Question: How to make a deep copy of gemmi.Structure in python about gemmi HOT 3 CLOSED

I just found some information from another project that had the same error from a pybind11 object:
google-deepmind/open_spiel#88

They point to the following in the pybind11 docs:
https://pybind11.readthedocs.io/en/stable/advanced/classes.html#pickling-support

I guess this could be quite an undertaking for a complex class though. Hopefully there'll be something simpler I'm missing. In the meantime I might just write the structure to disk and read it again.

from gemmi.

To have deepcopy working it would be probably sufficient to implement __deepcopy__ method. I was thinking about it, but in the end I added methods clone() to Structure, Model, Chain, Residue and Atom. It's a one-line function. I'm on the fence what's better: copy.deepcopy(st) or st.clone().

from gemmi.

Awesome, thanks. I think either approach is fine, unless you also wanted to implement a shallow copy but I can't think of a use case for that.

from gemmi.