Support for atomic and bond custom properties

[ghutchis]

There's often a need for key / array properties for atoms and bonds (e.g., atomic polarizabilities, Fukui indices, Mayer / Wiberg bond orders, etc.)

My suggestion would be something like this (in Python syntax):

atoms["properties"] = {
"polarizabilities" : [ 1.0, 1.4, 1.8 … ],
"chirality" : [ "", "R", … ]
}
bonds["properties"] = {
"Mayer_bond_orders" : [0.9, 1.0, 1.8 ],
}

Missing or optional values could be indicated with "" for string arrays or null / None for numeric or boolean arrays.

The one catch is how to deal with atomic partial charges, since the current specification handles them separately (i.e., a separate key / array set, not under atomic properties).

My vote would be to keep this as-is, so that atom / bond properties are key / array only rather than nesting "partial_charges" or something like that under atom properties. This also keeps backwards compatibility. But I'm open to suggestions.