MDAnalysis
Add example for writing to NamedStream StringIO buffer
We have plenty of examples of how to read a file from a StringIO buffer or similar using a NamedStream, but no examples of how to write to a StringIO buffer using a similar methodology. We should add a simple example like the following.
import MDAnalysis as mda
from io import StringIO
u = mda.Universe("pdb.pdb")
buf = StringIO()
prot = u.select_atoms("protein")
with mda.Writer(mda.lib.util.NamedStream(buf, "prot.xyz"), prot.n_atoms) as w:
w.write(prot)
buf.getvalue()
>>> # xyz file
This is an excellent and much-needed example! You're right @hmacdope , while reading from a NamedStream(StringIO, ...) is well-documented, the ability to write to an in-memory buffer is a highly useful pattern that currently lacks a clear example.
The proposed code snippet is perfect and demonstrates the usage of mda.lib.util.NamedStream with mda.Writer very clearly.
I'd be happy to open a Pull Request (PR) to add this example to the relevant section of the documentation (e.g., the User Guide or the mda.Writer documentation) to ensure it's easily discoverable for users.
@ChinmayRout9040895625 You are more than welcome to open a PR to fix things.
That being said, I have seen you respond in a few issues with (pardon me if I'm incorrect) what appears to be AI summaries of the issue.
May I recommend that you stick to resolving one issue first rather than trying to tackle many?
