diff --git a/ligands/bidentate/acac-acetylacetonate.png b/ligands/bidentate/acac-acetylacetonate.png index 1ebc2a6..be24627 100644 Binary files a/ligands/bidentate/acac-acetylacetonate.png and b/ligands/bidentate/acac-acetylacetonate.png differ diff --git a/ligands/bidentate/bpy-bipyridine.png b/ligands/bidentate/bpy-bipyridine.png index b94834f..3383745 100644 Binary files a/ligands/bidentate/bpy-bipyridine.png and b/ligands/bidentate/bpy-bipyridine.png differ diff --git a/ligands/bidentate/dithiolene.png b/ligands/bidentate/dithiolene.png index 18fc134..7700234 100644 Binary files a/ligands/bidentate/dithiolene.png and b/ligands/bidentate/dithiolene.png differ diff --git a/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png b/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png index 4c7fda6..0d7e267 100644 Binary files a/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png and b/ligands/bidentate/dmpe-1,2-bis(dimethylphosphino)ethane.png differ diff --git a/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.cjson b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.cjson new file mode 100644 index 0000000..ca581f1 --- /dev/null +++ b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.cjson @@ -0,0 +1,678 @@ +{ + "atoms": { + "coords": { + "3d": [ + 1.2733, + -0.2323, + 0.1547, + 2.81, + -0.4058, + 0.2484, + 3.4608, + 0.9877, + 0.3557, + 3.5947, + 1.6318, + 1.6022, + 4.2313, + 2.8703, + 1.725, + 4.7129, + 3.5201, + 0.5963, + 4.5343, + 2.9412, + -0.6552, + 3.9048, + 1.6962, + -0.7749, + 3.3463, + -1.29, + -0.9199, + 4.5531, + -2.0978, + -0.4131, + 4.622, + -1.9386, + 1.1328, + 4.8541, + -3.3227, + 1.7953, + 5.9962, + -4.0739, + 1.4603, + 6.2998, + -5.2621, + 2.1315, + 5.4681, + -5.7264, + 3.1469, + 4.325, + -5.0119, + 3.4822, + 4.0228, + -3.8221, + 2.8169, + 5.7034, + -0.9598, + 1.6666, + 6.5763, + -0.2258, + 0.8453, + 7.5029, + 0.6744, + 1.3864, + 7.593, + 0.8511, + 2.7623, + 6.7674, + 0.115, + 3.6021, + 5.8373, + -0.7771, + 3.0613, + 0.9088, + -0.2707, + 2.2992, + 0.631, + -0.0787, + -1.088, + -0.7599, + 0.0411, + -1.176, + -1.5369, + 0.0348, + -0.0215, + -0.9229, + -0.0746, + 1.2215, + 0.4676, + -0.1982, + 1.309, + 3.2282, + 1.1702, + 2.5142, + 4.3581, + 3.3164, + 2.7078, + 5.217, + 4.4775, + 0.6918, + 4.8858, + 3.4576, + -1.5442, + 3.7708, + 1.3023, + -1.7771, + 3.5952, + -0.7518, + -1.8376, + 2.582, + -2.0249, + -1.214, + 5.4616, + -1.8073, + -0.9443, + 4.387, + -3.1441, + -0.7035, + 6.6817, + -3.7168, + 0.6947, + 7.2012, + -5.813, + 1.876, + 5.7167, + -6.6381, + 3.6836, + 3.6735, + -5.368, + 4.2764, + 3.137, + -3.2839, + 3.1424, + 6.5471, + -0.2952, + -0.236, + 8.1432, + 1.2505, + 0.7234, + 8.3021, + 1.5619, + 3.1763, + 6.8396, + 0.235, + 4.6794, + 5.2094, + -1.3368, + 3.7511, + 2.806044634820382, + -1.3982756463973471, + 1.869136122172507, + -1.5244, + -0.0644, + 2.127, + 1.2053, + -0.0596, + -2.0102, + -1.2355, + 0.1399, + -2.148, + -2.6177, + 0.1256, + -0.0897 + ] + }, + "elements": { + "number": [ + 6, + 15, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 15, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 6, + 1, + 6, + 6, + 6, + 6, + 6, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 0, + 1, + 1, + 1, + 1 + ] + }, + "formalCharges": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "labels": [ + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "" + ], + "layer": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ] + }, + "bonds": { + "connections": { + "index": [ + 0, + 1, + 0, + 24, + 0, + 28, + 1, + 2, + 1, + 8, + 26, + 52, + 2, + 3, + 2, + 7, + 3, + 4, + 3, + 29, + 4, + 5, + 4, + 30, + 5, + 6, + 5, + 31, + 6, + 7, + 6, + 32, + 7, + 33, + 8, + 9, + 8, + 34, + 8, + 35, + 9, + 10, + 9, + 36, + 9, + 37, + 10, + 11, + 10, + 17, + 27, + 28, + 11, + 12, + 11, + 16, + 12, + 13, + 12, + 38, + 13, + 14, + 13, + 39, + 14, + 15, + 14, + 40, + 15, + 16, + 15, + 41, + 16, + 42, + 17, + 18, + 17, + 22, + 18, + 19, + 18, + 43, + 19, + 20, + 19, + 44, + 20, + 21, + 20, + 45, + 21, + 22, + 21, + 46, + 22, + 47, + 23, + 28, + 27, + 49, + 24, + 25, + 24, + 50, + 25, + 26, + 25, + 51, + 26, + 27, + 10, + 48, + 1, + 48 + ] + }, + "order": [ + 1, + 2, + 1, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 2, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 1, + 1, + 1, + 2, + 1, + 1, + 1, + 1 + ] + }, + "chemicalJson": 1, + "layer": { + "enable": { + "Ball and Stick": [ + true + ], + "Cartoons": [ + false + ], + "Close Contacts": [ + false + ], + "Crystal Lattice": [ + false + ], + "Force": [ + false + ], + "Labels": [ + false + ], + "Licorice": [ + false + ], + "Meshes": [ + false + ], + "Non-Covalent": [ + false + ], + "Van der Waals": [ + false + ], + "Wireframe": [ + false + ], + "undef": [ + false + ] + }, + "locked": [ + false, + false + ], + "settings": { + "Ball and Stick": [ + "true true 0.200000 0.100000" + ] + }, + "visible": [ + true, + true + ] + }, + "properties": { + "modelView": [ + [ + 0.6934791207313538, + 0.2202928066253662, + -0.6859722137451172, + -1.439110279083252 + ], + [ + -0.08278661221265793, + 0.9701640009880066, + 0.22786693274974823, + 1.0402475595474243 + ], + [ + 0.7157041430473328, + -0.1012318953871727, + 0.6910255551338196, + -25.00874137878418 + ], + [ + 0.0, + 0.0, + 0.0, + 1.0 + ] + ], + "projection": [ + [ + 0.1259332150220871, + 0.0, + 0.0, + -0.0 + ], + [ + 0.0, + 0.20000000298023224, + 0.0, + -0.0 + ], + [ + 0.0, + 0.0, + -0.033235739916563034, + -0.0 + ], + [ + 0.0, + 0.0, + 0.0, + 1.0 + ] + ], + "totalCharge": 0, + "totalSpinMultiplicity": 1 + } +} \ No newline at end of file diff --git a/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png index a0b5cad..1b51650 100644 Binary files a/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png and b/ligands/bidentate/dppe-1,2-bis(diphenylphosphino)ethane.png differ diff --git a/ligands/bidentate/en-ethylenediamine.png b/ligands/bidentate/en-ethylenediamine.png index c01a955..39290c8 100644 Binary files a/ligands/bidentate/en-ethylenediamine.png and b/ligands/bidentate/en-ethylenediamine.png differ diff --git a/ligands/bidentate/groups.smi b/ligands/bidentate/groups.smi index c8d0e8a..d1aa5db 100644 --- 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 index 39701de..192c332 100644 Binary files a/ligands/bidentate/oxalate.png and b/ligands/bidentate/oxalate.png differ diff --git a/ligands/bidentate/phenanthroline.png b/ligands/bidentate/phenanthroline.png index feb0634..b2b25e0 100644 Binary files a/ligands/bidentate/phenanthroline.png and b/ligands/bidentate/phenanthroline.png differ diff --git a/ligands/bidentate/tmeda-tetramethylethylenediamine.png b/ligands/bidentate/tmeda-tetramethylethylenediamine.png index 0b0c0c0..023dd90 100644 Binary files a/ligands/bidentate/tmeda-tetramethylethylenediamine.png and b/ligands/bidentate/tmeda-tetramethylethylenediamine.png