| """ |
| ActionExecutor β general-purpose molecular editing via a clean JSON Action protocol. |
| |
| Design: |
| - Graph-level: ChangeAtom, AddAtom, RemoveAtom, ChangeBond, AddBond, RemoveBond |
| - Shorthand: AddGroup, RemoveGroup |
| - Stereo: FlipChirality, FlipEZ |
| - Semantic: MoveSubstituent, SwapSubstituents |
| - Composite: Batch |
| |
| AtomRef (how to select an atom in the input SMILES): |
| {"map_num": 5} atom map number (preferred) |
| {"smarts": "[NH2]", "match_idx": 0} SMARTS pattern (most flexible) |
| {"idx": 3} raw atom index (fragile) |
| |
| BondRef: |
| {"atom1": <AtomRef>, "atom2": <AtomRef>} |
| |
| Usage: |
| ex = ActionExecutor() |
| new_smiles = ex.execute("CCO", {"type": "ChangeAtom", "atom": {"idx": 2}, "element": "N"}) |
| # β "CCN" |
| """ |
|
|
| import copy |
| import sys, os |
| sys.path.insert(0, os.path.dirname(__file__)) |
|
|
| from rdkit import Chem |
| from rdkit.Chem import rdmolops |
| from rdkit import RDLogger |
| RDLogger.DisableLog("rdApp.*") |
|
|
| from mol_ops import ( |
| BOND_TYPE_MAP, ELEM_TO_NUM, |
| add_functional_group, remove_functional_group, flip_ez, |
| ) |
|
|
|
|
| |
| |
| |
|
|
| class ActionError(Exception): |
| """Base class for all executor errors.""" |
|
|
| class AtomNotFoundError(ActionError): |
| """Raised when an AtomRef cannot be resolved.""" |
|
|
| class BondNotFoundError(ActionError): |
| """Raised when a BondRef cannot be resolved.""" |
|
|
| class InvalidMolError(ActionError): |
| """Raised when an operation produces an invalid molecule.""" |
|
|
| class UnknownActionError(ActionError): |
| """Raised for unsupported action types.""" |
|
|
|
|
| |
| |
| |
|
|
| BOND_STEREO_MAP = { |
| "E": Chem.BondStereo.STEREOE, |
| "Z": Chem.BondStereo.STEREOZ, |
| "CIS": Chem.BondStereo.STEREOZ, |
| "TRANS": Chem.BondStereo.STEREOE, |
| "NONE": Chem.BondStereo.STEREONONE, |
| } |
|
|
|
|
| def _sanitize(rw, context=""): |
| try: |
| Chem.SanitizeMol(rw) |
| except Exception as e: |
| raise InvalidMolError(f"Sanitization failed{' (' + context + ')' if context else ''}: {e}") |
|
|
|
|
| def _reset_atom_hs(atom): |
| """Clear explicit Hs and radical state so SanitizeMol recomputes implicit Hs.""" |
| atom.SetNumExplicitHs(0) |
| atom.SetNoImplicit(False) |
| atom.SetNumRadicalElectrons(0) |
|
|
|
|
| def _kekulize_rw(rw: Chem.RWMol) -> Chem.RWMol: |
| """Return a copy with aromatic bonds replaced by explicit single/double (KekulΓ© form).""" |
| rw2 = Chem.RWMol(copy.deepcopy(rw)) |
| Chem.Kekulize(rw2, clearAromaticFlags=True) |
| return rw2 |
|
|
|
|
| def _to_canonical(mol): |
| for a in mol.GetAtoms(): |
| a.SetAtomMapNum(0) |
| return Chem.MolToSmiles(mol) |
|
|
|
|
| def _shared_rings(mol, idx1, idx2): |
| """Return set of ring-atom-index sets that contain both idx1 and idx2.""" |
| ri = mol.GetRingInfo() |
| return [r for r in ri.AtomRings() if idx1 in r and idx2 in r] |
|
|
|
|
| |
| |
| |
|
|
| class ActionExecutor: |
| """ |
| Apply a JSON Action to a SMILES string and return the modified SMILES. |
| |
| Public API: |
| execute(smiles, action) β str |
| execute_batch(smiles, actions) β str |
| """ |
|
|
| |
|
|
| def _resolve_atom(self, mol, ref: dict) -> int: |
| """Resolve an AtomRef dict to a concrete atom index in mol.""" |
