Many thanks for the timely clarification! Indeed it works (attached fixed version) -- I will use this workaround. Can you somehow please advise when the bug is fixed (I am not sure how this works with RDKit, do you have a bug report for it on sourceforge I can check status on)? (The quick solution is probably for Nik to add this call at the end of his parsing routine, the proper way is to fix the parsing/molecule building code). If there is no bug, and the molecule is incorrect maybe we should get an error message (in the great rdkit philosophy that it doesn't try to guess what it going on).
ps. This mol.Debug() is really powerful. Jean-Paul Ebejer Early Stage Researcher On 24 August 2011 13:31, Greg Landrum <[email protected]> wrote: > Chem.AssignStereochemistry(mol,cleanIt=True,force=True)
#!/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) mol.Debug() # fix Chem.AssignStereochemistry(mol,cleanIt=True,force=True) mol.Debug() AllChem.Compute2DCoords(mol) Draw.MolToFile(mol, "broken_mol.png", (400,400))
<<attachment: fixed_mol.png>>
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