Use canonical rdkit import

doc/tutorial/interface/rdkit.rst

@@ -27,15 +27,14 @@ For a proper structural formula, we need to compute proper 2D coordinates first.
 
     import biotite.interface.rdkit as rdkit_interface
     import biotite.structure.info as struc
+    import rdkit.Chem.AllChem as Chem
     from rdkit.Chem.Draw import MolToImage
-    from rdkit.Chem.rdDepictor import Compute2DCoords
-    from rdkit.Chem.rdmolops import RemoveHs
 
     penicillin = struc.residue("PNN")
     mol = rdkit_interface.to_mol(penicillin)
     # We do not want to include explicit hydrogen atoms in the structural formula
-    mol = RemoveHs(mol)
-    Compute2DCoords(mol)
+    mol = Chem.RemoveHs(mol)
+    Chem.Compute2DCoords(mol)
     image = MolToImage(mol, size=(600, 400))
     display(image)
 
@@ -49,18 +48,13 @@ One way to to obtain them as :class:`.AtomArray` is passing a *SMILES* string to
 
 .. jupyter-execute::
 
-    from rdkit.Chem import MolFromSmiles
-    from rdkit.Chem.rdDistGeom import EmbedMolecule
-    from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
-    from rdkit.Chem.rdmolops import AddHs
-
     ERTAPENEM_SMILES = "C[C@@H]1[C@@H]2[C@H](C(=O)N2C(=C1S[C@H]3C[C@H](NC3)C(=O)NC4=CC=CC(=C4)C(=O)O)C(=O)O)[C@@H](C)O"
 
-    mol = MolFromSmiles(ERTAPENEM_SMILES)
+    mol = Chem.MolFromSmiles(ERTAPENEM_SMILES)
     # RDKit uses implicit hydrogen atoms by default, but Biotite requires explicit ones
-    mol = AddHs(mol)
+    mol = Chem.AddHs(mol)
     # Create a 3D conformer
-    conformer_id = EmbedMolecule(mol)
-    UFFOptimizeMolecule(mol)
+    conformer_id = Chem.EmbedMolecule(mol)
+    Chem.UFFOptimizeMolecule(mol)
     ertapenem = rdkit_interface.from_mol(mol, conformer_id)
     print(ertapenem)

src/biotite/interface/rdkit/mol.py

@@ -9,9 +9,7 @@
 import warnings
 from collections import defaultdict
 import numpy as np
-from rdkit.Chem.rdchem import Atom, Conformer, EditableMol, KekulizeException, Mol
-from rdkit.Chem.rdchem import BondType as RDKitBondType
-from rdkit.Chem.rdmolops import AddHs, Kekulize, SanitizeFlags, SanitizeMol
+import rdkit.Chem.AllChem as Chem
 from biotite.interface.version import requires_version
 from biotite.interface.warning import LossyConversionWarning
 from biotite.structure.atoms import AtomArray, AtomArrayStack
@@ -24,26 +22,26 @@
     BondType.TRIPLE: BondType.AROMATIC_TRIPLE,
 }
 _BIOTITE_TO_RDKIT_BOND_TYPE = {
-    BondType.ANY: RDKitBondType.UNSPECIFIED,
-    BondType.SINGLE: RDKitBondType.SINGLE,
-    BondType.DOUBLE: RDKitBondType.DOUBLE,
-    BondType.TRIPLE: RDKitBondType.TRIPLE,
-    BondType.QUADRUPLE: RDKitBondType.QUADRUPLE,
-    BondType.AROMATIC_SINGLE: RDKitBondType.AROMATIC,
-    BondType.AROMATIC_DOUBLE: RDKitBondType.AROMATIC,
-    BondType.AROMATIC_TRIPLE: RDKitBondType.AROMATIC,
-    BondType.AROMATIC: RDKitBondType.AROMATIC,
+    BondType.ANY: Chem.BondType.UNSPECIFIED,
+    BondType.SINGLE: Chem.BondType.SINGLE,
+    BondType.DOUBLE: Chem.BondType.DOUBLE,
+    BondType.TRIPLE: Chem.BondType.TRIPLE,
+    BondType.QUADRUPLE: Chem.BondType.QUADRUPLE,
+    BondType.AROMATIC_SINGLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC_DOUBLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC_TRIPLE: Chem.BondType.AROMATIC,
+    BondType.AROMATIC: Chem.BondType.AROMATIC,
     # Dative bonds may lead to a KekulizeException and may potentially be deprecated
     # in the future (https://github.com/rdkit/rdkit/discussions/6995)
-    BondType.COORDINATION: RDKitBondType.SINGLE,
+    BondType.COORDINATION: Chem.BondType.SINGLE,
 }
 _RDKIT_TO_BIOTITE_BOND_TYPE = {
-    RDKitBondType.UNSPECIFIED: BondType.ANY,
-    RDKitBondType.SINGLE: BondType.SINGLE,
-    RDKitBondType.DOUBLE: BondType.DOUBLE,
-    RDKitBondType.TRIPLE: BondType.TRIPLE,
-    RDKitBondType.QUADRUPLE: BondType.QUADRUPLE,
-    RDKitBondType.DATIVE: BondType.COORDINATION,
+    Chem.BondType.UNSPECIFIED: BondType.ANY,
+    Chem.BondType.SINGLE: BondType.SINGLE,
+    Chem.BondType.DOUBLE: BondType.DOUBLE,
+    Chem.BondType.TRIPLE: BondType.TRIPLE,
+    Chem.BondType.QUADRUPLE: BondType.QUADRUPLE,
+    Chem.BondType.DATIVE: BondType.COORDINATION,
 }
 
