more useful and easier to maintain to just abstract it more and make it datreant. @dotsdl can say more.

[kain88-de]

You can save everything that you can serialize in a sim object. In the end, they are just files on your hard drive. You can write objects to disk using the pickle module like this.

with open(treant['some_file_name'], 'w') as fh:
    pickle.dump(some_dic, fh)

and reading

with open(treant['some_file_name']) as fh:
    some_dic = pickle.load(fh)

With pickle functions should be possible to serialize too.

[sperezconesa]

Thanks for the help! I will try to get into datreant. Is datreant still mantained?

[kain88-de]

Yes it is still maintained. We work on bugs. We do consider the library feature complete though. So not many new things will appear.

…

On Thu 23. Jan 2020 at 11:35, Sergio Pérez Conesa ***@***.***> wrote: Thanks for the help! I will try to get into datreant. Is datreant still mantained? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#80?email_source=notifications&email_token=ABA2OVXON6CQDCQSMOK35G3Q7FXGXA5CNFSM4KDMZNLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJW5JUY#issuecomment-577623251>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABA2OVTHTJE4JRCWFQIVJXTQ7FXGXANCNFSM4KDMZNLA> .

[sperezconesa]

I am having problems pickling universe objects. How was this done in MDSynthesis, so I can do it in datreant?

[orbeckst]

Pickling universes is a hard problem, see MDAnalysis/mdanalysis#878 (and a whole bunch of somewhat related issues) so it does not work yet in MDAnalysis. (But we would really like it to work...)

In MDS we just stored the topology and trajectory and made Simulation.universe a managed attribute that would do a return mda.Universe(self.topology, self.trajectory) every time it was accessed. This worked (if you didn't care about any changes to the universe) but also was a bit problematic when people used in their code sim.universe instead of assigning it to a variableu = sim.universe because the former would load the universe every time, with poor performance. (I suppose, we really should have made it a function Simulation.get_Universe() to make clear that it does something expensive... poor UI choice.)

But the bottom line is that your best approach at the moment is to store in your Treant Universe.filename and Universe.trajectory.filename and then rebuild the Universe when you need it.

Feel free to ask questions on the MDAnalysis user list, people might also be able to give advice.

[orbeckst]

The lines in the MDS code

MDSynthesis/src/mdsynthesis/treants.py

Lines 89 to 109 in 980e9dd

	@property
	def universe(self):
	"""The universe of the Sim.
	Universes are interfaces to raw simulation data, with stored selections
	for this universe directly available via ``Sim.selections``.
	Setting this to a :class:`MDAnalysis.Universe` will set that as the
	universe definition for this Sim. Setting to ``None`` will remove
	the universe definition entirely.
	"""
	_args = self.universedef._args
	if _args != self._args:
	self._args = _args
	kwargs = self.universedef.kwargs
	if _args is None:
	self._universe = None
	else:
	self._universe = mda.Universe(*_args, **kwargs)
	return self._universe

[sperezconesa]

Ok, that clarifies things!
Thanks, I am really liking the library :)