Chemistry Terms

Understand identifiers, calculated properties, and structure-search results.

Names and identifiers

SMILES describes atoms and bonds as text; isomeric SMILES includes supported stereochemistry. CXSMILES adds annotations that simpler formats may not retain. InChI is a standardized structure identifier, and InChIKey is its compact key. RInChI describes reactions.

An IUPAC name describes a chemical structure. A successfully parsed or generated name is not necessarily the unique Preferred IUPAC Name. Standard and Fixed-H InChI identities capture different hydrogen/tautomer details; scan-name verification requires both to agree.

Calculated properties

Formula counts elements. Molecular weight, molar mass, and monoisotopic mass use different mass conventions. LogP estimates partitioning, TPSA is topological polar surface area, and hydrogen-bond donor/acceptor counts describe possible bonding sites.

Rotatable bonds and ring count summarize topology. Rule of Five is a screening heuristic, not a prediction of safety, efficacy, or suitability for use. Values depend on the parsed structure and calculation method.

Chemical search results

Similarity ranks molecule fingerprints by Tanimoto score from 0 to 1. A high score does not prove the query is contained in a result. Violet highlights show common regions found within a short time limit; a larger common region may exist. Results without a highlight keep their score and rank.

Substructure search checks atom-and-bond containment and highlights the match in red. MCIS / Target compares shared atoms with target size; tighter matches generally rank higher. These searches operate on repository molecules, not whole reactions.