| if "map_num" in ref: |
| mn = ref["map_num"] |
| for a in mol.GetAtoms(): |
| if a.GetAtomMapNum() == mn: |
| return a.GetIdx() |
| raise AtomNotFoundError(f"No atom with map_num={mn}") |
|
|
| if "smarts" in ref: |
| patt = Chem.MolFromSmarts(ref["smarts"]) |
| if patt is None: |
| raise AtomNotFoundError(f"Invalid SMARTS: {ref['smarts']!r}") |
| matches = mol.GetSubstructMatches(patt) |
| mi = ref.get("match_idx", 0) |
| if not matches or mi >= len(matches): |
| raise AtomNotFoundError( |
| f"SMARTS {ref['smarts']!r} match_idx={mi}: " |
| f"found {len(matches)} match(es)" |
| ) |
| return matches[mi][0] |
|
|
| if "idx" in ref: |
| idx = ref["idx"] |
| if idx < 0 or idx >= mol.GetNumAtoms(): |
| raise AtomNotFoundError(f"idx={idx} out of range (mol has {mol.GetNumAtoms()} atoms)") |
| return idx |
|
|
| raise AtomNotFoundError(f"AtomRef must have 'map_num', 'smarts', or 'idx': got {ref}") |
|
|
| def _resolve_bond(self, mol, bond_ref: dict): |
| """Resolve a BondRef to (idx1, idx2, Bond).""" |
| i1 = self._resolve_atom(mol, bond_ref["atom1"]) |
| i2 = self._resolve_atom(mol, bond_ref["atom2"]) |
| bond = mol.GetBondBetweenAtoms(i1, i2) |
| if bond is None: |
| raise BondNotFoundError(f"No bond between atom idx {i1} and {i2}") |
| return i1, i2, bond |
|
|
| |
|
|
| def _change_atom(self, rw: Chem.RWMol, action: dict): |
| idx = self._resolve_atom(rw, action["atom"]) |
| atom = rw.GetAtomWithIdx(idx) |
|
|
| if "element" in action: |
| n = ELEM_TO_NUM.get(action["element"]) |
| if n is None: |
| raise ActionError(f"Unknown element: {action['element']!r}") |
| atom.SetAtomicNum(n) |
| atom.SetNoImplicit(False) |
|
|
| if "charge" in action: |
| atom.SetFormalCharge(int(action["charge"])) |
| _reset_atom_hs(atom) |
|
|
| if "isotope" in action and action["isotope"] is not None: |
| atom.SetIsotope(int(action["isotope"])) |
|
|
| if "num_hs" in action and action["num_hs"] is not None: |
| atom.SetNumExplicitHs(int(action["num_hs"])) |
| atom.SetNoImplicit(True) |
|
|
| atom.UpdatePropertyCache(strict=False) |
| _sanitize(rw, "ChangeAtom") |
| return rw |
|
|
| def _add_atom(self, rw: Chem.RWMol, action: dict): |
| anchor_idx = self._resolve_atom(rw, action["anchor"]) |
| elem = action["element"] |
| n = ELEM_TO_NUM.get(elem) |
| if n is None: |
| raise ActionError(f"Unknown element: {elem!r}") |
|
|
| order = action.get("bond_order", "SINGLE").upper() |
| bond_type = BOND_TYPE_MAP.get(order) |
| if bond_type is None: |
| raise ActionError(f"Unknown bond order: {order!r}") |
|
|
| new_idx = rw.AddAtom(Chem.Atom(n)) |
| new_atom = rw.GetAtomWithIdx(new_idx) |
|
|
| if "charge" in action: |
| new_atom.SetFormalCharge(int(action["charge"])) |
| if "num_hs" in action and action["num_hs"] is not None: |
| new_atom.SetNumExplicitHs(int(action["num_hs"])) |
|
|
| _reset_atom_hs(rw.GetAtomWithIdx(anchor_idx)) |
|
|
| rw.AddBond(anchor_idx, new_idx, bond_type) |
| _sanitize(rw, "AddAtom") |
| return rw |
|
|
| def _remove_atom(self, rw: Chem.RWMol, action: dict): |
| idx = self._resolve_atom(rw, action["atom"]) |
| neighbors = [n.GetIdx() for n in rw.GetAtomWithIdx(idx).GetNeighbors()] |
| rw.RemoveAtom(idx) |
| for nidx in neighbors: |
