Elemental Atoms

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2.2 Elemental Atoms

The elemental atom class is used to match particular elemental atoms. Their names are either one or two characters and are the atomic symbols for atoms in the Periodic Table.

Examples

N[is=NC=O,N*=N]

Nitrogen is an amide group or a diimide.

N[not=NC=O,N:Any]

Nitrogen is not part of an amide and is not in an aromatic ring ("Any" is the arbitrary end of the aromatic bond).

Any[is=C,O,N&not=C=O, O:=Any,NC=O]

Either a carbon, oxygen, or nitrogen. It cannot be a carbonyl carbon, or an oxygen with either a double or aromatic bond, or an amide nitrogen.

Any[not=C,O,N|charge>0]

Atom that has a charge greater than 0 or is not a carbon, oxygen, or nitrogen.

NH(Any[not=C*[R]=O]) Any[not=C*[R]=O]

Secondary amine nitrogen atom that is not a cyclic amide.

C[1:RBC>2]:C[RBC>2]: C[RBC=2]:C[RBC=2]: C[RBC=2]:C[RBC=2]:@1

Phenyl ring which must match a fused ring system where atoms1 and 2 are in the fused ring, but atoms 2 through 6 are not.

Any[!f]-[!r]Any[!f]

Rotatable bonds, excluding terminal bonds.

CC[S=R]H(O)CC

CCH(O)CC where chirality at chiral center is R.

CC[S=R*]H(O)CC[S=S*] H(O)N

CCH(O)CCH(O)N entered as a single pure stereoisomer, where either the first chiral center is R and the second is S or the first chiral center is S and the second is R.

CC[S=RM]H(O)CC[S=SM] H(O)N

CCH(O)CCH(O)N entered as a mixture of the stereoisomer, where the first chiral center is R and the second is S and the stereoisomer where the first chiral center is S and the second is R.

`N[is=NC=O,N*=N]`	Nitrogen is an amide group or a diimide.
`N[not=NC=O,N:Any]`	Nitrogen is not part of an amide and is not in an aromatic ring ("Any" is the arbitrary end of the aromatic bond).
`Any[is=C,O,N&not=C=O, O:=Any,NC=O]`	Either a carbon, oxygen, or nitrogen. It cannot be a carbonyl carbon, or an oxygen with either a double or aromatic bond, or an amide nitrogen.
`Any[not=C,O,N\|charge>0]`	Atom that has a charge greater than 0 or is not a carbon, oxygen, or nitrogen.
`NH(Any[not=C[R]=O]) Any[not=C[R]=O]`	Secondary amine nitrogen atom that is not a cyclic amide.
`C[1:RBC>2]:C[RBC>2]: C[RBC=2]:C[RBC=2]: C[RBC=2]:C[RBC=2]:@1`	Phenyl ring which must match a fused ring system where atoms1 and 2 are in the fused ring, but atoms 2 through 6 are not.
`Any[!f]-[!r]Any[!f]`	Rotatable bonds, excluding terminal bonds.
`CC[S=R]H(O)CC`	CCH(O)CC where chirality at chiral center is R.
`CC[S=R]H(O)CC[S=S] H(O)`N	CCH(O)CCH(O)N entered as a single pure stereoisomer, where either the first chiral center is R and the second is S or the first chiral center is S and the second is R.
`CC[S=RM]H(O)CC[S=SM] H(O)N`	CCH(O)CCH(O)N entered as a mixture of the stereoisomer, where the first chiral center is R and the second is S and the stereoisomer where the first chiral center is S and the second is R.

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