Difference between topology_format vs format arguments in Universe constructor?

[jauy123]

Hi,

What's the fundamental difference between topology_format vs format in the Universe constructor. I've been experimenting with both here in this PR #4943

And it seems like you can just construct a universe by either passing Universe(topology_format='PDB') (from me messing around in the code) or Universe(format='pdb') (as linked here)

Is there any real fundamental difference in initalizing a universe between the two arguments?

[orbeckst]

topology_format specifies the file format of the topology file (the first arg in Universe(topology, trajectory). format is the file format for the trajectory file, or files (plural) because trajectory can also be a list of filenames, or you can just list multiple args and they are all being concatenated (using the "ChainReader"). See example below:

In [1]: import MDAnalysis as mda; import MDAnalysisTests.datafiles as data

In [6]: u = mda.Universe(data.TPR, data.TRR)

In [7]: u.trajectory.n_frames
Out[7]: 10

In [8]: u = mda.Universe(data.TPR, [data.TRR, data.TRR, data.XTC])

In [9]: u.trajectory.n_frames
Out[9]: np.int64(30)

In [10]: u = mda.Universe(data.TPR, data.TRR, data.TRR, data.XTC, data.TRR)

In [11]: u.trajectory.n_frames
Out[11]: np.int64(40)

In [12]: u.trajectory
Out[12]: <ChainReader containing adk_oplsaa.trr and 3 more with 40 frames of 47681 atoms>

Note that

• the length of the trajectory increases (10 frames for each repetition of the file)
• we can combine different trajectory files (as long as they match the topology, which is the case for the example TRR and XTC)
• the fact that we get np.int64(40) from the ChainReader instead of the Python integer 40 is a bit odd and an implementation detail.

In order to be able to clearly set the format for either topology or trajectory files with such a flexible way to specify topologies and trajectories we need the two different keywords. By the way, you can also provide a list of formats to format if you're reading multiple files. (EDIT: I thought that worked but the docs say otherwise... might need to check the docs).

Finally, there's the special case of creating a universe from a single file. The most common case are formats such as PDB or GRO or XYZ, which contain topology information (particle types etc) and coordinates. However, you can create a minimalist universe from a trajectory file, too (Universe(data.TRR)) which can be useful for just looking at coordinates.

[orbeckst]

See the docs for Universe for more details.