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Fig. 4 | Journal of Cheminformatics

Fig. 4

From: BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

Fig. 4

Graph database for storing rotamer library for fast searching. The figure illustrates a rooted graph layout of fragments where each node is a unique constitution. The child nodes originating from the root are such that the root (in this case, benzene fragment) is their immediate substructure among all the fragments shown in the graph. Fragments contained in the molecule of interest are colored in blue while those that are not are in red or black. For fragments in black no substructure search is performed because their parent fragments were not found in the molecule of interest. The edges represent all possible search paths for finding fragments contained in the molecule of interest. Paths in blue are the actual searches that were performed for finding fragments for the query molecule. Paths in red and black are never taken during the search. Red colored paths are redundant search paths that have already been covered in a previous search

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