29.1.1 Atom Primitives

Symbol	Description	Arg?	Default Value
`A`	Non-aromatic (aliphatic) atom	No
`a`	Aromatic atom	No
`D`n	Degree (explicit connections)	Yes	(No default)
`H`n	Total hydrogen count	Optional	Exactly one
`h`n	Implicit hydrogen count	Optional	Exactly one
`R`n	Ring count^29.1	Optional	Any ring atom
`r`n	Smallest ring size	Optional	Any ring atom
`v`n	Valence (total bond order)	Yes	(No default)
`X`n	Connectivity (total connections)	Yes	(No default)
`#`n	Atomic number	Yes	(No default)
`+`n	Positive charge	Optional	+1 cation ( is +2, etc)
`-`n	Negative charge	Optional	-1 anion ( is -2, etc)
`^`n	Atomic hybridization^29.2	Yes	(No default)
`@`	Anticlockwise local chirality	No
`@@`	Clockwise local chirality	No
`@`n	Chirality class	Optional	Anticlockwise
n	Explicit atomic mass	No

Footnotes

... count^29.1

The semantics of the ring count primitive, R, differs slightly between Daylight SMARTS and OpenEye SMARTS. In Daylight semantics, Rn means that an atom is in n rings of the chosen SSSR. As the choice of SSSR is non-deterministic, this interpretation can cause an arbitrary set of atoms to match depending upon input order. For example, in the symmetric molecule, cubane, four of the eight atoms will appear in two SSSR rings, and half of the atoms appear in three, but the choice is made almost randomly. Rather than attempt to reproduce these weak semantics, OpenEye strengthens the definition of Rn to mean the number of ring bonds to an atom, which is graph invariant and therefore independent of a molecule's input order. Notice, that the interpretation of [R] and [R0], i.e. ring membership, remains the same. Similarly, Daylight [R1] is approximately equal to OpenEye [R2], and Daylight [R2] is approximately equivalent to OpenEye [R3].

... hybridization^29.2

The atomic hybridization primtive, ^, is an OpenEye extension that is not available in Daylight SMARTS, but can be implemented using recursive SMARTS.

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1