Hi there everyone, Greg, Something is not quite right with the depiction of this molecule (broken_mol.png); the wedge bonds shouldn't be there...
I am attaching the script which generates this - is it a fault of the molecule definition (it looks fine in other, less stringent tools) or with the RDKit internal depiction code? I tried the savvy mol.Debug() trick - but I am none the wiser. Jean-Paul Ebejer Early Stage Researcher
#!/usr/bin/env python from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem import AllChem mol2block = """@<TRIPOS>MOLECULE MolPort-003-188-453_019_0.279709 50 52 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 S -8.6120 -7.0040 -0.3820 S.o2 1 <1> 1.4470 2 C -7.0270 -6.7750 0.3880 C.ar 1 <1> -0.0090 3 N -8.6130 -8.6280 -0.7820 N.am 1 <1> -0.8490 4 C 0.5110 0.3500 0.0410 C.3 1 <1> 1.1630 5 C -6.0660 -6.0670 -0.3340 C.ar 1 <1> -0.1500 6 H -6.2940 -5.7080 -1.3270 H 1 <1> 0.1500 7 C -3.8050 -5.0550 -0.5920 C.2 1 <1> 0.6340 8 C -4.7990 -5.8200 0.2300 C.ar 1 <1> 0.0860 9 O -8.6420 -6.2660 -1.6320 O.2 1 <1> -0.6500 10 O -9.6530 -6.7780 0.6050 O.2 1 <1> -0.6500 11 C -0.6720 -0.5690 -0.0670 C.ar 1 <1> -0.1430 12 C -6.7350 -7.2390 1.6700 C.ar 1 <1> -0.1430 13 O -2.6400 -4.9070 0.1040 O.3 1 <1> -0.4300 14 C -0.5740 -1.9010 -0.2360 C.ar 1 <1> -0.1500 15 H 0.4010 -2.3590 -0.3080 H 1 <1> 0.1500 16 O -4.0240 -4.6320 -1.7180 O.2 1 <1> -0.5700 17 C -4.5170 -6.2890 1.5150 C.ar 1 <1> -0.1500 18 H -3.5480 -6.1030 1.9550 H 1 <1> 0.1500 19 C -5.4820 -6.9970 2.2330 C.ar 1 <1> -0.1500 20 H -5.2580 -7.3580 3.2260 H 1 <1> 0.1500 21 F 0.5260 1.0200 1.2260 F 1 <1> -0.3400 22 F 0.5110 1.2930 -0.9410 F 1 <1> -0.3400 23 F 1.7040 -0.3010 -0.0500 F 1 <1> -0.3400 24 O -7.9970 -11.4510 -1.1640 O.3 1 <1> -0.5600 25 C -7.6930 -9.0950 -1.8440 C.3 1 <1> 0.1960 26 H1 -6.6700 -9.0540 -1.4690 H 1 <1> 0.0800 27 H2 -7.7890 -8.4380 -2.7090 H 1 <1> 0.0800 28 C -8.6850 -9.6120 0.3440 C.3 1 <1> 0.1960 29 H1 -9.4870 -9.3200 1.0220 H 1 <1> 0.0800 30 H2 -7.7360 -9.6090 0.8810 H 1 <1> 0.0800 31 C -1.6000 -4.1920 -0.5520 C.3 1 <1> 0.2630 32 H1 -1.6500 -4.3920 -1.6220 H 1 <1> 0.0800 33 H2 -0.6380 -4.5270 -0.1640 H 1 <1> 0.0800 34 C -1.7360 -2.7110 -0.3210 C.ar 1 <1> -0.1430 35 C -2.0060 0.1090 0.0270 C.ar 1 <1> -0.1500 36 H -2.0990 1.1760 0.1660 H 1 <1> 0.1500 37 C -8.0090 -10.5360 -2.2750 C.3 1 <1> 0.1200 38 H1 -8.9970 -10.5560 -2.7360 H 1 <1> 0.0800 39 H2 -7.2630 -10.8570 -3.0020 H 1 <1> 0.0800 40 C -8.9620 -11.0340 -0.1800 C.3 1 <1> 0.1200 41 H1 -8.9300 -11.7290 0.6590 H 1 <1> 0.0800 42 H2 -9.9540 -11.0540 -0.6310 H 1 <1> 0.0800 43 C -3.1060 -0.7160 -0.0750 C.ar 1 <1> -0.1500 44 H -4.0910 -0.2770 -0.0170 H 1 <1> 0.1500 45 C -7.7440 -8.0100 2.5250 C.3 1 <1> -0.0970 46 H1 -8.6740 -8.1290 1.9700 H 1 <1> 0.0800 47 H2 -7.9380 -7.4580 3.4450 H 1 <1> 0.0800 48 H3 -7.3380 -8.9920 2.7690 H 1 <1> 0.0800 49 C -2.9950 -2.0970 -0.2500 C.ar 1 <1> -0.1500 50 H -3.8880 -2.6990 -0.3320 H 1 <1> 0.1500 @<TRIPOS>BOND 1 1 2 1 2 1 3 am 3 1 9 2 4 1 10 2 5 2 5 ar 6 2 12 ar 7 3 25 1 8 3 28 1 9 4 11 1 10 4 21 1 11 4 22 1 12 4 23 1 13 5 6 1 14 5 8 ar 15 7 8 1 16 7 13 1 17 7 16 2 18 8 17 ar 19 11 14 ar 20 11 35 ar 21 12 19 ar 22 12 45 1 23 13 31 1 24 14 15 1 25 14 34 ar 26 17 18 1 27 17 19 ar 28 19 20 1 29 24 37 1 30 24 40 1 31 25 26 1 32 25 27 1 33 25 37 1 34 28 29 1 35 28 30 1 36 28 40 1 37 31 32 1 38 31 33 1 39 31 34 1 40 34 49 ar 41 35 36 1 42 35 43 ar 43 37 38 1 44 37 39 1 45 40 41 1 46 40 42 1 47 43 44 1 48 43 49 ar 49 45 46 1 50 45 47 1 51 45 48 1 52 49 50 1 """ mol=AllChem.MolFromMol2Block(mol2block) AllChem.Compute2DCoords(mol) Draw.MolToFile(mol, "broken_mol.png", (400,400))
<<attachment: broken_mol.png>>
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