Unexpected atoms while working with XYZ files in rdkit

Question

I am processing some XYZ files using the rdkit library in python. I came across some strange/unexpected behaviour.

Consider a sample XYZ file of methanol with coordinates in Angstroms:

6
Methanol
  H      1.2001      0.0363      0.8431
  H      0.9877      0.8943     -0.7114
  H      1.0155     -0.8918     -0.6742
  C      0.7031      0.0083     -0.1305
  O     -0.6582     -0.0067      0.1730
  H     -1.1326     -0.0311     -0.6482

I am using the following code to visualise this compound. I am running the below code on Google Colab.

!pip install rdkit
from rdkit.Chem.rdmolfiles import  MolFromXYZFile

coord_filepath = '/content/drive/MyDrive/input_files/methanol.xyz'
mol = MolFromXYZFile(coord_filepath)
display(mol)

The output from the display looks like this:

I am a bit puzzled about the extra Hydrogens in the image. I tried to double check the atoms in the rdkit mol

for atom in mol.GetAtoms():
  print(atom.GetSymbol())

It displays as expected:

H
H
H
C
O
H

With coordinates in nanometers, the behaviour persists, with a bit better spacing between the various atoms/molecules.

So is this behaviour a bug or am I missing something conceptually?

Answer 1

Here is a demo how to work with MolFromXYZ.

You can choose rdDetermineBonds.DetermineConnectivity for bonds or rdDetermineBonds.DetermineBondsfor bonds and bond orders.

from rdkit import Chem
from rdkit.Chem import rdDetermineBonds

xyz = '''6
Methanol
  H      1.2001      0.0363      0.8431
  H      0.9877      0.8943     -0.7114
  H      1.0155     -0.8918     -0.6742
  C      0.7031      0.0083     -0.1305
  O     -0.6582     -0.0067      0.1730
  H     -1.1326     -0.0311     -0.6482'''

mol = Chem.MolFromXYZBlock(xyz)

conn_mol = Chem.Mol(mol)
rdDetermineBonds.DetermineConnectivity(conn_mol)
conn_mol