Data structures for molecular graphs

The data structure used for molecular graphs depends on the purpose and on the problem to be solved. For example, if an efficient formula-based structure generation plays a central role, an optimal random access to the bonds is important, and so the matrix of multiplicities will be used. However, this method has rather high memory requirements. In other situations, e.g. a substructure search, fast sequential access will be favorable and only the neighborhood list is needed. A neighborhood list keeps a list of all adjacent atoms for each atom, up to three labels as well as the associated information about atoms and bonds. 

Alternatively, the storage space is important where fast access to atoms and bonds may be irrelevant. This holds, for example, when performing structure generation with canonical numbering. In this case the matrix of multiplicities still plays an important role but each covalent bond only needs to be mentioned once. 

In the following we describe the data format used in MOLGEN for a compact storage of molecular graphs. It uses the fact that H atoms can be represented either explicitly or implicitly. Moreover, it allows the storage of 2D and 3D placements of molecules. 

1 Byte Specification of amount and form of the data stored or to be stored Bit 0 bName (1, if a neune is to be stored) 

4 Byte Number k of characters in the name (unsigned int) k Byte Name of the molecular graph 

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