Merge pull request #20 from nbehrnd/correction_b

structural & visual corrections on non-haptic ligands
OpenChemistry · Jan 18, 2024 · 8dc711a · 8dc711a
2 parents 9211de8 + 4a2e647
commit 8dc711a
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Showing 44 changed files with 699 additions and 22 deletions.
diff --git a/ligands/bidentate/acac-acetylacetonate.png b/ligands/bidentate/acac-acetylacetonate.png
diff --git a/ligands/bidentate/bpy-bipyridine.png b/ligands/bidentate/bpy-bipyridine.png
diff --git a/ligands/bidentate/dithiolene.png b/ligands/bidentate/dithiolene.png
diff --git a/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png b/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png
diff --git a/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.cjson b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.cjson
diff --git a/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png
diff --git a/ligands/bidentate/en-ethylenediamine.png b/ligands/bidentate/en-ethylenediamine.png
diff --git a/ligands/bidentate/groups.smi b/ligands/bidentate/groups.smi
@@ -1,6 +1,8 @@
 [CH3]C([O][*]1)=CC(=[O]1)[CH3] a acac-acetylacetonate
 C12=CC=CC=[N]1[*][N]3=C2C=CC=C3 a bpy-bipyridine
 [*]1[SH0][CH][CH][SH0]1 a dithiolene
+C[P]1(C)CC[P](C)(C)*1 a dmpe-1,2-bis(dimethylphosphino)ethane
+c1([P]2(c3ccccc3)CC[P](c3ccccc3)(c3ccccc3)*2)ccccc1 a dppe-1,2-bis(diphenylphosphino)ethane
 [NH2]1CC[NH2][*]1 a en-ethylenediamine
 [CH3][N]1([CH3])CC[N]([CH3])([CH3])[*]1 a tmeda-tetramethylethylenediamine
 [O]=C([O-][*][O-]1)C1=[O] a oxalate

diff --git a/ligands/bidentate/oxalate.png b/ligands/bidentate/oxalate.png
diff --git a/ligands/bidentate/phenanthroline.png b/ligands/bidentate/phenanthroline.png
diff --git a/ligands/bidentate/tmeda-tetramethylethylenediamine.png b/ligands/bidentate/tmeda-tetramethylethylenediamine.png
diff --git a/ligands/monodentate/ammine.png b/ligands/monodentate/ammine.png
diff --git a/ligands/monodentate/aqua.png b/ligands/monodentate/aqua.png
diff --git a/ligands/monodentate/azido.png b/ligands/monodentate/azido.png
diff --git a/ligands/monodentate/carbonyl.png b/ligands/monodentate/carbonyl.png
diff --git a/ligands/monodentate/cyano.png b/ligands/monodentate/cyano.png
diff --git a/ligands/monodentate/ethyl.png b/ligands/monodentate/ethyl.png
diff --git a/ligands/monodentate/groups.smi b/ligands/monodentate/groups.smi
@@ -4,7 +4,6 @@
 *C#[O] a carbonyl
 *C#[N] a cyano
 *C[CH3] a ethyl
-Cc1cc(C)cc(c1N1CCN(C1*)c1c(C)cc(cc1C)C)C a imes
 *[N]#[C] a isocyano
 *C([CH3])[CH3] a isopropyl
 *[CH3] a methyl
@@ -13,6 +12,7 @@ Cc1cc(C)cc(c1N1CCN(C1*)c1c(C)cc(cc1C)C)C a imes
 *[PH3] a phosphine
 *CC[CH3] a propyl
 *[N](C=C1)=CC=C1 a pyridyl
+Cc1cc(C)cc(c1N1CCN(C1=*)c1c(C)cc(cc1C)C)C a simes
 *C([CH3])([CH3])[CH3] a t-butyl
 *[N]=C=[S] a thiocyanato-N
 *[SH0]C#[NH0] a thiocyano

