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Table 1 A summary of the features used to define structure-based classes, either singly or in combination

From: Structure-based classification and ontology in chemistry

Abbrev.

Feature

Description

Examples of features

Examples of classes

IP.1

Skeleton

The main carbon backbone of the molecule

A porphyrin skeleton

Porphyrins, pyridines

IP.2

Attached group

A functional group attached in some position on a skeleton

A methyl group on a pyridine skeleton

Methylpyridine

IP.3

Arbitrary part

A group or atom present in any position within the molecule

A carboxy group, an oxygen atom

Carboxylic acid, oxygen molecular entity

IP.4

Count of parts

The specific number, or a constraint on the number, of parts of a specified type

Three carboxy groups

Tricarboxylic acid

IP.5

Relative arrangement of parts

Relative arrangement of parts of a specified type

Relative arrangement of hydroxy group and amino group

Allothreonine, threonine

CP.1

Basic chemical properties such as charge

Presence of a specific number of charges, or unpaired electrons

Presence of a single positive charge

Anion, cation, dication

TF.1

Topological features - presence of cycles

Whether a molecule contains cycles of specified types

Presence of a cycle containing a hetero atom

Heterocyclic molecule

TF.2

Topological features - count of cycles

Presence of the specified number of distinct (smallest) cycles

Presence of two cycles

Bicyclic molecule, tricyclic molecule

TF.3

Topological features - interrelation between cycles (fusing, arrangements)

Relative arrangements and fusing between cycles

Presence of two cycles sharing one bond

Ortho-fused molecule

TF.4

Topological features

Overall aspects of connectivity, such as ring arrangements

Arrangement of rings into a cage shape

Polycyclic cage, fullerene, nanotube

MC.1

Mechanical connectivity

Mechanical connectivity/interlocking

Molecule with interlinked rotating parts

Rotaxanes, catenanes

MC.2

Mechanical shape of molecule

Features of overall shape of molecule

Knot-shaped molecule

Molecular Möbius strips, molecular knots

SF.1

Structural formula - atomic

A schema for structural formulae in terms of the overall atomic constitution

Molecule with formula C n H2n

Hydrocarbons, alkanes

SF.2

Structural formula - repeating substructural units (polymers)

Structural formulae in terms of relative numbers of substructural units

Macromolecule with repeated ethylene units

poly(ethylene), poly(propylene)