Re: [Rdkit-discuss] HasSubStructureMatch error

Hi, The problem is connected with the lack of explicit Hs in the aromatic version of the SMILES. The general rule is that if an aromatic heteroatom needs to have an H on it in order for the valence to make sense, then you need to include that in the SMILES. This does not hold when you express the

[Rdkit-discuss] HasSubStructureMatch error

Dear all, There are several questions I want to ask for help. 1. When I read a molecular by MolFromSmiles and MolFromSmarts,it throw an exception，As shown below , the molecule “n1c(=O)nc(=O)cc1” can’t be read by MolFromSmiles while MolFromSmarts work well.So what the difference between

Re: [Rdkit-discuss] Strange behavior with MMFFHasAllMoleculeParams()

Dear Sereina, I'll have a look. I suspect it might have something to do with the MMFF94 aromaticity model, but it could also be a bug. I'll get back to you later. Cheers, p. > On 3 Aug 2016, at 08:00, Sereina wrote: > > Dear all, > > I stumbled upon a - to me -

[Rdkit-discuss] Strange behavior with MMFFHasAllMoleculeParams()

Dear all, I stumbled upon a - to me - rather strange behavior with MMFFHasAllMoleculeParams(). I want to generate a molecule from SMILES, check if all MMFF parameters are present, add hydrogens and generate conformers. However, the outcome (error or not error) depends on the order of checking