The R group is an atom or group of atoms that determines the chemical properties of an organic compound. Common functional groups are olefins, alcohols, phenols, ethers, aldehydes, ketones, etc. Organic chemical reactions mainly occur in functional groups. Functional groups play a decisive role in the properties of organic substances. -X, -OH, -CHO, -COOH, -NO2, -SO3H, -NH2, RCO-, these functional groups determine the chemical properties of halogenated hydrocarbons, alcohols or phenols, aldehydes, carboxylic acids, nitro compounds or nitrites, sulfonic acid organics, amines, and amides in organic substances.
R-group decomposition is a special kind of substructure search that aims at finding a central structure - scaffold - and identify its ligands at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups. These R-groups are simple R-group atoms without R-group definitions. An example of query structure is shown below:
Note that two R1 atoms are referring to symmetrical ligand positions. By default, this means that the matching ligands should be identical. You can change this behavior by setting parameter, in which case the same RGroup ID is only used to denote symmetrical positions on the scaffold and different ligands at these positions are also accepted.
Ligand attachments are not allowed at implicit H atoms, that is, each decomposition corresponds to a full fragment match.
To add R-atoms in place of implicit H atoms, use the --query-modification query transformation option. Applying this to the query above, you get the following:
Take the following targets:
Decompositions using the different query options (no modification, add R-groups) are shown below. By default, decomposition is generated for the first hit only.
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