differ diff --git a/ligands/monodentate/ammine.png b/ligands/monodentate/ammine.png index 626bfaa..5e830cd 100644 Binary files a/ligands/monodentate/ammine.png and b/ligands/monodentate/ammine.png differ diff --git a/ligands/monodentate/aqua.png b/ligands/monodentate/aqua.png index 0b4b9ed..c9562db 100644 Binary files a/ligands/monodentate/aqua.png and b/ligands/monodentate/aqua.png differ diff --git a/ligands/monodentate/azido.png b/ligands/monodentate/azido.png index 81d21f5..b76e2dd 100644 Binary files a/ligands/monodentate/azido.png and b/ligands/monodentate/azido.png differ diff --git a/ligands/monodentate/carbonyl.png b/ligands/monodentate/carbonyl.png index eaf4deb..1bfa6d2 100644 Binary files a/ligands/monodentate/carbonyl.png and b/ligands/monodentate/carbonyl.png differ diff --git a/ligands/monodentate/cyano.png b/ligands/monodentate/cyano.png index 4e3a573..129a83a 100644 Binary files a/ligands/monodentate/cyano.png and b/ligands/monodentate/cyano.png differ diff --git a/ligands/monodentate/ethyl.png b/ligands/monodentate/ethyl.png index ef8a52c..edce06a 100644 Binary files a/ligands/monodentate/ethyl.png and b/ligands/monodentate/ethyl.png differ diff --git a/ligands/monodentate/groups.smi b/ligands/monodentate/groups.smi index c82d68d..bf2049c 100644 --- 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 deleted file mode 100644 index d6c6c62..0000000 Binary files a/ligands/monodentate/imes.png and /dev/null differ diff --git a/ligands/monodentate/isocyano.png b/ligands/monodentate/isocyano.png index 7ad0fa9..606c367 100644 Binary files a/ligands/monodentate/isocyano.png and b/ligands/monodentate/isocyano.png differ diff --git a/ligands/monodentate/isopropyl.png b/ligands/monodentate/isopropyl.png index 97bff23..340020d 100644 Binary files a/ligands/monodentate/isopropyl.png and b/ligands/monodentate/isopropyl.png differ diff --git a/ligands/monodentate/methyl.png b/ligands/monodentate/methyl.png index 3187846..2d38a49 100644 Binary files a/ligands/monodentate/methyl.png and b/ligands/monodentate/methyl.png differ diff --git a/ligands/monodentate/nitro.png b/ligands/monodentate/nitro.png index 2981bee..7dbe551 100644 Binary files a/ligands/monodentate/nitro.png and b/ligands/monodentate/nitro.png differ diff --git a/ligands/monodentate/nitrosyl.png b/ligands/monodentate/nitrosyl.png index 645350c..8d0a1e8 100644 Binary files a/ligands/monodentate/nitrosyl.png and b/ligands/monodentate/nitrosyl.png differ diff --git a/ligands/monodentate/phosphine.png b/ligands/monodentate/phosphine.png index 4bb35a2..6ab6ca7 100644 Binary files a/ligands/monodentate/phosphine.png and b/ligands/monodentate/phosphine.png differ diff --git a/ligands/monodentate/propyl.png b/ligands/monodentate/propyl.png index a368b28..abffc59 100644 Binary files a/ligands/monodentate/propyl.png and b/ligands/monodentate/propyl.png differ diff --git a/ligands/monodentate/pyridyl.png b/ligands/monodentate/pyridyl.png index d73e0ff..2f500f3 100644 Binary files a/ligands/monodentate/pyridyl.png and b/ligands/monodentate/pyridyl.png differ diff --git a/ligands/monodentate/imes.cjson b/ligands/monodentate/simes.cjson similarity index 96% rename from ligands/monodentate/imes.cjson rename to ligands/monodentate/simes.cjson index 976d8c9..0cb88b6 100644 --- a/ligands/monodentate/imes.cjson +++ b/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 new file mode 100644 