[BUG] `DEPRECATION WARNING: please use GetValence(Chem.ValenceType.EXPLICIT) instead`

[njzjz]

Bug summary

I notice the CI has the following warning:

[07:15:17] DEPRECATION WARNING: please use GetValence(Chem.ValenceType.EXPLICIT) instead

dpdata Version

latest

Input Files, Running Commands, Error Log, etc.

See the recent CI logs.

Steps to Reproduce

See the recent CI logs.

Further Information, Files, and Links

No response

[dosubot]

The deprecated call is in dpdata/rdkit/sanitize.py at line 13, where atom.GetExplicitValence() is used inside the get_explicit_valence() function [1].

The fix would be replacing:

exp_val = atom.GetExplicitValence()

with:

exp_val = atom.GetValence(Chem.ValenceType.EXPLICIT)

You'd also need to ensure Chem (from rdkit) is imported in that module. It may be worth checking which RDKit version introduced the new GetValence(Chem.ValenceType.EXPLICIT) API to set the minimum supported version accordingly.

To reply, just mention @dosu.

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