General Structure Search Introduction Atom lists, not lists Generic atoms
	Reaction Search Simple query structure in reaction Query structure in reaction components Atom maps Component identification

Introduction
In the simplest case two molecular structures are compared. An exact structure search determines whether they have the same topology or not. Chemists are more often interested in substructure search, that is, whether one molecular structure contains the other one as a substructure or not. By definition, the examined molecule is called a target, the structure we are looking for is called a query, and a target molecule matching the query structure is called a hit (Table 1).

Table 1 Exact structure search, substructure search

query	target	hit
		exact structure search	substructure search

Atom lists, not lists
It is possible to define the type of an atom in a custom atom list. If the type of the corresponding atom in the target molecular structure is a member of the list, it is considered a matching atom (Table 2). Not lists can be used to specify atoms to be excluded (Table 3).

Table 2 Atom lists

		target
query

Table 3 Atom not lists

		target
query

Generic atoms
Applying atom lists and not lists is a practical solution when the number of included or excluded atoms is small. However, generic atom types are helpful to avoid long atom lists (Table 4). JChem handles two generic atom types, Any and Hetero (the set of available generic atoms will be extended soon).

 Any         any (any atom except hydrogen)
 Q           hetero (any atom except hydrogen and carbon)

Table 4 Generic query atoms

		target
query

Simple query structure in reaction
Structures to the left of the reaction arrow are reactants (starting materials), structures to the right of the reaction arrow are products, and those molecules drawn just above or below the arrow are agents (ingredients). Corresponding atoms containing changing bonds (created, destroyed or modified) are marked with map numbers both in the reactants and in the products (Table 5).

Searching for a substructure in a reaction equation does not differ from the classical substructure search process described above. Any matching in any reaction components (reactants, agents, products) is a hit. This is not the case when the query itself is a reaction.

Table 5 Searching for simple query structure in reaction

		target
query

Query structure in reaction components
Reaction queries are not necessarily complete reactions. Reaction queries sometimes contain reactants only. In this case, the search engine retrieves reactions containing reactants matching to the given structure. When just a product is specified in the query, those reactions will be returned which contain matching products (Table 6).

Table 6 Searching for query structure in reaction components

		target
query

Atom maps
When a reaction query has mapped atoms, the reaction center of a matching reaction is mapped correspondingly. Although, the actual value of the map numbers might be different in the query and the target, the hit atoms have to be paired exactly as they are in the query (Table 7).

Table 7 Searching by mapped reaction queries

		target
query

Component identification
A query structure occasionally consists of some disjunct fragments. Since these fragments belong to a single reaction component in the query, their corresponding hits must belong to a single component as well. Two components of a reaction query are matching to two components of a target reaction (Table 13).

Table 13 Component identification during reaction search

		target
query