Reaction Query Features

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A reaction structure query will retrieve reactions that include the reactants, reagents, or products that you draw, either as complete structures, or as substructures. As when searching for substances, you can apply substructure query features to narrow or broaden the search for the substructures embedded in the substances matched.

Other query features are specific to reaction structure queries and are used to focus the search on the reaction transformation:

Specifying Reaction Roles

You can specify the reaction roles of the structures by drawing a reaction arrow. Structures to the left of the arrow are assigned as reactants. Structures to the right are assigned as products.


In ChemDoodle, use the Arrow_tool.png tool. In CAS Draw, use the Arrow_tool.png tool. Click the drawing area to place the arrow.

Alternatively, you can define the reaction role for each structure as Product, Reactant, Reagent, Reactant/Reagent, or Any Role. For example:


In ChemDoodle, use the Arrow_tool.png tool. In CAS Draw, use the CASDraw-ReactionRole.png tool. Click the structure, and then select the role from the menu that appears.

Marking Reaction Sites

Mark bonds that are changed (broken, formed, or change bond order) in the reaction. The bonds are marked with a double line.


In ChemDoodle, use the Mark_Bond_tool.png tool. In CAS Draw, use the MarkBondTool.png tool. Click the bond to mark it as a reaction site.

Mapping Atom Pairs

Specify corresponding pairs of atoms present in the reactant and product.

Note: When you submit a reaction structure query with mapped atoms, the results include multi-step reactions with mapping available. 


In ChemDoodle, use the Map_tool.png tool. In CAS Draw, use the AtomMapTool.png tool. Click the atom in the reactant, and then click the atom in the product. Map numbers appear on the atom pair.