Why is there a PDB Loader and no SDF Loader?

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IMO, there was simply no demand so far for loading SDF molecule definitions, especially since there is a PDBLoader around. Looking at the SDF/Mol File Format Specification, a loader shouldn’t be that complicated to implement. However, I would suggest a different approach like with PDBLoader.

It might make more sense to write a three.js independent library that takes SDF text content as an input and returns a JSON representation. We could then add an external three.js example that imports the lib, parse a loaded SDF with it and then visualizes the result with a CSS renderer or with WebGL/WebGPU.

Unlike other loaders for OBJ, FBX or glTF, the visualization of molecule data is quite application specific. So instead of writing a SDFLoader that returns mesh definitions, I would just focus on JSON and let the application do anything else.

The JSON could have the following structure:

{
  "molecules": [
    {
      "name": "Molecule 1 Name (from header if available, or generate one)",
      "atoms": [
        {
          "id": 1,
          "element": "C",
          "x": 0.0,
          "y": 0.0,
          "z": 0.0,
          "charge": 0
        },
        {
          "id": 2,
          "element": "O",
          "x": 1.2,
          "y": 0.0,
          "z": 0.0,
          "charge": -1
        }
        // ... more atoms
      ],
      "bonds": [
        {
          "from_atom": 1,
          "to_atom": 2,
          "type": 1, // 1 for single, 2 for double, etc.
          "stereo": 0
        },
        // ... more bonds
      ],
      "properties": {
        "logP": 2.5,
        "ExactMass": 123.45,
        "Source": "Some_Database"
        // ... other properties from the SDF/MOL file
      }
    },
    // ... more molecules if it's an SDF file
  ]
}
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