| adj = nidx if nidx < idx else nidx - 1 |
| if adj < rw.GetNumAtoms(): |
| _reset_atom_hs(rw.GetAtomWithIdx(adj)) |
| _sanitize(rw, "RemoveAtom") |
| return rw |
|
|
| def _change_bond(self, rw: Chem.RWMol, action: dict): |
| i1, i2, bond = self._resolve_bond(rw, action["bond"]) |
| order = action["order"].upper() |
| bond_type = BOND_TYPE_MAP.get(order) |
| if bond_type is None: |
| raise ActionError(f"Unknown bond order: {order!r}") |
| bond.SetBondType(bond_type) |
|
|
| if "stereo" in action and action["stereo"]: |
| stereo = BOND_STEREO_MAP.get(action["stereo"].upper()) |
| if stereo is not None: |
| bond.SetStereo(stereo) |
|
|
| for idx in (i1, i2): |
| _reset_atom_hs(rw.GetAtomWithIdx(idx)) |
| _sanitize(rw, "ChangeBond") |
| return rw |
|
|
| def _add_bond(self, rw: Chem.RWMol, action: dict): |
| i1 = self._resolve_atom(rw, action["bond"]["atom1"]) |
| i2 = self._resolve_atom(rw, action["bond"]["atom2"]) |
| if rw.GetBondBetweenAtoms(i1, i2) is not None: |
| raise ActionError(f"Bond already exists between atoms {i1} and {i2}") |
| order = action.get("order", "SINGLE").upper() |
| bond_type = BOND_TYPE_MAP.get(order) |
| if bond_type is None: |
| raise ActionError(f"Unknown bond order: {order!r}") |
| rw.AddBond(i1, i2, bond_type) |
| for idx in (i1, i2): |
| _reset_atom_hs(rw.GetAtomWithIdx(idx)) |
| _sanitize(rw, "AddBond") |
| return rw |
|
|
| def _remove_bond(self, rw: Chem.RWMol, action: dict): |
| i1, i2, _ = self._resolve_bond(rw, action["bond"]) |
| rw.RemoveBond(i1, i2) |
| for idx in (i1, i2): |
| _reset_atom_hs(rw.GetAtomWithIdx(idx)) |
| _sanitize(rw, "RemoveBond") |
| return rw |
|
|
| def _add_group(self, rw: Chem.RWMol, action: dict): |
| anchor = self._resolve_atom(rw, action["anchor"]) |
| group = action["group"] |
| result = add_functional_group(rw, anchor_idx=anchor, group_name=group) |
| if result is None: |
| raise InvalidMolError(f"AddGroup failed: group={group!r} anchor={anchor}") |
| return Chem.RWMol(result) |
|
|
| def _remove_group(self, rw: Chem.RWMol, action: dict): |
| anchor = self._resolve_atom(rw, action["anchor"]) |
| group = action["group"] |
| result, removed = remove_functional_group(rw, anchor_idx=anchor, group_name=group) |
| if result is None: |
| raise InvalidMolError( |
| f"RemoveGroup failed: group={group!r} not found at anchor={anchor}" |
| ) |
| rw2 = Chem.RWMol(result) |
| _reset_atom_hs(rw2.GetAtomWithIdx(anchor)) |
| _sanitize(rw2, "RemoveGroup") |
| return rw2 |
|
|
| def _flip_chirality(self, rw: Chem.RWMol, action: dict): |
| idx = self._resolve_atom(rw, action["atom"]) |
| atom = rw.GetAtomWithIdx(idx) |
| chi = atom.GetChiralTag() |
| if chi == Chem.ChiralType.CHI_TETRAHEDRAL_CW: |
| atom.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW) |
| elif chi == Chem.ChiralType.CHI_TETRAHEDRAL_CCW: |
| atom.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW) |
| else: |
| raise ActionError(f"Atom idx={idx} has no specified chirality to flip") |
| _sanitize(rw, "FlipChirality") |
| return rw |
|
|
| def _flip_ez(self, smiles: str, action: dict) -> str: |
| """ |
| FlipEZ: invert E/Z at SMILES level. |
| If 'bond' is provided, validates it's a double bond first. |
| """ |
| mol = Chem.MolFromSmiles(smiles) |
| if mol is None: |
