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Merged
YZY-stack merged 1 commit into from
Jun 1, 2026
Merged

Preserve stereochemistry and explicit aromatic '<-->' bonds in Mermaid↔RDKit converters #1

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130 changes: 85 additions & 45 deletions molecode/markush/mermaid_to_rdkit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ class MermaidMolParser:
'---': Chem.BondType.SINGLE,
'===': Chem.BondType.DOUBLE,
'-.-': Chem.BondType.TRIPLE,
'<-->': Chem.BondType.AROMATIC,
'-->': Chem.BondType.DATIVE, # 配位键
}

Expand Down Expand Up @@ -88,7 +89,7 @@ def _parse_line(self, line: str):

# 尝试匹配普通键连接: atom1 bond_type atom2
# 原子ID可能包含手性后缀 (_R 或 _S)
bond_pattern = r'([\w_]+)\s*(---|\===|-\.-|-->)\s*([\w_]+)'
bond_pattern = r'([\w_]+)\s*(<-->|---|\===|-\.-|-->)\s*([\w_]+)'
bond_match = re.search(bond_pattern, line)

if bond_match:
Expand Down Expand Up @@ -241,17 +242,10 @@ def _build_mol(self) -> Optional[Chem.Mol]:
atom_obj = mol.GetAtomWithIdx(idx)
atom_obj.SetProp("_abbreviation", self.abbreviations[atom_id])

# 设置手性（如果有）
if atom_id in self.chirality:
chirality_type = self.chirality[atom_id]
atom_obj = mol.GetAtomWithIdx(idx)

if chirality_type == 'R':
atom_obj.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)
elif chirality_type == 'S':
atom_obj.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW)

# 添加键
# 添加键。双键 E/Z 和四面体 R/S 都需要在完整拓扑存在后设置，
# 因此这里先记录，待 SanitizeMol 后统一恢复。
stereo_bonds = []
aromatic_atom_idxs = set()
for bond_info in self.bonds:
if len(bond_info) == 3:
# 普通键: (atom1_id, atom2_id, bond_type_str)
Expand All @@ -270,40 +264,16 @@ def _build_mol(self) -> Optional[Chem.Mol]:

mol.AddBond(idx1, idx2, bond_type)

# 设置立体化学（稍后统一处理，需要先添加所有键）
if bond_type_str == '<-->':
aromatic_atom_idxs.update((idx1, idx2))
bond = mol.GetBondBetweenAtoms(idx1, idx2)
bond.SetIsAromatic(True)

if stereo_type:
# 记录需要设置立体化学的键
if not hasattr(mol, '_stereo_bonds'):
mol._stereo_bonds = []
mol._stereo_bonds.append((idx1, idx2, stereo_type))

# 在转换为不可编辑的Mol之前，设置立体化学
if hasattr(mol, '_stereo_bonds'):
for idx1, idx2, stereo_type in mol._stereo_bonds:
bond = mol.GetBondBetweenAtoms(idx1, idx2)

# 获取双键两端原子的邻接原子（用于定义立体化学）
atom1 = mol.GetAtomWithIdx(idx1)
atom2 = mol.GetAtomWithIdx(idx2)

# 找到idx1的邻居（除了idx2）
neighbors1 = [n.GetIdx() for n in atom1.GetNeighbors() if n.GetIdx() != idx2]
# 找到idx2的邻居（除了idx1）
neighbors2 = [n.GetIdx() for n in atom2.GetNeighbors() if n.GetIdx() != idx1]

# 如果两端都有邻居，设置立体化学
if neighbors1 and neighbors2:
# 使用第一个邻居作为参考原子
bond.SetStereoAtoms(neighbors1[0], neighbors2[0])

if stereo_type == 'E':
bond.SetStereo(Chem.BondStereo.STEREOE)
elif stereo_type == 'Z':
bond.SetStereo(Chem.BondStereo.STEREOZ)
elif stereo_type == 'CIS':
bond.SetStereo(Chem.BondStereo.STEREOCIS)
elif stereo_type == 'TRANS':
bond.SetStereo(Chem.BondStereo.STEREOTRANS)
stereo_bonds.append((idx1, idx2, stereo_type))

for idx in aromatic_atom_idxs:
mol.GetAtomWithIdx(idx).SetIsAromatic(True)