 
@@ -128,11 +126,11 @@ def to_mol(
     else:
         atoms = atoms[..., ~hydrogen_mask]
 
-    mol = EditableMol(Mol())
+    mol = Chem.EditableMol(Chem.Mol())
 
     has_charge_annot = "charge" in atoms.get_annotation_categories()
     for i in range(atoms.array_length()):
-        rdkit_atom = Atom(atoms.element[i].capitalize())
+        rdkit_atom = Chem.Atom(atoms.element[i].capitalize())
         if has_charge_annot:
             rdkit_atom.SetFormalCharge(atoms.charge[i].item())
         if explicit_hydrogen:
@@ -162,11 +160,8 @@ def to_mol(
         # Handle AtomArray and AtomArrayStack consistently
         coord = coord[None, :, :]
     for model_coord in coord:
-        conformer = Conformer(mol.GetNumAtoms())
-        # RDKit silently expects the data to be in C-contiguous order
-        # Otherwise the coordinates would be completely misassigned
-        # (https://github.com/rdkit/rdkit/issues/8221)
-        conformer.SetPositions(np.ascontiguousarray(model_coord, dtype=np.float64))
+        conformer = Chem.Conformer(mol.GetNumAtoms())
+        conformer.SetPositions(model_coord.astype(np.float64))
         conformer.Set3D(True)
         mol.AddConformer(conformer)
 
@@ -239,8 +234,8 @@ def from_mol(mol, conformer_id=None, add_hydrogen=None):
     if add_hydrogen is None:
         add_hydrogen = not _has_explicit_hydrogen(mol)
     if add_hydrogen:
-        SanitizeMol(mol, SanitizeFlags.SANITIZE_ADJUSTHS)
-        mol = AddHs(mol)
+        Chem.SanitizeMol(mol, Chem.SanitizeFlags.SANITIZE_ADJUSTHS)
+        mol = Chem.AddHs(mol)
 
     rdkit_atoms = mol.GetAtoms()
     if rdkit_atoms is None:
@@ -274,15 +269,15 @@ def from_mol(mol, conformer_id=None, add_hydrogen=None):
 
     rdkit_bonds = list(mol.GetBonds())
     is_aromatic = np.array(
-        [bond.GetBondType() == RDKitBondType.AROMATIC for bond in rdkit_bonds]
+        [bond.GetBondType() == Chem.BondType.AROMATIC for bond in rdkit_bonds]
     )
     if np.any(is_aromatic):
         # Determine the kekulized order of aromatic bonds
         # Copy as 'Kekulize()' modifies the molecule in-place
-        mol = Mol(mol)
+        mol = Chem.Mol(mol)
         try:
-            Kekulize(mol)
-        except KekulizeException:
+            Chem.Kekulize(mol)
+        except Chem.KekulizeException:
             warnings.warn(
                 "Kekulization failed, "
                 "using 'BondType.AROMATIC' instead for aromatic bonds instead",