| raise InvalidMolError(f"Cannot parse SMILES: {smiles!r}") |
|
|
| if "bond" in action: |
| i1, i2, bond = self._resolve_bond(mol, action["bond"]) |
| if bond.GetBondType() != Chem.BondType.DOUBLE: |
| raise ActionError( |
| f"FlipEZ: bond between atoms {i1} and {i2} is not a double bond" |
| ) |
|
|
| smi = Chem.MolToSmiles(mol, isomericSmiles=True) |
| if "/" not in smi and "\\" not in smi: |
| raise ActionError("FlipEZ: SMILES has no E/Z notation to flip") |
|
|
| result = flip_ez(smi) |
| if result is None or result == smi: |
| raise ActionError("FlipEZ: flip produced no change or invalid molecule") |
| |
| mol_r = Chem.MolFromSmiles(result) |
| if mol_r is None: |
| raise InvalidMolError(f"FlipEZ produced invalid SMILES: {result!r}") |
| return _to_canonical(mol_r) |
|
|
| def _move_substituent(self, rw: Chem.RWMol, action: dict): |
| """ |
| Detach `substituent` from `from_atom` and reattach it to `to_atom`. |
| Works on aromatic rings by operating in KekulΓ© form. |
| """ |
| sub_idx = self._resolve_atom(rw, action["substituent"]) |
| from_idx = self._resolve_atom(rw, action["from_atom"]) |
| to_idx = self._resolve_atom(rw, action["to_atom"]) |
|
|
| bond = rw.GetBondBetweenAtoms(from_idx, sub_idx) |
| if bond is None: |
| raise BondNotFoundError( |
| f"MoveSubstituent: no bond between from_atom={from_idx} and substituent={sub_idx}" |
| ) |
| bond_type = bond.GetBondType() |
| |
| if bond_type == Chem.BondType.AROMATIC: |
| bond_type = Chem.BondType.SINGLE |
|
|
| if rw.GetBondBetweenAtoms(to_idx, sub_idx) is not None: |
| raise ActionError( |
| f"MoveSubstituent: bond already exists between to_atom={to_idx} and substituent={sub_idx}" |
| ) |
|
|
| rw = _kekulize_rw(rw) |
| rw.RemoveBond(from_idx, sub_idx) |
| |
| for i in (from_idx, to_idx): |
| _reset_atom_hs(rw.GetAtomWithIdx(i)) |
| rw.AddBond(to_idx, sub_idx, bond_type) |
| _sanitize(rw, "MoveSubstituent") |
| return rw |
|
|
| def _swap_substituents(self, rw: Chem.RWMol, action: dict): |
| """ |
| Swap all non-ring substituents between two atoms (typically ring atoms). |
| Works on aromatic rings by operating in KekulΓ© form. |
| """ |
| idx1 = self._resolve_atom(rw, action["atom1"]) |
| idx2 = self._resolve_atom(rw, action["atom2"]) |
|
|
| if idx1 == idx2: |
| raise ActionError("SwapSubstituents: atom1 and atom2 are the same atom") |
|
|
| shared_ring_atoms = set() |
| for ring in _shared_rings(rw, idx1, idx2): |
| shared_ring_atoms.update(ring) |
|
|
| def get_substituents(center, other_center): |
| subs = [] |
| for nb in rw.GetAtomWithIdx(center).GetNeighbors(): |
| nidx = nb.GetIdx() |
| if nidx in shared_ring_atoms and nidx != other_center: |
| continue |
| if nidx == other_center: |
| continue |
| subs.append((nidx, rw.GetBondBetweenAtoms(center, nidx).GetBondType())) |
| return subs |
|
|
| subs1 = get_substituents(idx1, idx2) |
| subs2 = get_substituents(idx2, idx1) |
|
|
| rw = _kekulize_rw(rw) |
|
|
| for sub_idx, _ in subs1: |
| rw.RemoveBond(idx1, sub_idx) |
| for sub_idx, _ in subs2: |
| rw.RemoveBond(idx2, sub_idx) |
|
|
| |
| for center in (idx1, idx2): |
| _reset_atom_hs(rw.GetAtomWithIdx(center)) |
|
|
| for sub_idx, btype in subs1: |
| bt = Chem.BondType.SINGLE if btype == Chem.BondType.AROMATIC else btype |
