Ralf Gugisch

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 (2D) 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.

Many-Valued Context Analysis Using Descriptions

We propose an approach to many-valued contexts using formal descriptions instead of scaling. The underlying idea is the philosphical definition of a concept as a set of objects together with the most precise description. We introduce a formal description as a mapping from the set of attributes to the power set of the values (which is extended appropriately to empty cells), assigning to each attribute the set of allowed values. Descriptions are naturally ordered by preciseness. Using this, we can introduce extent and intent according to the philosophical idea, and thus we define concepts. We present a way to restrict the amount of concepts for a many-valued context by preselecting some descriptions of interest. Furthermore, we introduce implications on descriptions, allowing to investigate relationships between attributes. Within this approach, we reformulate the known theory under a different point of view. It certainly does not provide a better analysis than scaling, but it allows to avoid the generation of a huge one-valued context.

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.

Manual construction and mathematics- and computer-aided counting of stereoisomers. The example of oligoinositols

Two methods to obtain numbers of stereoisomers and of achiral stereoisomers of a given molecular structure are detailed on the example of di- and triinositols. The first method is manual exhaustive construction free of redundance of all stereoisomers, which is rendered feasible by symmetry considerations despite the large number of isomeric triinositols (82176). The second method is counting without constructing, made possible by use of a mathematical tool, the Cauchy-Frobenius lemma, which actually is a formalized manner of considering symmetry. The results are compared to those obtained by computer-aided stereoisomer generation using the program MOLGEN 3.5. It is demonstrated that in their results all three methods agree.

A Construction of Isomorphism Classes of Oriented Matroids

We developed a computer program for generating all oriented matroids corresponding to a prescribed underlying matroid. The generation process and its output can be controlled via a variety of possible restrictions allowing to generate specific sets of oriented matroids.

Advances in Mathematical Chemistry and Applications Volume 1 (Revised Edition)

Volume 1 includes chapters on mathematical structural descriptors of molecules and biomolecules, applications of partially ordered sets (posets) in chemistry, optimal characterization of molecular complexity using graph theory, different connectivity matrices and their polynomials, use of 2D fingerprints in similaritybased virtual screening, mathematical approaches to molecular structure generation, comparability graphs, applications of molecular topology in drug design, density functional theory of chemical reactivity, application of mathematical descriptors in the quantification of drug-likeness, utility of pharmacophores in drug design, and much more.

Chapter 6 – 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 describe the version MOLGEN 5.0 of this new series.