Fix enhanced CLI explicit-donor handling and writeout tuple unpacking

[mikec-ai]

run_build_complex() imported pydentate before checking whether any ligand was actually missing coordinating atoms. That made commands with explicit --usercatoms fail in environments where pydentate was not installed, even though donor prediction was not needed for the run.

After fixing that, the same enhanced CLI path hit a second bug: it overwrote mol with the full return value of enforce_metal_ligand_distances_and_optimize(...), which returns a tuple. The later mol.writexyz(...) call then failed with:

AttributeError: 'tuple' object has no attribute 'writexyz'

This patch defers the pydentate import until it is actually needed, unpacks the return value of enforce_metal_ligand_distances_and_optimize(...) before writeout, and adds a CLI regression test for the explicit --usercatoms path.

Repro before

python -m molSimplify \
  --ligand NCCCOCCN \
  --usercatoms '[0,7]' \
  --occupancy 3 \
  --metal Fe \
  --ox 2 \
  --spin 1 \
  --geometry octahedral \
  --run-dir /tmp/molsimplify-cli-probe-repro

In an environment without pydentate, this failed immediately with:

ModuleNotFoundError: No module named 'pydentate'

After the lazy-import change, the same command progressed to the next bug in the same CLI path:

AttributeError: 'tuple' object has no attribute 'writexyz'

With both fixes in place, the command completes and writes the expected output files.

Test

conda run -n materials-cli-molsimplify python -m pytest -q tests/test_cli.py

2 passed

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 40.68%. Comparing base (44c0b8e) to head (48a8da1).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
molSimplify/__main__.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #541      +/-   ##
==========================================
+ Coverage   40.26%   40.68%   +0.41%     
==========================================
  Files          93       93              
  Lines       30325    30327       +2     
==========================================
+ Hits        12211    12339     +128     
+ Misses      18114    17988     -126     

Flag	Coverage Δ
unittests	40.68% <50.00%> (+0.41%)	⬆️

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[rolan701]

Everything looks good here!

Thanks,

• Roland