| rw.AddBond(idx2, sub_idx, bt) |
| for sub_idx, btype in subs2: |
| bt = Chem.BondType.SINGLE if btype == Chem.BondType.AROMATIC else btype |
| rw.AddBond(idx1, sub_idx, bt) |
|
|
| _sanitize(rw, "SwapSubstituents") |
| return rw |
|
|
| |
|
|
| _SMILES_LEVEL = {"FlipEZ", "Batch"} |
|
|
| def _dispatch(self, smiles: str, action: dict) -> str: |
| atype = action.get("type") |
| if not atype: |
| raise UnknownActionError("Action dict missing 'type' key") |
|
|
| |
| if atype == "Batch": |
| for sub in action["actions"]: |
| smiles = self.execute(smiles, sub) |
| return smiles |
|
|
| |
| if atype == "FlipEZ": |
| return self._flip_ez(smiles, action) |
|
|
| |
| mol = Chem.MolFromSmiles(smiles) |
| if mol is None: |
| raise InvalidMolError(f"Cannot parse SMILES: {smiles!r}") |
| rw = Chem.RWMol(copy.deepcopy(mol)) |
|
|
| handlers = { |
| "ChangeAtom": self._change_atom, |
| "AddAtom": self._add_atom, |
| "RemoveAtom": self._remove_atom, |
| "ChangeBond": self._change_bond, |
| "AddBond": self._add_bond, |
| "RemoveBond": self._remove_bond, |
| "AddGroup": self._add_group, |
| "RemoveGroup": self._remove_group, |
| "FlipChirality": self._flip_chirality, |
| "MoveSubstituent": self._move_substituent, |
| "SwapSubstituents": self._swap_substituents, |
| } |
|
|
| handler = handlers.get(atype) |
| if handler is None: |
| raise UnknownActionError( |
| f"Unknown action type: {atype!r}. " |
| f"Valid types: {sorted(handlers) + ['FlipEZ', 'Batch']}" |
| ) |
|
|
| result_rw = handler(rw, action) |
| return _to_canonical(result_rw) |
|
|
| |
|
|
| def execute(self, smiles: str, action: dict) -> str: |
| """ |
| Apply a single Action to smiles. |
| |
| Args: |
| smiles: input SMILES string (with or without atom map numbers) |
| action: Action dict with 'type' key and type-specific fields |
| |
| Returns: |
| Canonical SMILES after applying the action. |
| |
| Raises: |
| AtomNotFoundError, BondNotFoundError, InvalidMolError, UnknownActionError |
| """ |
| return self._dispatch(smiles, action) |
|
|
| def execute_batch(self, smiles: str, actions: list) -> str: |
| """ |
| Apply a list of Actions sequentially. |
| |
| Equivalent to: execute(smiles, {"type": "Batch", "actions": actions}) |
| """ |
| return self._dispatch(smiles, {"type": "Batch", "actions": actions}) |
|
|
|
|
| |
| |
| |
|
|
| if __name__ == "__main__": |
| ex = ActionExecutor() |
| passed = failed = 0 |
|
|
| def test(name, smiles, action, expected): |
| global passed, failed |
| try: |
| result = ex.execute(smiles, action) |
| exp_canon = Chem.MolToSmiles(Chem.MolFromSmiles(expected)) |
| if result == exp_canon: |
| print(f" PASS {name}") |
| passed += 1 |
| else: |
| print(f" FAIL {name}") |
| print(f" input: {smiles}") |
| print(f" expected: {exp_canon}") |
| print(f" got: {result}") |
| failed += 1 |
| except Exception as e: |
| print(f" ERROR {name}: {e}") |
| failed += 1 |
|
|
| print("=" * 60) |
| print("ActionExecutor β inline tests") |
| print("=" * 60) |
|
|
| |
| test("ChangeAtom/element", |
| "CCCO", |
| {"type": "ChangeAtom", "atom": {"idx": 2}, "element": "N"}, |
| "CCNO") |
|
|
| |
| test("ChangeAtom/charge", |
| "CC(=O)[O-]", |
| {"type": "ChangeAtom", "atom": {"smarts": "[O-]"}, "charge": 0}, |
