Scaffold-oriented universal line system

One or more non-transitory computer-readable media storing instructions that, when executed by one or more processors, cause a system to perform operations, the operations comprising:

• obtaining a chemical structure with a computing system;
• and
• converting the chemical structure to a computer-readable scaffold-oriented line notation, the scaffold-oriented line notation comprising:
• a scaffold sequence of a plurality of atom identifiers arranged in a line notation that defines a scaffold of the chemical structure of a molecule, wherein the scaffold sequence includes at least one decoration marker, each decoration marker being adjacent to an atom identifier of a linking atom of the scaffold that is linked to a decoration, wherein in the chemical structure of the molecule the decoration is a chemical moiety that is bonded to the linking atom of the scaffold;
• a decoration separator following a last atom identifier or a last decoration marker of the scaffold sequence;
• at least one decoration having at least one atom identifier in a line notation that defines a chemical structure of the chemical moiety of the decoration that is attached to the linking atom of the scaffold of the molecule;
• wherein:
• in the scaffold sequence, an order of the at least one decoration marker defines an order of the at least one decoration;
• in the at least one decoration, the first decoration follows the first decoration separator;
• and
• in the at least one decoration, the first decoration is defined as being attached to a first linking atom identifier in the plurality of atom identifiers between a first atom identifier and the last atom identifier, wherein the first linking atom is any atom including a first atom or last atom or any atom therebetween in the scaffold sequence.