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: image.png]
Chem.AllChem.EmbedMolecule(mol)
Chem.MolToXYZFile(mol, "rdkit_mol.xyz")
mol2 = Chem.MolFromXYZFile('rdkit_mol.xyz')
mol2
[image: image.png]
Is there a bug on the XYZ code, or am I missing something?
Thanks!
--
Gustavo Seabra.
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