diff --git a/ligands/monodentate/imes.png b/ligands/monodentate/imes.png
diff --git a/ligands/monodentate/isocyano.png b/ligands/monodentate/isocyano.png
diff --git a/ligands/monodentate/isopropyl.png b/ligands/monodentate/isopropyl.png
diff --git a/ligands/monodentate/methyl.png b/ligands/monodentate/methyl.png
diff --git a/ligands/monodentate/nitro.png b/ligands/monodentate/nitro.png
diff --git a/ligands/monodentate/nitrosyl.png b/ligands/monodentate/nitrosyl.png
diff --git a/ligands/monodentate/phosphine.png b/ligands/monodentate/phosphine.png
diff --git a/ligands/monodentate/propyl.png b/ligands/monodentate/propyl.png
diff --git a/ligands/monodentate/pyridyl.png b/ligands/monodentate/pyridyl.png
diff --git a/ligands/monodentate/imes.cjson → ligands/monodentate/simes.cjson b/ligands/monodentate/imes.cjson → ligands/monodentate/simes.cjson
@@ -107,9 +107,9 @@
         0.2950375115703756,
         5.787283005672643,
         -0.04225011908470685,
-        -2.0127886908519845,
-        2.9643793621189234,
-        1.482464801318469,
+        -2.0015869140625,
+        2.9280271530151367,
+        1.5361080169677734,
         -2.5618258495945945,
         6.954602279166593,
         -0.7736460696173343,
@@ -151,10 +151,7 @@
         -0.5435772796487052,
         1.719928229050943,
         2.231726756953255,
-        -2.233810736757843,
-        -1.0575294494628906,
-        3.1812362670898438,
-        1.9747276306152344
+        -2.233810736757843
       ]
     },
     "elements": {
@@ -194,6 +191,7 @@
         1,
         1,
         1,
+        0,
         1,
         1,
         1,
@@ -207,9 +205,7 @@
         1,
         1,
         1,
-        1,
-        1,
-        0
+        1
       ]
     },
     "formalCharges": [
@@ -262,7 +258,6 @@
       0,
       0,
       0,
-      0,
       0
     ],
     "labels": [
@@ -315,7 +310,6 @@
       "",
       "",
       "",
-      "",
       ""
     ],
     "layer": [
@@ -368,7 +362,6 @@
       0,
       0,
       0,
-      0,
       0
     ]
   },
@@ -478,9 +471,7 @@
         22,
         48,
         22,
-        49,
-        12,
-        50
+        49
       ]
     },
     "order": [
@@ -521,8 +512,7 @@
       1,
       1,
       1,
-      1,
-      1,
+      2,
       1,
       1,
       1,
@@ -580,6 +570,7 @@
       ]
     },
     "locked": [
+      false,
       false
     ],
     "settings": {
@@ -588,6 +579,7 @@
       ]
     },
     "visible": [
+      true,
       true
     ]
   },

diff --git a/ligands/monodentate/simes.png b/ligands/monodentate/simes.png
diff --git a/ligands/monodentate/t-butyl.png b/ligands/monodentate/t-butyl.png
diff --git a/ligands/monodentate/thiocyanato-N.png b/ligands/monodentate/thiocyanato-N.png
diff --git a/ligands/monodentate/thiocyano.png b/ligands/monodentate/thiocyano.png
diff --git a/ligands/monodentate/thiol.png b/ligands/monodentate/thiol.png
diff --git a/ligands/monodentate/trimethylammonium.png b/ligands/monodentate/trimethylammonium.png
diff --git a/ligands/monodentate/trimethylphosphine.png b/ligands/monodentate/trimethylphosphine.png
diff --git a/ligands/monodentate/triphenylphosphine.png b/ligands/monodentate/triphenylphosphine.png
diff --git a/ligands/tetradentate/phthalocyanine.png b/ligands/tetradentate/phthalocyanine.png
diff --git a/ligands/tetradentate/porphin.png b/ligands/tetradentate/porphin.png
diff --git a/ligands/tridentate/9-ane-S3.png b/ligands/tridentate/9-ane-S3.png
diff --git a/ligands/tridentate/dien-diethylenetriamine.png b/ligands/tridentate/dien-diethylenetriamine.png
diff --git a/ligands/tridentate/tacn-147-triazacyclononane.png b/ligands/tridentate/tacn-147-triazacyclononane.png
diff --git a/ligands/tridentate/terpyridine.png b/ligands/tridentate/terpyridine.png
diff --git a/ligands/tridentate/tp-scorpionate.png b/ligands/tridentate/tp-scorpionate.png
diff --git a/scripts/depict_ligands.py b/scripts/depict_ligands.py
@@ -56,14 +56,19 @@ def is_transition_metal(atom):
     )
 
 
-def set_dative_bonds(mol, fromAtoms=(6, 7, 8, 15, 16)):  # i.e., C, N, O, P, S
+def reset_dative_bonds(mol, fromAtoms=(6, 7, 8, 15, 16)):  # i.e., C, N, O, P, S
     """convert some bonds to dative
 
     Replace any single bond between the dummy atom/transition metals and atoms
     with atomic numbers in fromAtoms with dative bonds.  This approach differs
     to the original approach[1] to highlight the denticity of every ligand.
+    Because of a discussion in the user forum of RDKit,[2] the use of a dative
+    bond indicated by an arrow however is dropped; because results are depicted
+    and are not starting point of additional computation, single bonds appear
+    a suitable alternative to use.
 
     [1] http://rdkit.org/docs/Cookbook.html#organometallics-with-dative-bonds
+    [2] https://github.com/rdkit/rdkit/discussions/6995
 
     Returns the modified molecule.
 
@@ -82,7 +87,7 @@ def set_dative_bonds(mol, fromAtoms=(6, 7, 8, 15, 16)):  # i.e., C, N, O, P, S
                 == Chem.BondType.SINGLE
             ):
                 rwmol.RemoveBond(nbr.GetIdx(), metal.GetIdx())
-                rwmol.AddBond(nbr.GetIdx(), metal.GetIdx(), Chem.BondType.DATIVE)
+                rwmol.AddBond(nbr.GetIdx(), metal.GetIdx(), Chem.BondType.SINGLE)
     return rwmol
 
 
@@ -96,7 +101,7 @@ def generate_previews(line):
         smiles = "*" + smiles
 
     mol = Chem.MolFromSmiles(smiles, sanitize=False)
-    mol = set_dative_bonds(mol)
+    mol = reset_dative_bonds(mol)
     svg = svgDepict(mol).replace("*", "")
 
     # save the SVG