rdkit

# rdkit RDKit is the cheminformatics toolkit: a molecule is a graph (`Chem.Mol`), written as SMILES, queried with SMARTS, given coordinates by distance geometry. Tools: `$RDKIT_PYTHON` (the pinned venv, with numpy and pandas), `harness_rdkit` on `PYTHONPATH` (build, embed, write, compare), `$RDKIT_TOOLCHAIN/verdict.py` (the pane header). Never install another RDKit. ## Build, write, verdict ```bash "$RDKIT_PYTHON" molecules/hello.py # runs the script → out/<name>.sdf and the rest "$RDKIT_PYTHON" "$RDKIT_TOOLCHAIN/verdict.py" # judges the newest molecule → pane header "$RDKIT_PYTHON" "$RDKIT_TOOLCHAIN/harness_rdkit.py" design "CCO" ethanol # the same, without a script ``` ```python from harness_rdkit import design, mol_from_smiles, embed_conformers, embed_3d, write_outputs, properties, similarity, substructure design("CC(C)Cc1ccc(cc1)C(C)C(=O)O", "ibuprofen") # parse → 10 conformers → minimise → describe → write design("CC(C)(O)Cc1ccc(C(C)C(=O)O)cc1", "ibuprofen_oh", parent="ibuprofen") # an analogue: name its parent mol = mol_from_smiles("CN1C=NC2=C1C(=O)N(C)C(=O)N2C", "caffeine") # the steps, when work happens between confs = embed_conformers(mol, n=10, seed=7) # ETKDGv3 + MMFF94, deduplicated, lowest first, aligned write_outputs(confs, "caffeine", parent=False) # False: not an analogue of anything here ``` What `design`/`write_outputs` write to `out/`, and what each is for: | file | what it is...