fetch_mmtf no longer works

[IAlibay]

Expected behavior

Calling fetch_mmtf will return an MMTF of the provided PDB entry.

Actual behavior

Calling fetch_mmtf leads to the following error:

URLError: <urlopen error [Errno -2] Name or service not known>

Why

As of the 2nd of July 2024, the PDB no longer services MMTF files, which means that attempts at retreiving such files no longer works.

Suggested path forward

My suggestion would be to remove the fetch_mmtf method and deprecate the MMTF Reader as no longer relevant.

Current version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") develop
• Which version of Python (python -V)? 3.10+
• Which operating system? Any

[RMeli]

Thanks @IAlibay, the suggested path forward sounds sensible to me.

[orbeckst]

Yes, I agree.

I would like to remove MMTFReader but on the off-chance that some has actual mmtf files they want to read, they get fair warning.

[orbeckst]

Removing MMTF also helps us with relicensing https://www.mdanalysis.org/2023/09/22/licensing-update/#removing-apache-20-dependencies