index 0000000..cfce280 Binary files /dev/null and b/ligands/monodentate/simes.png differ diff --git a/ligands/monodentate/t-butyl.png b/ligands/monodentate/t-butyl.png index 3a8cc9c..7058e9b 100644 Binary files a/ligands/monodentate/t-butyl.png and b/ligands/monodentate/t-butyl.png differ diff --git a/ligands/monodentate/thiocyanato-N.png b/ligands/monodentate/thiocyanato-N.png index 426afa2..7900336 100644 Binary files a/ligands/monodentate/thiocyanato-N.png and b/ligands/monodentate/thiocyanato-N.png differ diff --git a/ligands/monodentate/thiocyano.png b/ligands/monodentate/thiocyano.png index b1f64d3..a3b7366 100644 Binary files a/ligands/monodentate/thiocyano.png and b/ligands/monodentate/thiocyano.png differ diff --git a/ligands/monodentate/thiol.png b/ligands/monodentate/thiol.png index 08d8478..39896dc 100644 Binary files a/ligands/monodentate/thiol.png and b/ligands/monodentate/thiol.png differ diff --git a/ligands/monodentate/trimethylammonium.png b/ligands/monodentate/trimethylammonium.png index dcefde2..55d369e 100644 Binary files a/ligands/monodentate/trimethylammonium.png and b/ligands/monodentate/trimethylammonium.png differ diff --git a/ligands/monodentate/trimethylphosphine.png b/ligands/monodentate/trimethylphosphine.png index cd4193b..15fca6a 100644 Binary files a/ligands/monodentate/trimethylphosphine.png and b/ligands/monodentate/trimethylphosphine.png differ diff --git a/ligands/monodentate/triphenylphosphine.png b/ligands/monodentate/triphenylphosphine.png index ad14dce..c5663c1 100644 Binary files a/ligands/monodentate/triphenylphosphine.png and b/ligands/monodentate/triphenylphosphine.png differ diff --git a/ligands/tetradentate/phthalocyanine.png b/ligands/tetradentate/phthalocyanine.png index ca1c854..e1fcae6 100644 Binary files a/ligands/tetradentate/phthalocyanine.png and b/ligands/tetradentate/phthalocyanine.png differ diff --git a/ligands/tetradentate/porphin.png b/ligands/tetradentate/porphin.png index 150d1e2..91539a0 100644 Binary files a/ligands/tetradentate/porphin.png and b/ligands/tetradentate/porphin.png differ diff --git a/ligands/tridentate/9-ane-S3.png b/ligands/tridentate/9-ane-S3.png index aa3697f..ed457fc 100644 Binary files a/ligands/tridentate/9-ane-S3.png and b/ligands/tridentate/9-ane-S3.png differ diff --git a/ligands/tridentate/dien-diethylenetriamine.png b/ligands/tridentate/dien-diethylenetriamine.png index 9d5f5ca..672412f 100644 Binary files a/ligands/tridentate/dien-diethylenetriamine.png and b/ligands/tridentate/dien-diethylenetriamine.png differ diff --git a/ligands/tridentate/tacn-147-triazacyclononane.png b/ligands/tridentate/tacn-147-triazacyclononane.png index c834e06..79cd419 100644 Binary files a/ligands/tridentate/tacn-147-triazacyclononane.png and b/ligands/tridentate/tacn-147-triazacyclononane.png differ diff --git a/ligands/tridentate/terpyridine.png b/ligands/tridentate/terpyridine.png index a5fa50e..3994738 100644 Binary files a/ligands/tridentate/terpyridine.png and b/ligands/tridentate/terpyridine.png differ diff --git a/ligands/tridentate/tp-scorpionate.png b/ligands/tridentate/tp-scorpionate.png index 8a1a2bf..0791bd2 100644 Binary files a/ligands/tridentate/tp-scorpionate.png and b/ligands/tridentate/tp-scorpionate.png differ diff --git a/scripts/depict_ligands.py b/scripts/depict_ligands.py index 55fb381..9a18ec1 100644 --- 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