Hi Guys,
I'm sorry it took me this long to try it... But I could finally get to it,
and it works well now. Thanks for your help!
--
Gustavo Seabra.
On Tue, Apr 11, 2023 at 3:19 AM Jan Halborg Jensen <jhjen...@chem.ku.dk>
wrote:
> Hi Gustavo
>
> raw_mol = Chem.MolFromXYZFile('acetate.xyz')
> mol = Chem.Mol(raw_mol)
> rdDetermineBonds.DetermineBonds(mol,charge=-1)
>
> Best regards, Jan
>
> On 7 Apr 2023, at 22.57, Gustavo Seabra <gustavo.sea...@gmail.com> wrote:
>
> Hi everyone,
>
> I'm having difficulties using RDKit to read molecules from an XYZ file,
> and I would really appreciate some help.
>
> The problem is that whenever i read a molecule from an XYZ file, I get
> just a disconnected clump of atoms, not a molecule. For example: the
> following code:
>
> import rdkit
> from rdkit import Chem
> from rdkit.Chem import Draw, rdmolfiles
> mol = Chem.MolFromSmiles('COC1=C(O)C[C@@](O)(CO)CC1=O')
> mol = Chem.AddHs(mol)
> mol
>
> <image.png>
>
> Chem.AllChem.EmbedMolecule(mol)
> Chem.MolToXYZFile(mol, "rdkit_mol.xyz")
> mol2 = Chem.MolFromXYZFile('rdkit_mol.xyz')
> mol2
> <image.png>
> Is there a bug on the XYZ code, or am I missing something?
>
> Thanks!
> --
> Gustavo Seabra.
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