MoleculeValue option IncludeHydrogens does not work everywhere?

Question

The coordination number property of a molecule seems to ignore the IncludeHydrogens flag. Adjacency matrix, on the other hand, seems to respect it.

mol = Molecule["CCCCC", IncludeHydrogens -> False]
dV = MoleculeValue[mol, "CoordinationNumber", IncludeHydrogens -> "ExplicitOnly"]
Out: {4,4,4,4}
dV = MoleculeValue[mol, "CoordinationNumber", IncludeHydrogens -> None]
Out: {4,4,4,4}

However, the adjacency matrix correctly interprets that there are no H atoms

aM = MoleculeValue[mol, "AdjacencyMatrix", IncludeHydrogens -> None]

The matrix form of that output is

{{0, 1, 0, 0, 0}, {1, 0, 1, 0, 0}, {0, 1, 0, 1, 0}, {0, 0, 1, 0, 
1}, {0, 0, 0, 1, 0}}

This does not include H atoms. Is there another way to get the coordination number of non-Hydrogen atoms in a molecule?

Thank you,

Version: "13.0.0 for Linux x86 (64-bit) (December 3, 2021)"

IncludeHydrogens should only change the length of the results, not their value — Jason B., Mar 04 '22 at 00:35

score 1 · Accepted Answer · answered Mar 03 '22 at 22:50

Is there another way to get the coordination number of non-Hydrogen atoms in a molecule?

The property you want is called "HeavyAtomCoordinationNumber"

mol = Molecule["CCCCC"];
mol["HeavyAtomCoordinationNumber"]
(* {1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1} *)
AtomList[mol, Except["H"], "HeavyAtomCoordinationNumber"]
(* {1, 2, 2, 2, 1} *)

MoleculeValue option IncludeHydrogens does not work everywhere?

1 Answers1