SMILES - 3D : das weiterentwickelte Konzept zur Codierung dreidimensionaler Molekülstruktur in einer linearen Notation und die programmtechnische Umsetzung in der Software WinSmiles - 3D

The SMILES - 3D (Simplified Molecular Input Line Entry System) notation to encode three-dimensional molecular structures in a linear string will be reported and the implementation of the concept into the software WinSmiles - 3D will also be described. The SMILES - 3D notation expresses the three-dimensional molecular structure in a compact and easy understandable string by using only a few notation-rules. The three-dimensional structure will be encoded by assigning a cell to each atom in the molecule. The cell represents the stereo-arrangement of electron groups in the sense of the VSEPR (Valence Shell Electron Pair Repulsion) concept. The properties of atoms (charge, oxidation state, etc.) and the properties of bonds (bond length, etc.) can be specified optionally in the linear SMILES - 3D string. Furthermore, it is possible to assign the SMILES - 3D string of a molecular fragment to a template and also to integrate these templates into another SMILES - 3D notation. The SMILES - 3D concept is implemented into the software WinSmiles - 3D. The program WinSmiles - 3D generates the three-dimensional molecular structure based on the linear SMILES - 3D string input. The software WinSmiles - 3D is a 32-bit Windows application written in the object-oriented programming language C++. The internal programming structure of the software WinSmiles - 3D is described and the algorithm for the automatic generation of the SMILES - 3D string based on the program representation of the molecular structure is explained.