# 转换为不可编辑的Mol对象
mol = mol.GetMol()
Expand All @@ -322,9 +292,79 @@ def _build_mol(self) -> Optional[Chem.Mol]:
# 完全失败，返回未清理的版本
pass

self._assign_chirality_from_ids(mol, atom_id_to_idx)
self._assign_double_bond_stereo(mol, stereo_bonds)

return mol


def _assign_chirality_from_ids(self, mol: Chem.Mol, atom_id_to_idx: Dict[str, int]):
"""根据 atom id 的 _R/_S 后缀恢复绝对 CIP 手性。"""
if not self.chirality:
return

for atom_id, desired_cip in self.chirality.items():
idx = atom_id_to_idx.get(atom_id)
if idx is None:
continue

atom = mol.GetAtomWithIdx(idx)
matched = False

for chiral_tag in (
Chem.ChiralType.CHI_TETRAHEDRAL_CW,
Chem.ChiralType.CHI_TETRAHEDRAL_CCW,
):
atom.SetChiralTag(chiral_tag)
try:
Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
except Exception:
continue

if atom.HasProp('_CIPCode') and atom.GetProp('_CIPCode') == desired_cip:
matched = True
break

if not matched:
atom.SetChiralTag(Chem.ChiralType.CHI_UNSPECIFIED)

try:
Chem.AssignStereochemistry(mol, cleanIt=False, force=True)
except Exception:
pass

def _assign_double_bond_stereo(self, mol: Chem.Mol, stereo_bonds: List[Tuple[int, int, str]]):
"""恢复 ===|E| / ===|Z| 双键构型。"""
for idx1, idx2, stereo_type in stereo_bonds:
bond = mol.GetBondBetweenAtoms(idx1, idx2)
if bond is None:
continue

atom1 = mol.GetAtomWithIdx(idx1)
atom2 = mol.GetAtomWithIdx(idx2)
neighbors1 = [n.GetIdx() for n in atom1.GetNeighbors() if n.GetIdx() != idx2]
neighbors2 = [n.GetIdx() for n in atom2.GetNeighbors() if n.GetIdx() != idx1]

if not neighbors1 or not neighbors2:
continue

bond.SetStereoAtoms(neighbors1[0], neighbors2[0])

if stereo_type == 'E':
bond.SetStereo(Chem.BondStereo.STEREOE)
elif stereo_type == 'Z':
bond.SetStereo(Chem.BondStereo.STEREOZ)
elif stereo_type == 'CIS':
bond.SetStereo(Chem.BondStereo.STEREOCIS)
elif stereo_type == 'TRANS':
bond.SetStereo(Chem.BondStereo.STEREOTRANS)

try:
Chem.AssignStereochemistry(mol, cleanIt=False, force=True)
except Exception:
pass


def has_invalid_atoms(mol: Chem.Mol) -> bool:
"""
检查分子是否包含无效原子（Dummy Atom）
Expand Down
22 changes: 10 additions & 12 deletions molecode/markush/rdkit_to_mermaid.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -163,18 +163,16 @@ def _generate_atom_id(self, atom: Chem.Atom) -> str:
# 基础ID
base_id = f"{clean_name}_{symbol}_{count}"

# 检测手性并添加后缀
chiral_tag = atom.GetChiralTag()

if chiral_tag == Chem.ChiralType.CHI_TETRAHEDRAL_CW:
# 顺时针 (R构型)
return f"{base_id}_R"
elif chiral_tag == Chem.ChiralType.CHI_TETRAHEDRAL_CCW:
# 逆时针 (S构型)
return f"{base_id}_S"
else:
# 无手性或未指定
return base_id
# 使用 RDKit 计算出的绝对 CIP 构型，而不是直接把
# CHI_TETRAHEDRAL_CW/CCW 当作 R/S。CW/CCW 依赖原子顺序，
# 只有 _CIPCode 才是可序列化的绝对 R/S 标签。
if atom.HasProp('_CIPCode'):
cip_code = atom.GetProp('_CIPCode')
if cip_code in ('R', 'S'):
return f"{base_id}_{cip_code}"

