Search Types

Exact structure search, substructure search

Chemists are most 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).

If special molecular features are present on the query (eg. stereochemistry, charge, etc.), only those targets match which also contain the feature. However, if a feature is missing from the query, it is not checked by default.

An exact structure search finds molecules that are equal (in size) to the query structure. (No additional fragments or heavy atoms are allowed.) Molecular features (by default) are evaluated the same way as described above for substructure search.

Table 1. Exact structure search, substructure search

query target hit

exact structure search substructure search

Other search types

Besides the above, JChem supports similarity, perfect, superstructure and exact fragment type searches.

Similarity is only used in database searches, and its similarity concept is based on hashed binary chemical fingerprints with Tanimoto metrics. (For a more detailed description, see the Developers Guide.) For a more sophisticated approach of similarity, we provide the Screen package.

Perfect search is mainly used before database inserts to check whether the given molecule already appears in the database or not. All molecular features need to be equal here, eg. non-stereo query will only match non-stereo target, etc.

Superstructure search is the opposite of substructure search: It searches for those target molecules which can be found in the given superstructure query. (In this case the roles of the query and target molecules are simply exchanged, so query properties should be specified on the target!)

Exact fragment search is between substructure and exact search: the query must exactly match to a full fragment of the target. Other fragments may be present in the target, they are ignored. This search type is useful to perform an "Exact search" that ignores salts or solvents beside the main structure in the target.

Table 2. details the main differences amongst these search types.

Table 2. Search type differences

Search type Search feature

Similarity Tests if target
contains query Tests if query
contains target Full fragment
coverage Exact topology
matching Exact stereo
matching Exact atom
features matching Exact bond
matching

SUBSTRUCTURE n/a

SUPERSTRUCTURE n/a

EXACT_FRAGMENT n/a

EXACT n/a

PERFECT n/a

SIMILARITY n/a n/a n/a n/a n/a n/a n/a

The definition of the search features are:

Similarity: similarity search using chemical hashed binary fingerprint and Tanimoto metrics.
Full fragment coverage: the query must cover a whole fragment of the target, but the target may contain other fragments. (Implicit and explicit hydrogens are treated equal.)
Exact topology matching: the whole molecular graph must match (Implicit and explicit hydrogens are treated equal.)
Exact stereo matching: equality is needed in stereochemistry, eg. non-stereo query only matches non-stereo target.
Exact atom features matching: whether matching of certain atom properties should be switched to "exact". This requires equality of the properties (eg. uncharged query only matches uncharged target), and includes the following switches:
- chargeMatching : exact
- isotopeMatching : exact
- exactQueryAtomMatching : true
- radicalMatching : exact
- valenceMatching : exact
Exact bond matching: generic bonds are not evaluated, equality is needed.

Table 3. illustrates the most important differences between EXACT and PERFECT searches.

Table 3. EXACT and PERFECT search differences

Query Target Hit Remark

EXACT PERFECT

with option DoubleBondStereoMatching
set to DBS_MARKED (default)

(A) denotes aliphatic query property

The diagrams below show further examples of substructure, exact fragment, exact and perfect searches. The arrow between a query and target molecules denotes matching.

Searching in the database

Searching in the database contains a rapid prefiltering step, which screens out many of the targets not matching the query. This step uses chemical hashed fingerprints. To learn more about this step and how to fine-tune fingerprint generation to your needs, see the following document: Parameters for Generating Chemical Hashed Fingerprints

Comparison levels

Graph topology

Graphs consist of nodes and edges. When we compare structures represented as graphs, the graph patterns must match. Atoms correspond to nodes and bonds are edges.

Atom types

In the case of molecular structures, it is certainly not enough to simply compare the graph patterns, the type of atoms and bonds must be checked as well.

Stereo configuration

Even if both the topology and the type of the corresponding atoms and bonds are matching, we still have to examine the stereochemical configuration. Two molecules having the same kind of atoms connected by the same kind of bonds can be stereochemically different. The relative position of ligands connected to a chiral atom (R/S isomers), the enhanced stereo labels on chiral atoms and relative position of atoms located on rings or double bonds (cis/trans or E/Z isomers) determine the stereochemical configuration of the molecule.

For the different stereo features, see section Stereochemistry.

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