{
  "context": "This criteria evaluates how effectively an engineer uses RDKit's molecular alignment capabilities, including 3D conformation generation, molecular alignment functions, and RMSD calculations. The focus is exclusively on correct usage of RDKit's API for 3D molecular operations.",
  "type": "weighted_checklist",
  "checklist": [
    {
      "name": "Molecular I/O",
      "description": "Uses appropriate RDKit functions for reading molecules from different formats: MolFromSmiles() for SMILES files and MolFromMolBlock() or MolFromMolFile() for MOL files. Correctly handles file reading and molecule parsing.",
      "max_score": 15
    },
    {
      "name": "3D Conformer Generation",
      "description": "Uses EmbedMolecule() or EmbedMultipleConfs() from rdkit.Chem.AllChem to generate 3D coordinates for molecules that lack them. Properly checks if molecules need 3D coordinate generation.",
      "max_score": 20
    },
    {
      "name": "Force Field Optimization",
      "description": "Applies force field optimization using MMFFOptimizeMolecule() or UFFOptimizeMolecule() from rdkit.Chem.AllChem to optimize generated 3D conformations.",
      "max_score": 15
    },
    {
      "name": "Molecular Alignment",
      "description": "Uses AlignMol() function from rdkit.Chem.AllChem to align the query molecule to the reference molecule. Correctly passes the probe molecule (query) and reference molecule in the right order, ensuring the alignment is performed on heavy atoms.",
      "max_score": 25
    },
    {
      "name": "RMSD Calculation",
      "description": "Calculates RMSD either by capturing the return value from AlignMol() or by using GetConformerRMS() or CalcRMS() functions. Correctly reports the RMSD value between aligned structures.",
      "max_score": 15
    },
    {
      "name": "MOL Output",
      "description": "Uses MolToMolBlock() or MolToMolFile() to write the aligned query molecule with 3D coordinates to an output file. Ensures the output preserves the 3D conformation of the aligned molecule.",
      "max_score": 10
    }
  ]
}