ZINCv: A Chemical Visualization and Molecular Construction System

This research effort aims to develop a chemical modeling software tool that integrates the functionality of chemical visualization and molecular builder into one. ZINCv, which stands for “ZINCv Is Not just a Chemical visualizer”, is developed using Visualization Toolkit and FLTK, which makes it a cross-platform tool. Using ZINCv one can build and visualize from simple molecules to complex protein structures. ZINCv Visualizer supports nearly 45 different chemical file formats including PDB. Babel chemical file converter is integrated into ZINCv so that this can visualize datasets in numerous chemical file formats. Currently ZINCv supports both ball-and-stick and space-filling visualization paradigms for molecules. ZINCv allows bond types to be represented in an intuitive manner by color -coding the same for single, double and triple bonds. ZINCv Builder is tightly integrated with Visualizer and with the integration of Babel as a built -in module, it can import and export molecules data in numerous chemical formats. The builder has several user-friendly features such as adding, modifying and deleting of atoms and bonds using simple mouse clicks. ZINCv has an internal database containing atomic radii, Van der Waals radii and bond numbers of all the elements. Using this database, the Visualizer can automatically create bonds between atoms using the Van der Waals radii as the threshold distance between two atoms in case of visualizing data with formats like XYZ, which does not have any connectivity information. Also, the database is used by the ZINCv Builder to automatically create bonds for an atom based on its bond number. Using ZINCv, molecules can be visualized on large stereoscopic displays as well as high resolution, tiled displays to get a better understanding of complex molecular structures in 3D.