Table of Atom attributes

[rapodaca]

A table of Atom attributes should be present. It should use exactly the same terms used elsewhere in the ms.

Attribute Name	Description	Type	Nullable	Meaning if null	Constraints	Default Value
index	A unique identifier	unsigned integer	no	N/A	-	N/A
isotope	The sum of proton and neutron counts.	unsigned integer	yes	Natural abundance	0 <= value < 1000	null
element	The atom's element.	enumeration	yes	unknown element	An IUPAC-approved element symbol.	null
virtual_hydrogens	The number of virtual hydrogens	unsigned integer	Yes	zero virtual hydrogens	0 <= value < 10	0
algorithmic_hydrogens	If true hydrogens are counted algorithmically.	boolean	No	-	-	true
configuration	Configurational descriptor	enumeration	Yes	No configuration	tetracoordinate	Null
extension	Application-specific data	integer	Yes	No extension	0 <= value < 1000	Null
selected	Whether the atom is selected.	boolean	No	-	element must be one of C, N, O, P, or S.	-

... and so on.

[rapodaca]

This table implies that [*] has an isotope value of 1. Does this make sense? Probably, not, but neither does [*] with an isotope of 0. It's an arbitrary convention.

[rapodaca]

An alternative approach:

Data Type	Description	Values
Index	Unsigned integer	0...232
Option<Type>	Optional value	None, Type
Ten	Integer count	0..10
PlusMinusTen	Integer count	-9...10
Thousand	Integer count	0...1000
Element	IUPAC-approved element symbol	Ac, Ag, Al, ... Zn
HydrogenCount	Hydrogen count	Implicit, Ten
Configuration	Configurational descriptor	Clockwise, Counterclockwise
boolean	Boolean	true, false

Attribute	Description	Type	Default
index	A unique identifier	Index	-
isotope	Sum of proton and neutron counts	Option<Thousand>	None
element	Elemental symbol	Option<Element>	None
hydrogens	Hydrogen count	HydrogenCount	0
configuration	Configurational descriptor	Option<Configuration>	None
charge	Formal charge	PlusMinusTen	0
extension	Application-specific data	Option<Thousand>	None
selected	Whether the atom is selected	boolean	false