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Fig. 1 | Journal of Cheminformatics

Fig. 1

From: DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism

Fig. 1

Examples of a an asymmetric ligand (PDB Ligand ID: CFF); b a slightly symmetric ligand (PDB Ligand ID: IBP); c a highly symmetric ligand (PDB Ligand ID: QN3). d An example ligand structure (left) and the resulting ligand structure when the atoms are reordered according to the optimal query-template atomic correspondence generated by the Hungarian method (right). Since the Hungarian method only takes atom type into account and not the bonds between atoms, the hypothetical molecule proposed by the Hungarian correspondence is physically impossible

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