Re: [Rdkit-discuss] Another Can't kekulize mol observation

2017-04-27 Thread Markus Metz
but both of them can represented by >>>> "c1nncn1" >>>> >>>> There's two solutions I suggest: >>>> 1. use `Chem.MolFromSmiles('c1ccc(cc1)-c1nnc(n1)-c1c1',False)` >>>> (reference: http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfi &

Re: [Rdkit-discuss] Another Can't kekulize mol observation

2017-04-27 Thread Greg Landrum
i >>> les-module.html#MolFromSmiles) >>> >>> 2. Manually Kekulize it: >>> `Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')` >>> . This indicate the H is on the 4'N. >>> >>> >>> -- >>> Hon

Re: [Rdkit-discuss] Another Can't kekulize mol observation

2017-04-27 Thread Markus Metz
cc1)-c1nnc(n1)-c1c1',False)` >> (reference: http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfi >> les-module.html#MolFromSmiles) >> >> 2. Manually Kekulize it: >> `Chem.MolFromSmiles('c1ccc(cc1)-C1=NN=C(N1)-c1c1')` >> . This indicate the H is on the 4'N. >&g

Re: [Rdkit-discuss] Another Can't kekulize mol observation

2017-04-27 Thread Peter S. Shenkin
; > > *From:* Markus Metz <metm...@gmail.com> > *Date:* 2017-04-27 09:30 > *To:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net> > *Subject:* [Rdkit-discuss] Another Can't kekulize mol observation > Hello all: > > I obtained this smiles string: > c1cc

Re: [Rdkit-discuss] Another Can't kekulize mol observation

2017-04-26 Thread Hongbin Yang
Hi Markus,“c1ccc(cc1)-c1nnc(n1)-c1c1” is different from "c1ccc(cc1)-c1nncn1-c1c1", so you cannot remove the parentheses. The error "Can't kekulize mol." is caused by the triazole in your molecule. "c1nncn1" tells that the molecule is aromatic, but it do not tell where the H is. For

[Rdkit-discuss] Another Can't kekulize mol observation

2017-04-26 Thread Markus Metz
Hello all: I obtained this smiles string: c1ccc(cc1)-c1nnc(n1)-c1c1 by removing atoms from the n1 in parentheses. Using: mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nnc(n1)-c1c1") throws an error: Can't kekulize mol. Using mol = Chem.MolFromSmiles("c1ccc(cc1)-c1nncn1-c1c1") works fine.