History and Progress of the Generation of Structural Formulae in Chemistry and its Applications

After a few remarks on the history of molecular modelling we describe certain mathematical aspects of the generation of molecular structural formulae. The focus is on the automatic generation of structural formulae for the purpose of molecular structure elucidation and the examination of molecular libraries. The aim is to give a review and to point to relevant literature. We demonstrate an application in the area of quantitative structure-property/activity relationships. Then, we give a glance on ongoing research in the generation of 3Dstructures (stereoisomers and conformers), and finally we mention two problems that should be solved in the near future, the possible use of hypergraphs, and the generation of patent libraries

MOLGEN–CID, A Canonizer for Molecules and Graphs Accessible through the Internet

The MOLGEN Chemical Identifier MOLGEN-CID is a software module freely accessible via the Internet. For a molecule or graph entered in molfile format it produces, by a canonical renumbering procedure, a canonical molfile and a unique character string that is easily compared by computer to a similar string. The mode of operation of MOLGEN-CID is detailed and visualized with examples

MOLGEN 5.0, A Molecular Structure Generator

MOLGEN 5.x combines the efficiency of the molecular generator MOLGEN 3.5 and the flexibility of MOLGEN 4.x. To achieve this, the software was reimplemented based on a totally new concept. The most visible new features are fuzzy molecular formula input and explicit use of atom state patterns. We here describe the first version MOLGEN 5.0 of this new series