Daylight Summer School 2001, June 5-7, Santa Fe, NM
Reaction SMILES and SMIRKS
Just as a SMILES represents a molecule, a reaction SMILES
represents the molecules in a chemical reaction.
Reaction SMILES consist of potentially three parts each separated by a ">":
- Daylight system is designed to be able to represent and store both
completely specified reactions (graph-like reactions) and information-deficient
reactions in a repeatable and searchable fashion.
- Only pure structural information is stored in a lexical representation
of the reaction
- Additional data is not stored as part of the reaction but rather
stored separately in the database. (e.g. stoichiometry, equilibrium constants,
- Daylight system is oriented towards single-step reactions
- Reactant: A starting material. It is expected to participate
in the reaction by contributing one or more atoms to the products.
- Agent: Agents are molecules which do not contribute atoms to the
product, or accept atoms from the reactants. Agents are commonly
used for catalysts, solvents and other adjunts which are indirect participants.
- Product: Molecules which are the final result of the reaction. All
atoms in the product should come from the reactants.
Reaction processing occurs by the use of Atom Maps. The atom
map tells the computer which atoms are the same on the reactant and
products sides of the reaction.
- The map is always the last part of the atom expression delimited
by a colon
- Values are numbers without intrinsic meaning
- If a hydrogen is mapped, it is also "special" and must be shown (Hydrogens
are normally omitted from SMILES)
- Extend SMARTS with '>' operator, like SMILES, with optional atom map.
- Any valid Reaction SMILES is a valid SMARTS query.
- Any valid Molecule SMARTS can be a component of a Reaction
- Recursive SMARTS supports only molecule expressions.
- All valid SMIRKS are valid reaction queries
Matches any reaction with a reactant acid and a product ester. Includes all
esterification reactions, plus any reaction which happens to have the
appropriate functionality in its components.
Matches esterification reactions.
Matches any intra-molecular esterification reaction.
Matches any inter-molecular esterification reaction.
Example Reaction SMARTS:
A transform is a generic reaction defined in the Daylight
world by a SMIRKS. SMIRKS is a hybrid language of SMILES
and SMARTS which meets the requirements of reaction expressions:
The SMIRKS rules are as follows:
- Expression of a reaction graph
- Expression of indirect effects
- Atoms can be added or deleted during a transformation
- Atomic SMARTS expressions can be used for atoms directly
involved in the reaction (the reaction center)
- Stoichiometry is defined to be 1-1 for all atoms in the reactant and product for a transformation.
- Explicit hydrogens that are used on one side of a transformation must appear explicitly on the other side of the transformation must be mapped.
- Bond expressions must be valid SMILES (no bond queries allowed)
- Atomic expressions may be any valid atomic SMARTS expression for nodes where the bonding (connectivity & bond order) doesn't change.
- Nitro group conversion
- Enumeration of a combinatorial library - aminothiazole transformation
Contrast this with the "fragment marking approach"
Reference: J.Chem.Inf. Comput. Sci., Vol 39, No. 6,1999,p.1161-1172
Daylight Chemical Information Systems Inc.