# 无手性或未指定
return base_id

def _generate_atom_label(self, atom: Chem.Atom) -> str:
"""
Expand Down
133 changes: 88 additions & 45 deletions molecode/molecule/mermaid_to_rdkit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ class MermaidMolParser:
'---': Chem.BondType.SINGLE,
'===': Chem.BondType.DOUBLE,
'-.-': Chem.BondType.TRIPLE,
'<-->': Chem.BondType.AROMATIC,
'-->': Chem.BondType.DATIVE, # 配位键
}

Expand Down Expand Up @@ -86,7 +87,7 @@ def _parse_line(self, line: str):

# 尝试匹配普通键连接: atom1 bond_type atom2
# 原子ID可能包含手性后缀 (_R 或 _S)
bond_pattern = r'([\w_]+)\s*(---|\===|-\.-|-->)\s*([\w_]+)'
bond_pattern = r'([\w_]+)\s*(<-->|---|\===|-\.-|-->)\s*([\w_]+)'
bond_match = re.search(bond_pattern, line)

if bond_match:
Expand Down Expand Up @@ -215,17 +216,10 @@ def _build_mol(self) -> Optional[Chem.Mol]:
idx = mol.AddAtom(atom)
atom_id_to_idx[atom_id] = idx

# 设置手性（如果有）
if atom_id in self.chirality:
chirality_type = self.chirality[atom_id]
atom_obj = mol.GetAtomWithIdx(idx)

if chirality_type == 'R':
atom_obj.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)
elif chirality_type == 'S':
atom_obj.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW)

# 添加键
# 添加键。双键 E/Z 和四面体 R/S 都需要在完整拓扑存在后设置，
# 因此这里先记录，待 SanitizeMol 后统一恢复。
stereo_bonds = []
aromatic_atom_idxs = set()
for bond_info in self.bonds:
if len(bond_info) == 3:
# 普通键: (atom1_id, atom2_id, bond_type_str)
Expand All @@ -244,40 +238,16 @@ def _build_mol(self) -> Optional[Chem.Mol]:

mol.AddBond(idx1, idx2, bond_type)

# 设置立体化学（稍后统一处理，需要先添加所有键）
if bond_type_str == '<-->':
aromatic_atom_idxs.update((idx1, idx2))
bond = mol.GetBondBetweenAtoms(idx1, idx2)
bond.SetIsAromatic(True)

if stereo_type:
# 记录需要设置立体化学的键
if not hasattr(mol, '_stereo_bonds'):
mol._stereo_bonds = []
mol._stereo_bonds.append((idx1, idx2, stereo_type))

# 在转换为不可编辑的Mol之前，设置立体化学
if hasattr(mol, '_stereo_bonds'):
for idx1, idx2, stereo_type in mol._stereo_bonds:
bond = mol.GetBondBetweenAtoms(idx1, idx2)

# 获取双键两端原子的邻接原子（用于定义立体化学）
atom1 = mol.GetAtomWithIdx(idx1)
atom2 = mol.GetAtomWithIdx(idx2)

# 找到idx1的邻居（除了idx2）
neighbors1 = [n.GetIdx() for n in atom1.GetNeighbors() if n.GetIdx() != idx2]
# 找到idx2的邻居（除了idx1）
neighbors2 = [n.GetIdx() for n in atom2.GetNeighbors() if n.GetIdx() != idx1]

# 如果两端都有邻居，设置立体化学
if neighbors1 and neighbors2:
# 使用第一个邻居作为参考原子
bond.SetStereoAtoms(neighbors1[0], neighbors2[0])

if stereo_type == 'E':
bond.SetStereo(Chem.BondStereo.STEREOE)
elif stereo_type == 'Z':
bond.SetStereo(Chem.BondStereo.STEREOZ)
elif stereo_type == 'CIS':
bond.SetStereo(Chem.BondStereo.STEREOCIS)
elif stereo_type == 'TRANS':
bond.SetStereo(Chem.BondStereo.STEREOTRANS)
stereo_bonds.append((idx1, idx2, stereo_type))

for idx in aromatic_atom_idxs:
mol.GetAtomWithIdx(idx).SetIsAromatic(True)

