Re: [Rdkit-discuss] Problem with getting hybridization from mol object

I'm not sure if this helps, but maybe... If you have xyz files, how about trying xyz2mol: https://github.com/jensengroup/xyz2mol -greg On Wed, Oct 23, 2019 at 4:57 PM Navid Shervani-Tabar wrote: > Thanks for the prompt response Greg, these are from QM9 dataset (from the > original paper). Do y

Re: [Rdkit-discuss] Problem with getting hybridization from mol object

Thanks for the prompt response Greg, these are from QM9 dataset (from the original paper). Do you know of any package that has already fixed them by any chance? I used to use Chainer Chemistry to load the dataset, but those seem not to have coordinate information included. Navid On Wed, Oct 23, 2

Re: [Rdkit-discuss] Problem with getting hybridization from mol object

Given that those molecules are not chemically reasonable, I would suggest either fixing them by hand or removing them. On Wed, 23 Oct 2019 at 16:46, Navid Shervani-Tabar wrote: > Thanks Dan, > > There are two more issues after sanitizing: > > 1. For some molecules (e.g; c1ccnc1), I get the follo

Re: [Rdkit-discuss] Problem with getting hybridization from mol object

Thanks Dan, There are two more issues after sanitizing: 1. For some molecules (e.g; c1ccnc1), I get the following error: Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 2. For some molecules (e.g; C#CC#CN#N), I get the following error: ValueError: Sanitization error: Explicit valence for atom

Re: [Rdkit-discuss] Problem with getting hybridization from mol object

Navid- You probably need to "sanitize" the mol: rdkit.Chem.rdmolops.SanitizeMol(mol) *dan nealschneider* | senior developer [image: Schrodinger Logo] On Tue, Oct 22, 2019 at 6:31 PM Navid Shervani-Tabar wrote: > Hello, > > I am trying to load a dataset using a v

[Rdkit-discuss] Problem with getting hybridization from mol object

Hello, I am trying to load a dataset using a vector of atoms (e.g [6,6,7,6,6,8]) and the corresponding adjacency matrix. I am using the following script to transform these into a mol object: def MolFromGraphs(node_list, adjacency_matrix): # create empty editable mol object mol = Chem.RWM