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

2017-04-27 Thread Markus Metz
it do not tell >>>> where the H is. >>>> >>>> For example, "C1=NN=CN1" is "4H-1,2,4-triazole" and "C1=NC=NN1" is >>>> 1H-1,2,4-triazole. >>>> They are different in Kekulize but both of them can represented by >>>> "c1n

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

2017-04-27 Thread Greg Landrum
th of them can represented by "c1nncn1" >>> >>> There's two solutions I suggest: >>> 1. use `Chem.MolFromSmiles('c1ccc(cc1)-c1nnc(n1)-c1ccccc1',False)` >>> (reference: http://www.rdkit.org/docs/api/rdkit.Chem.rdmolfi >>> les

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

2017-04-27 Thread Markus Metz
c1',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. >

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

2017-04-26 Thread Peter S. Shenkin
alse)` > (reference: http://www.rdkit.org/docs/api/rdkit.Chem. > rdmolfiles-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. > > >

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. I