Reaction Languages: Reaction SMARTS
Reaction SMARTS, the reaction query language, is a strict superset of molecule
SMARTS. The extensions for SMARTS which describe reaction query features are
essentially the same as those described for reaction SMILES. The semantics
are described here.
These are pretty straightforward. Each component of the reaction query
describes a substructure which appears within that component role during a
substructure match.
The behavior when mixing molecule and reaction SMARTS with molecule and
reaction targets is worth describing. Molecule SMARTS (SMARTS without
">" characters) can match anywhere in a reaction target
(reactant, agent, or product). Reaction queries never match molecule targets.
Another way to think of these cases is to consider the "role" of
each atom a searchable property... a molecule query is a search for a
collection of atoms and bonds where we haven't specified a role, hence the
molecule query potentially will match any role in a reaction. A reaction
query, on the other hand, specifies roles for all the atoms and bonds in it's
query, and since the atoms in the target molecule don't have specified roles,
these can't match.
Simple Reaction SMARTS Matching
| Target Reaction |
SMARTS and remark |
 |
C=C
The SMARTS matches double-bonded carbons anywhere in the target.
NOTE: All matches are highlighted in red. |
 |
>>C=C
Looking for double-bonded carbons in product components. This query
never matches a molecule target (since molecule SMILES don't have
"products"). |
 |
C=C>>CC
This matches a pair of double-bonded carbons in the reactant and
two single-bonded carbons in product. It matches a double bond
reduction reaction, and also matches any case where each component
appears separately (see the next example).
|
 |
C=C>>CC
This would be a 'false hit' if looking for a reduction reaction.
Atom maps must be used to refine the query and eliminate these
false hits.
|
SMARTS atom maps allow specification the correspondance between reactant and
product atoms within the target reaction. As with reaction SMILES, atom maps
are numeric labels which represent classes and are normally paired (i.e., one
reactant and one product atom have the same map-class). Atom mapped reaction
SMARTS atomic expressions never match unmapped target atoms. Hence, mapped
reaction queries will never hit unmapped reaction targets.
When atom maps in the SMARTS are pairwise (a reactant and a product atom
have the same map class label), the SMARTS says that these two atoms are in
the same class in the target. The actual values of the map classes in the
pattern and target need not match (eg. SMARTS [C:1]>>[C:1] does match the
target [CH2:2]=[CH2:3]>>[CH3:2][CH3:3]) but the two target atoms must be
in the same map classes as one another. Furthermore, it is possible
that additional atoms in the target to be mapped to the same class (eg. SMARTS
[C:1]>>[C:1] also matches the target
[CH2:2]=[CH2:2]>>[CH3:2][CH3:2]).
It is legal in SMARTS for many atoms to have the same map class. The
semantics of atom maps in SMARTS, when multiple reactant and product atoms
have the same class labels uses "or" logic. The SMARTS will match
if each reactant atom of the ambiguous class matches at least one product in
the class, and each product in the class matches at least one reactant. It is
not necessary that all atoms in the target be in the same atom map class. In
effect, using ambiguous atom maps in a query makes that query broader; it will
match ambiguous targets as well as specifically mapped ones.
Atom maps in SMARTS must always be the final part of an atom expression and
has the lowest-precedence and between the atom map and the rest of the
expression. An expression like: [C;:6&:7] is not legal.
Atom-mapped Reaction SMARTS
| Target Reaction |
SMARTS and remark |
 |
[C:1]=[C:2]>>[C:1][C:2]
This matches a double-bond reduction reaction. |
 |
[C:1]=[C:2]>>[C:1][C:2]
This query correctly does not match the atom-mapped reaction
target, eliminating the false hit. |
This final table gives examples to clarify the nuances of atom map query
semantics.
More Atom-mapped Reaction SMARTS
| SMARTS Query:
| Target:
| Match count:
| Comment:
|
| C>>C
| CC>>CC
| 4
| No maps, normal match.
|
| C>>C
| [CH3:7][CH3:8]>> [CH3:7][CH3:8]
| 4
| No maps in query, maps in target are ignored.
|
| [C:1]>>[C:1]
| CC>>CC
| 0
| No maps in target, hence no matches.
|
| [C:1]>>C
| [CH3:7][CH3:8]>> [CH3:7][CH3:8]
| 4
| Unpaired map in query ignored.
|
| [C:?1]>>[C:?1]
| CC>>CC
| 4
| Query says mapped as shown or not present.
|
| [C:1]>>[C:1]
| [CH3:7][CH3:8]>> [CH3:7][CH3:8]
| 2
| Matches for target 7,7 and 8,8 atom pairs.
|
| [C:1]>>[C:2]
| [CH3:7][CH3:8]>> [CH3:7][CH3:8]
| 4
| When a query class is not found on both sides of the query, it is
ignored; this query does NOT say that the atoms are in different
classes.
|
| [C:1][C:1]>>[C:1]
| [CH3:7][CH3:7]>> [CH3:7][CH3:7]
| 4
| Atom maps match with "or" logic. All atoms get bound to
class 7.
|
| [C:1][C:1]>>[C:1]
| [CH3:7][CH3:8]>> [CH3:7][CH3:8]
| 4
| The reactant atoms are bound to classes 7 and 8. Note that having
the first query atom bound to class 7 does not preclude binding the
second atom. Next, the product atom can bind to classes 7 or 8.
|
| [C:1][C:1]>>[C:1]
| [CH3:7][CH3:7]>> [CH3:7][CH3:8]
| 2
| The reactants are bound to class 7. The product atom can bind to
class 7 only.
|
Forward to "Reaction SMIRKS".
Return to table of contents.
Daylight Chemical Information Systems, Inc.
jjdelany@daylight.com