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 <nshe...@gmail.com> wrote: > 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, 2019 at 10:53 AM Greg Landrum <greg.land...@gmail.com> > wrote: > >> >> 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 <nshe...@gmail.com> >> wrote: >> >>> 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 # 4 N, 4, is >>> greater than permitted >>> >>> I asked a similar question few weeks ago, where I got a similar error >>> while having SMILES as my input, but non of the suggestions helped. Should >>> I just get rid of these molecules? >>> >>> Thanks, >>> Navid >>> >>> On Tue, Oct 22, 2019 at 11:57 PM Dan Nealschneider < >>> dan.nealschnei...@schrodinger.com> wrote: >>> >>>> Navid- >>>> You probably need to "sanitize" the mol: >>>> >>>> rdkit.Chem.rdmolops.SanitizeMol(mol) >>>> >>>> *dan nealschneider* | senior developer >>>> [image: Schrodinger Logo] <https://www.schrodinger.com/> >>>> >>>> >>>> On Tue, Oct 22, 2019 at 6:31 PM Navid Shervani-Tabar <nshe...@gmail.com> >>>> wrote: >>>> >>>>> 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.RWMol() >>>>> >>>>> # add atoms to mol and keep track of index >>>>> node_to_idx = {} >>>>> for i in range(len(node_list)): >>>>> a = Chem.Atom(node_list[i].item()) >>>>> molIdx = mol.AddAtom(a) >>>>> node_to_idx[i] = molIdx >>>>> >>>>> # add bonds between adjacent atoms >>>>> for ix, row in enumerate(adjacency_matrix): >>>>> for iy, bond in enumerate(row): >>>>> >>>>> # only traverse half the matrix >>>>> if iy <= ix: >>>>> continue >>>>> >>>>> # add relevant bond type (there are many more of these) >>>>> if bond == 0: >>>>> continue >>>>> elif bond == 1: >>>>> bond_type = Chem.rdchem.BondType.SINGLE >>>>> mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type) >>>>> elif bond == 2: >>>>> bond_type = Chem.rdchem.BondType.DOUBLE >>>>> mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type) >>>>> elif bond == 3: >>>>> bond_type = Chem.rdchem.BondType.TRIPLE >>>>> mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type) >>>>> elif bond == 1.5: >>>>> bond_type = Chem.rdchem.BondType.AROMATIC >>>>> mol.AddBond(node_to_idx[ix], node_to_idx[iy], bond_type) >>>>> >>>>> # Convert RWMol to Mol object >>>>> mol = mol.GetMol() >>>>> >>>>> return mol >>>>> >>>>> >>>>> When I try to get the hybridization of atoms using the mol object >>>>> generated from the function above, I get *UNSPECIFIED.* >>>>> >>>>> To make sure that this function works, I used *MolToSmiles *to >>>>> generate a SMILES string from the generated mol object and it matched the >>>>> actual SMILES from the dataset. Interestingly, when I regenerate the mol >>>>> object from the SMILES that I already generated from the above function, I >>>>> can get the hybridization from the new mol object with no problem. I was >>>>> wondering if there is a flag or variable that I should set in the above >>>>> function to be able to get hybridization from the generated mol object. >>>>> >>>>> Thanks! >>>>> Navid >>>>> >>>>> _______________________________________________ >>>>> Rdkit-discuss mailing list >>>>> Rdkit-discuss@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>>> >>>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>
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