Add PACMOF2 module for charge prediction#7
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Wraps the pacmof2 library to allow users to predict partial atomic charges on single CIF files or directories of CIFs. Adds CLI command (matkit pacmof2 predict), optional dependency, and typed result contract.
…ubstitution The template had a hardcoded component block with literal "ADSORBATE" as the MoleculeName, which was never replaced by setup_simulation(). Replace it with the __COMPONENTS__ placeholder that generate_component_blocks() already handles.
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Summary
pacmof2module wrapping the PACMOF2 library for predicting partial atomic charges in MOFsrun_charge_prediction()matkit pacmof2 predict --cif-dir <dir> --outdir <out>pacmof2as an optional dependency (pip install matkit[pacmof2])Test plan
pip install -e ".[pacmof2]"and verify import:from matkit.pacmof2 import run_charge_predictionmatkit pacmof2 predict --cif-dir <cifs> --outdir <out>on a folder of CIFs_atom_site_chargeannotationsmatkit pacmof2 predict --helprenders correctly