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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,
)
# ---------------------------------------------------------------------------
# Exceptions
# ---------------------------------------------------------------------------
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."""
# ---------------------------------------------------------------------------
# Helpers
# ---------------------------------------------------------------------------
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]
# ---------------------------------------------------------------------------
# ActionExecutor
# ---------------------------------------------------------------------------
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
"""
# ββ Atom / Bond resolution βββββββββββββββββββββββββββββββββββββββββββββββ
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
# ββ Action handlers ββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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")
# Strip atom map numbers and return canonical form
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()
# Use SINGLE for substituent attachment (aromatic bond β substituent is always single)
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)
# Reset explicit Hs on both endpoints so valence is recomputed by sanitize
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)
# Reset explicit Hs on swap targets so valence is recomputed
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
# ββ Dispatch βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
_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")
# Batch: apply actions sequentially at SMILES level
if atype == "Batch":
for sub in action["actions"]:
smiles = self.execute(smiles, sub)
return smiles
# FlipEZ: SMILES-level operation
if atype == "FlipEZ":
return self._flip_ez(smiles, action)
# All other ops: work on RWMol
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)
# ββ Public API ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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})
# ---------------------------------------------------------------------------
# Inline tests
# ---------------------------------------------------------------------------
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)
# 1. ChangeAtom β element
test("ChangeAtom/element",
"CCCO",
{"type": "ChangeAtom", "atom": {"idx": 2}, "element": "N"},
"CCNO")
# 2. ChangeAtom β charge
test("ChangeAtom/charge",
"CC(=O)[O-]",
{"type": "ChangeAtom", "atom": {"smarts": "[O-]"}, "charge": 0},
"CC([O])=O") # canonical RDKit form of acetic acid
# 3. AddAtom β via idx
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
# 4. RemoveAtom β via smarts
test("RemoveAtom",
"CCO",
{"type": "RemoveAtom", "atom": {"smarts": "[OH]"}},
"CC")
# 5. ChangeBond β DOUBLEβSINGLE (C=O β C-O in acetaldehyde)
test("ChangeBond",
"CC=O",
{"type": "ChangeBond",
"bond": {"atom1": {"idx": 1}, "atom2": {"idx": 2}},
"order": "SINGLE"},
"CCO")
# 6. AddBond
test("AddBond",
"CCCC",
{"type": "AddBond",
"bond": {"atom1": {"idx": 0}, "atom2": {"idx": 3}},
"order": "SINGLE"},
"C1CCC1")
# 7. RemoveBond
test("RemoveBond",
"C1CCC1",
{"type": "RemoveBond",
"bond": {"atom1": {"smarts": "[CH2]", "match_idx": 0},
"atom2": {"smarts": "[CH2]", "match_idx": 3}}},
"CCCC")
# 8. AddGroup
test("AddGroup",
"c1ccccc1",
{"type": "AddGroup", "anchor": {"idx": 0}, "group": "OH"},
"Oc1ccccc1")
# 9. RemoveGroup
test("RemoveGroup",
"Oc1ccccc1",
{"type": "RemoveGroup", "anchor": {"smarts": "[c;r6]", "match_idx": 0}, "group": "OH"},
"c1ccccc1")
# 10. FlipChirality β via smarts
test("FlipChirality",
"C[C@@H](O)F",
{"type": "FlipChirality", "atom": {"smarts": "[C@@H]"}},
"C[C@H](O)F")
# 11. FlipEZ
test("FlipEZ",
"C/C=C/C",
{"type": "FlipEZ",
"bond": {"atom1": {"idx": 1}, "atom2": {"idx": 2}}},
"C/C=C\\C")
# 12. MoveSubstituent β move Cl from position 1 to position 3 on pyridine
# pyridine with Cl at C2: Clc1ccccn1 β move Cl to C4: c1cc(Cl)ccn1
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")
# 13. SwapSubstituents β on o-chlorotoluene, swap Cl and CH3
# Cc1ccccc1Cl β Clc1ccccc1C (same thing, test canonical form)
try:
mol_in = Chem.MolFromSmiles("Cc1ccccc1Cl")
# assign map nums for stable ref
rw = Chem.RWMol(mol_in)
for a in rw.GetAtoms():
a.SetAtomMapNum(a.GetIdx() + 1)
mapped = Chem.MolToSmiles(rw)
# find the two substituted ring carbons
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
# 14. Batch β two actions
test("Batch",
"CCO",
{"type": "Batch", "actions": [
{"type": "ChangeAtom", "atom": {"idx": 2}, "element": "N"},
{"type": "AddGroup", "anchor": {"idx": 2}, "group": "CH3"},
]},
"CCN(C)")
# 15. map_num AtomRef (with pre-mapped SMILES)
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)
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