RdKit Coordinates for atoms in a molecule

Question

Hey everyone I need some help formatting coordinates for atoms in a molecule and I'm coding with Python. What I am needing is along the lines of:

(atom) x y z coordinates

For every atom in the molecule. So far my code is:

for molecule in mol_list:
    molecule = Chem.AddHs(molecule)
    print(molecule.GetNumAtoms())
    AllChem.EmbedMolecule(molecule)
    AllChem.UFFOptimizeMolecule(molecule)
    molecule.GetConformer()

    print()

    for atom in molecule.GetAtoms():
        # positions = molecule.GetConformer().GetAtomPosition(0)
        positions = molecule.GetConformer().GetPositions()
        print(atom.GetSymbol(), positions)
    
        print()

But this gives me the output of:

(Atom) x y z coordinates for every atom

This repeats so that every atom in the molecule has the entire molecule's x, y, and z coordinates. mol_list in the for loop is a list of strings that I converted to the object: rdkit.Chem.rdchem.Mol . I've tried the geometry.xyz function in Chemml , but ran into issues with the Molecule object. Also, I've tried using the RdKit function getAtomPos() with no luck. Any help with this would be awesome!

Answer 1

You have to pass the atom number to get its coordinates. The following code snippet should do what you're looking for

for molecule in mol_list:
    molecule = Chem.AddHs(molecule)
    print(molecule.GetNumAtoms())
    AllChem.EmbedMolecule(molecule)
    AllChem.UFFOptimizeMolecule(molecule)
    molecule.GetConformer()
    print()

    for i, atom in enumerate(molecule.GetAtoms()):
        positions = molecule.GetConformer().GetAtomPosition(i)
        print(atom.GetSymbol(), positions.x, positions.y, positions.z)