How does MolToPDBFile() determine the order of atoms?

[fyy623]

it seems that molecules with similar structures can always get similar results in terms of atom order, for example, i noticed that for several molecules that have a benzene ring, the carbon atom on that benzene ring always have the same index across all those moleculres. so i wonder if there is a specific rule that rdkit/pdb file follows.

[greglandrum]

@fyy623 the atoms are written to the PDB output in the same order they are in the molecule.
Here's an example, three different atom orderings for ethanol:

In [2]: print(Chem.MolToPDBBlock(Chem.MolFromSmiles('CCO')))
HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
HETATM    3  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
CONECT    1    2
CONECT    2    3
END


In [3]: print(Chem.MolToPDBBlock(Chem.MolFromSmiles('OCC')))
HETATM    1  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
CONECT    1    2
CONECT    2    3
END


In [4]: print(Chem.MolToPDBBlock(Chem.MolFromSmiles('C(O)C')))
HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
HETATM    2  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
HETATM    3  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
CONECT    1    2    3
END