I just checked in the bug fix. Here's the new behavior:
In [2]: mol = Chem.MolFromSmiles('N1C=CC=C1')
In [3]: Chem.Kekulize(mol,clearAromaticFlags=True)
In [4]: tempMol = Chem.EditableMol(mol)
In [5]: idx = tempMol.AddAtom(Chem.Atom(0))
In [6]: tempMol.AddBond(idx,0,Chem.BondType.SINGLE)
Out[6]: 6
In [7]: nm = tempMol.GetMol()
In [8]: print Chem.MolToSmiles(nm)
[*]N1C=CC=C1-greg On Tue, Oct 29, 2013 at 5:56 PM, Nicholas Firth <[email protected]>wrote: > Cheers Greg. I will clean up the mess manually for the time being and > update the code if needs be. > > Best, > Nick > > *Nicholas C. Firth* | PhD Student | Cancer Therapeutics**** > The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | > Surrey | SM2 5NG**** > > *T* 020 8722 4033 | *E* [email protected] | *W* www.icr.ac.uk | * > Twitter* @ICRnews <https://twitter.com/ICRnews>**** > > *Facebook* www.facebook.com/theinstituteofcancerresearch**** > > *Making the discoveries that defeat cancer* > > > On 29 Oct 2013, at 04:19, Greg Landrum <[email protected]> wrote: > > There was a typo in my earlier message. > > The last example I intended to send was: > >>> mol = Chem.MolFromSmiles('N1C=CC=C1') > >>> Chem.Kekulize(mol,clearAromaticFlags=True) > >>> for atom in mol.GetAtoms(): > if atom.GetAtomicNum() in (7,15,16) and atom.GetNumExplicitHs()==1: > atom.SetNumExplicitHs(0) > ... > >>> tempMol = Chem.EditableMol(mol) > >>> idx = tempMol.AddAtom(Chem.Atom(0)) > >>> tempMol.AddBond(idx,0,Chem.BondType.SINGLE) > 6 > >>> nm = tempMol.GetMol() > >>> print Chem.MolToSmiles(nm) > [*]N1C=CC=C1 > > The earlier message included a spurious "sanitize=False" argument to the > Chem.MolFromSmiles() call. > > -greg > > > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the addressee only. If > the message is received by anyone other than the addressee, please return > the message to the sender by replying to it and then delete the message > from your computer and network. >
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