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YiiP Protein Example | ||
==================== | ||
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To get started immediately with *Zarrtraj*, we have made the topology and trajectory of the | ||
[YiiP protein in a POPC membrane](https://www.mdanalysis.org/MDAnalysisData/yiip_equilibrium.html) | ||
publicly available for streaming. The trajectory is stored in in the `zarrmd` format | ||
for optimal streaming performance. | ||
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To access the trajectory, follow this example: | ||
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```python | ||
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" | ||
) | ||
for ts in u.trajectory: | ||
# Do something | ||
``` | ||
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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! |
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