| "CC([O])=O") |
|
|
| |
| try: |
| r = ex.execute("CCO", {"type": "AddAtom", "anchor": {"idx": 1}, "element": "C"}) |
| assert Chem.MolFromSmiles(r) is not None |
| print(" PASS AddAtom") |
| passed += 1 |
| except Exception as e: |
| print(f" FAIL AddAtom: {e}") |
| failed += 1 |
|
|
| |
| test("RemoveAtom", |
| "CCO", |
| {"type": "RemoveAtom", "atom": {"smarts": "[OH]"}}, |
| "CC") |
|
|
| |
| test("ChangeBond", |
| "CC=O", |
| {"type": "ChangeBond", |
| "bond": {"atom1": {"idx": 1}, "atom2": {"idx": 2}}, |
| "order": "SINGLE"}, |
| "CCO") |
|
|
| |
| test("AddBond", |
| "CCCC", |
| {"type": "AddBond", |
| "bond": {"atom1": {"idx": 0}, "atom2": {"idx": 3}}, |
| "order": "SINGLE"}, |
| "C1CCC1") |
|
|
| |
| test("RemoveBond", |
| "C1CCC1", |
| {"type": "RemoveBond", |
| "bond": {"atom1": {"smarts": "[CH2]", "match_idx": 0}, |
| "atom2": {"smarts": "[CH2]", "match_idx": 3}}}, |
| "CCCC") |
|
|
| |
| test("AddGroup", |
| "c1ccccc1", |
| {"type": "AddGroup", "anchor": {"idx": 0}, "group": "OH"}, |
| "Oc1ccccc1") |
|
|
| |
| test("RemoveGroup", |
| "Oc1ccccc1", |
| {"type": "RemoveGroup", "anchor": {"smarts": "[c;r6]", "match_idx": 0}, "group": "OH"}, |
| "c1ccccc1") |
|
|
| |
| test("FlipChirality", |
| "C[C@@H](O)F", |
| {"type": "FlipChirality", "atom": {"smarts": "[C@@H]"}}, |
| "C[C@H](O)F") |
|
|
| |
| test("FlipEZ", |
| "C/C=C/C", |
| {"type": "FlipEZ", |
| "bond": {"atom1": {"idx": 1}, "atom2": {"idx": 2}}}, |
| "C/C=C\\C") |
|
|
| |
| |
| test("MoveSubstituent", |
| "Clc1ccccn1", |
| {"type": "MoveSubstituent", |
| "substituent": {"smarts": "[Cl]"}, |
| "from_atom": {"smarts": "[c;r6]", "match_idx": 0}, |
| "to_atom": {"smarts": "[c;r6]", "match_idx": 2}}, |
| "c1cc(Cl)ccn1") |
|
|
| |
| |
| try: |
| mol_in = Chem.MolFromSmiles("Cc1ccccc1Cl") |
| |
| rw = Chem.RWMol(mol_in) |
| for a in rw.GetAtoms(): |
| a.SetAtomMapNum(a.GetIdx() + 1) |
| mapped = Chem.MolToSmiles(rw) |
|
|
| |
| c_idx = next(a.GetIdx() for a in rw.GetAtoms() |
| if a.GetAtomicNum() == 6 and not a.GetIsAromatic() |
| and any(nb.GetIsAromatic() for nb in a.GetNeighbors())) |
| cl_nb = next(a for a in rw.GetAtoms() if a.GetAtomicNum() == 17) |
| cl_ring = next(nb.GetIdx() for nb in cl_nb.GetNeighbors()) |
| ch3_ring = next(nb.GetIdx() for nb in rw.GetAtomWithIdx(c_idx).GetNeighbors() |
| if nb.GetIsAromatic()) |
|
|
| r = ex.execute(mapped, { |
| "type": "SwapSubstituents", |
| "atom1": {"map_num": ch3_ring + 1}, |
| "atom2": {"map_num": cl_ring + 1}, |
| }) |
| mol_r = Chem.MolFromSmiles(r) |
| assert mol_r is not None |
| print(f" PASS SwapSubstituents ({Chem.MolToSmiles(mol_in)} β {r})") |
| passed += 1 |
| except Exception as e: |
| print(f" FAIL SwapSubstituents: {e}") |
| failed += 1 |
|
|
| |
| test("Batch", |
| "CCO", |
| {"type": "Batch", "actions": [ |
| {"type": "ChangeAtom", "atom": {"idx": 2}, "element": "N"}, |
| {"type": "AddGroup", "anchor": {"idx": 2}, "group": "CH3"}, |
| ]}, |
| "CCN(C)") |
|
|
| |
| test("AtomRef/map_num", |
| "[CH3:1][CH2:2][OH:3]", |
| {"type": "ChangeAtom", "atom": {"map_num": 3}, "element": "N"}, |
| "CCN") |
|
|
| print("=" * 60) |
| print(f"Results: {passed} passed, {failed} failed out of {passed+failed} tests") |
| print("=" * 60) |
|
|