YiiP Protein Example

To get started immediately with Zarrtraj, we have made the topology and trajectory of the YiiP protein in a POPC membrane publicly available for streaming (no read/write credentials are needed as in the walkthrough). The trajectory is stored in in the ZarrMD format for optimal streaming performance.

To access the trajectory, you can copy and paste this code into a python script:

import zarrtraj
import MDAnalysis as mda
import fsspec

with fsspec.open("gcs://zarrtraj-test-data/YiiP_system.pdb", "r") as top:

    u = mda.Universe(
        top, "gcs://zarrtraj-test-data/yiip.zarrmd", topology_format="PDB"
    )
    protein = u.select_atoms("protein")

    for ts in u.trajectory[::100]:
        print(f"{ts.frame}, {ts.time}, {protein.center_of_mass()}")

In this example, we first import all necessary packages:

zarrtraj for the functionality to read a trajectory from cloud-storage; it automatically hooks into MDAnalysis to make the trajectory available as part of a Universe

Note

Whenever you want to read or write the ZarrMD format, you need to import zarrtraj. You do not have to explicitly call any functions or classes inside the zarrtraj package because on import it automatically registers itself as a reader/writer with MDAnalysis. The import zarrtraj together with importing MDAnalysis (in any order) is sufficient for MDAnalysis to “know” how to work with trajectories stored in the cloud in zarr and h5md format.
fsspec to access a simple file in cloud storage with a file-like interface

Note

While there is not yet an officially recommended way to access cloud-stored topologies, this method of opening a Python File-like object from the topology URL in PDB format using fsspec works with MDAnalysis 2.7.0. Check back later for further development!

We then create the basic MDAnalysis data structure, the Universe, from the topology file “YiiP_system.pdb” (which contains static information about the individual atoms such as their names, types, and organization as a biomolecule) and the data that change over time, namely the positions of the atoms in the trajectory “yiip.zarrmd”. Both topology and trajectory files can be stored in the cloud (here in Google Cloud Storage). The specific URI string for the trajectory tells MDAnalysis to use zarrtraj to access the file.

We then use standard MDAnalysis functionality to first select a part of the system for analysis, namely, the protein, and then iterate over the trajectory in steps of 100 frames. For each loaded frame, we print information about the frame number and recorded time in the trajectory and perform a simple analysis task by calculating and printing the center of mass (see AtomGroup.center_of_mass of the protein.