SMARTS Pattern Matching¶
SMARTS Syntax¶
SMARTS is a line notation developed by Daylight Chemical Information Systems for compactly representing molecular substructure queries. The SMARTS language can be considered an extension or generalization of Daylight’s SMILES notation for representing discrete molecules.
Atom Primitives¶
| Symbol | Description | Argument? | Default Value |
|---|---|---|---|
| A | non-aromatic (aliphatic) atom | no | (no default) |
| a | aromatic atom | no | (no default) |
| 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 bond count [1] | optional | any ring atom |
| x<n> | ring bond count [2] | 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 [3] | yes | (no default) |
| @ | anticlockwise local chirality | no | |
| @@ | clockwise local chirality | no | |
| @<n> | chirality class | optional | anticlockwise |
| n explicit | atomic mass no |
Table footnote:
[1] The semantics of the ring count primitive, R, differs slightly between Daylight SMARTS and OpenEye SMARTS. In Daylight semantics, R<n> 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 R<n> 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].
[2] Note that [x] was implemented by Daylight v4.9 and OEChem TK 1.5, and is exactly synonymous to OEChem TK‘s [R].
[3] The atomic hybridization primitive, ^, is an OpenEye* extension that is not available in Daylight SMARTS, but can be implemented using recursive SMARTS.
Bond Primitives¶
| Syntax | Description |
|---|---|
| default (single or | aromatic) |
| - | single bond (not aromatic) |
| = | double bond (not aromatic) |
| # | triple bond |
| ~ | any bond (wildcard) |
| : | aromatic bond |
| @ | ring bond |
| / | directional single ‘up’ bond |
| \ | directional single ‘down’ bond |
| /? | directional ‘up’ or unspecified |
| \? | directional ‘down’ or unspecified |
Logical Operators¶
| Syntax | Description |
|---|---|
| !e | not e |
| e1 & e2 | e1 and e2 (high precedence) |
| e1,e2 | e1 or e2 |
| e1;e2 | e1 and e2 (low precedence) |
Examples¶
| SMARTS: [C;$([*@]([*])([*]))] |
|
| SMARTS: [C;!$([*@]([*])([*]))] |
|