to_rdkit_molecule converter implemented

version BUMP

CGRtools/utils/rdkit.py

@@ -16,7 +16,7 @@
 #  You should have received a copy of the GNU Lesser General Public License
 #  along with this program; if not, see <https://www.gnu.org/licenses/>.
 #
-from rdkit.Chem import BondType
+from rdkit.Chem import BondType, Atom, RWMol, SanitizeMol, Conformer
 from ..containers import MoleculeContainer
 
 
@@ -38,7 +38,7 @@ def from_rdkit_molecule(data):
             atom['isotope'] = isotope
         radical = a.GetNumRadicalElectrons()
         if radical:
-            atom['multiplicity'] = 2 if radical == 1 else 3
+            atom['multiplicity'] = radical + 1
 
     conformers = data.GetConformers()
     if conformers:
@@ -56,7 +56,39 @@ def from_rdkit_molecule(data):
     return m
 
 
-_rdkit_bond_map = {BondType.SINGLE: 1, BondType.DOUBLE: 2, BondType.TRIPLE: 3, BondType.AROMATIC: 4}
+def to_rdkit_molecule(data):
+    """
+    MoleculeContainer to RDKit molecule object converter
+    """
+    mol = RWMol()
+    conf = Conformer()
+    mapping = {}
+    is_3d = False
+    for n, a in data.atoms():
+        ra = Atom(a.number)
+        ra.SetAtomMapNum(n)
+        if a.charge:
+            ra.SetFormalCharge(a.charge)
+        if a.isotope != a.common_isotope:
+            ra.SetIsotope(a.isotope)
+        if a.radical:
+            ra.SetNumRadicalElectrons(a.radical)
+        mapping[n] = m = mol.AddAtom(ra)
+        conf.SetAtomPosition(m, (a.x, a.y, a.z))
+        if a.z:
+            is_3d = True
+    if not is_3d:
+        conf.Set3D(False)
+
+    for n, m, b in data.bonds():
+        mol.AddBond(mapping[n], mapping[m], _bond_map[b.order])
 
+    mol.AddConformer(conf)
+    SanitizeMol(mol)
+    return mol
+
+
+_rdkit_bond_map = {BondType.SINGLE: 1, BondType.DOUBLE: 2, BondType.TRIPLE: 3, BondType.AROMATIC: 4}
+_bond_map = {1: BondType.SINGLE, 2: BondType.DOUBLE, 3: BondType.TRIPLE, 4: BondType.AROMATIC}
 
-__all__ = ['from_rdkit_molecule']
+__all__ = ['from_rdkit_molecule', 'to_rdkit_molecule']

setup.py

@@ -23,7 +23,7 @@
 
 setup(
     name='CGRtools',
-    version='3.1.3',
+    version='3.1.4',
     packages=['CGRtools', 'CGRtools.algorithms', 'CGRtools.attributes', 'CGRtools.containers', 'CGRtools.files',
               'CGRtools.files.dll', 'CGRtools.periodictable', 'CGRtools.utils'],
     url='https://github.com/cimm-kzn/CGRtools',