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On Mon, Aug 24, 2015 at 3:29 AM, S.L. Chan <[email protected]> wrote: > Dear colleagues, > > I used Chem.MolFromMolFile to read in an sd file with stereo info on some > atoms. But the stereo info seems to be lost. Could you spot what I missed? > > The input file is attached. On the atom lines, the third column after the > element name should contain the stereo data. I simply used mol.Debug() to > dump out the atoms' info. > According to the CTAB spec, those parity flags are supposed to be ignored on reading the file. This is what the RDKit does. You can assign stereochemistry using the 3D coordinates: In [16]: m = Chem.MolFromMolFile('r3.sdf') In [17]: Chem.AssignAtomChiralTagsFromStructure(m) In [18]: Chem.AssignStereochemistry(m,force=True,cleanIt=True) In [19]: m.Debug() Atoms: 0 7 N chg: 1 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 1 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: 4 arom?: 0 chi: 2 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 0 chi: 0 3 8 O chg: 0 deg: 1 exp: 2 imp: 0 hyb: 3 arom?: 0 chi: 0 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 5 6 C chg: 0 deg: 3 exp: 3 imp: 1 hyb: 4 arom?: 0 chi: 0 6 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 7 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 Bonds: 0 0->1 order: 1 conj?: 0 aromatic?: 0 1 1->2 order: 1 conj?: 0 aromatic?: 0 2 1->4 order: 1 conj?: 0 aromatic?: 0 3 2->3 order: 2 conj?: 0 aromatic?: 0 4 4->5 order: 1 conj?: 0 aromatic?: 0 5 5->6 order: 1 conj?: 0 aromatic?: 0 6 5->7 order: 1 conj?: 0 aromatic?: 0 That second step (line 18) is needed to remove the chiral specification that is otherwise added to carbon 5. If you would like to provide information about stereochemistry in an SDF without needing to perceive it from the coordinates, you can wedge the bonds. Here's the example for your molecule: In [6]: m = Chem.MolFromMolFile('r3.sdf') In [7]: Chem.AssignAtomChiralTagsFromStructure(m) In [8]: Chem.AssignStereochemistry(m,force=True,cleanIt=True) In [9]: from rdkit.Chem import AllChem In [10]: AllChem.Compute2DCoords(m) Out[10]: 0 In [11]: print Chem.MolToMolBlock(m) 2tmn RDKit 2D 8 7 0 0 1 0 0 0 0 0999 V2000 -2.5981 -1.1250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 -0.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2990 1.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.8750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 -0.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 1.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 2 3 1 0 2 5 1 0 3 4 2 0 5 6 1 0 6 7 1 0 6 8 1 0 M CHG 1 1 1 M END I hope this helps, -greg
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