# 转换为不可编辑的Mol对象
mol = mol.GetMol()
Expand All @@ -296,9 +266,82 @@ def _build_mol(self) -> Optional[Chem.Mol]:
# 完全失败，返回未清理的版本
pass

self._assign_chirality_from_ids(mol, atom_id_to_idx)
self._assign_double_bond_stereo(mol, stereo_bonds)

return mol


def _assign_chirality_from_ids(self, mol: Chem.Mol, atom_id_to_idx: Dict[str, int]):
"""根据 atom id 的 _R/_S 后缀恢复绝对 CIP 手性。"""
if not self.chirality:
return

for atom_id, desired_cip in self.chirality.items():
idx = atom_id_to_idx.get(atom_id)
if idx is None:
continue

atom = mol.GetAtomWithIdx(idx)
matched = False

for chiral_tag in (
Chem.ChiralType.CHI_TETRAHEDRAL_CW,
Chem.ChiralType.CHI_TETRAHEDRAL_CCW,
):
atom.SetChiralTag(chiral_tag)
try:
Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
except Exception:
continue

if atom.HasProp('_CIPCode') and atom.GetProp('_CIPCode') == desired_cip:
matched = True
break

if not matched:
atom.SetChiralTag(Chem.ChiralType.CHI_UNSPECIFIED)

try:
Chem.AssignStereochemistry(mol, cleanIt=False, force=True)
except Exception:
pass

def _assign_double_bond_stereo(self, mol: Chem.Mol, stereo_bonds: List[Tuple[int, int, str]]):
"""恢复 ===|E| / ===|Z| 双键构型。"""
for idx1, idx2, stereo_type in stereo_bonds:
bond = mol.GetBondBetweenAtoms(idx1, idx2)
if bond is None:
continue

# 获取双键两端原子的邻接原子（用于定义立体化学）
atom1 = mol.GetAtomWithIdx(idx1)
atom2 = mol.GetAtomWithIdx(idx2)

neighbors1 = [n.GetIdx() for n in atom1.GetNeighbors() if n.GetIdx() != idx2]
neighbors2 = [n.GetIdx() for n in atom2.GetNeighbors() if n.GetIdx() != idx1]

if not neighbors1 or not neighbors2:
continue

bond.SetStereoAtoms(neighbors1[0], neighbors2[0])

if stereo_type == 'E':
bond.SetStereo(Chem.BondStereo.STEREOE)
elif stereo_type == 'Z':
bond.SetStereo(Chem.BondStereo.STEREOZ)
elif stereo_type == 'CIS':
bond.SetStereo(Chem.BondStereo.STEREOCIS)
elif stereo_type == 'TRANS':
bond.SetStereo(Chem.BondStereo.STEREOTRANS)

try:
# 不使用 cleanIt=True，避免清掉刚刚从 EGL 明确恢复的 E/Z 标记。
Chem.AssignStereochemistry(mol, cleanIt=False, force=True)
except Exception:
pass


def has_invalid_atoms(mol: Chem.Mol) -> bool:
"""
检查分子是否包含无效原子（Dummy Atom）
Expand Down
22 changes: 10 additions & 12 deletions molecode/molecule/rdkit_to_mermaid.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -158,18 +158,16 @@ def _generate_atom_id(self, atom: Chem.Atom) -> str:
# 基础ID
base_id = f"{clean_name}_{symbol}_{count}"

# 检测手性并添加后缀
chiral_tag = atom.GetChiralTag()

if chiral_tag == Chem.ChiralType.CHI_TETRAHEDRAL_CW:
# 顺时针 (R构型)
return f"{base_id}_R"
elif chiral_tag == Chem.ChiralType.CHI_TETRAHEDRAL_CCW:
# 逆时针 (S构型)
return f"{base_id}_S"
else:
# 无手性或未指定
return base_id
# 使用 RDKit 计算出的绝对 CIP 构型，而不是直接把
# CHI_TETRAHEDRAL_CW/CCW 当作 R/S。CW/CCW 依赖原子顺序，
# 只有 _CIPCode 才是可序列化的绝对 R/S 标签。
if atom.HasProp('_CIPCode'):
cip_code = atom.GetProp('_CIPCode')
if cip_code in ('R', 'S'):
return f"{base_id}_{cip_code}"

# 无手性或未指定
return base_id

def _generate_atom_label(self, atom: Chem.Atom) -> str:
"""
Expand Down
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