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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)