• cheminformatics
• molecular perception
• Proxima
• SSSR

Molecular perception is the set of theories and methods for the automatic determination of the fundamental molecular properties of a system, such as the atom types, the graph structure representing bonds (the molecular connectivity), bond orders, etc.
This work of thesis is focused on the development and the validation of a new software, called Proxima, for the Automatic Molecular Perception of different molecular properties on the base of atomic coordinates and atom types as structural informations. The library also includes a parser for the PDB file format. Molecular Perception of covalent bond connectivity is traditionally performed by comparing the distance between atoms with a theoretical distance resulting from the sum of the relative covalent radii. In the development of Proxima, the additional contribution of the electronegativity is included, as proposed by Schomaker and Stevenson [V.Schomaker and D. P. Stevenson, “Some revisions of the covalent radii and the additivity rule for the lengths of partially ionic single covalent bonds”, Journal of the American Chemical Society, 1941]. The contribution of the electronegativity is especially useful in the case of ionic interactions, such as in the potassium channel (PDB ID: 1BL8), where most common software (such as OpenBabel [Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison, “Open Babel: An open chemical toolbox”, Journal of Cheminformatics, 2011]) overestimate the number of bonds by adding covalent bonds to the potassium atoms. The intensity of hydrogen bonds between a triad of atoms, instead, is computed according to the model proposed by Dr. Pagliai [M. Pagliai, F. Muniz-Miranda, G. Cardini, R. Righini, and V. Schettino, “Hydrogen bond dynamics of methyl acetate in methanol,” The Journal of Physical Chemistry Letters, 2010]. In addition to hydrogen bond and covalent bond connectivity, algorithms for the perception of atomic hybridisation, partial charges and molecular rings have been implemented in Proxima. The hybridisation is computed by using the information about the angles and the geometry of an atom. The molecular perception of chemical rings, instead, is performed by means of the Horton's algorithm for the computation of the SSSR (the Smallest Set of Smallest Rings) [Horton J. D.(1987) A polynomial-time algorithm to find the shortest cycle basis of a graph. SIAM J. Comput.]. Finally, the molecular perception of partial charges is performed by using the Gasteiger method [Johann Gasteiger and Mario Marsili. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron, 36(22):3219 - 3228, 1980.]