The kick script is based on the stochastic search procedure originally defined by M. Saunders: "Stochastic Search for Isomers on a Quantum Mechanical Surface" M. Saunders, J. Comput. Chem. 2004, 25, 621 - 626.
The original Fortran code was rewritten in Javascript for web version.
This version is the first adaptation of the original procedure, where one molecular fragment is defined,
and kept frozen while the rest is "kicked" around.
Articles published with this procedure in our group include:
"Prereactive complexes in chlorination of benzene, triazine, and tetrazine: A quantum chemical study"
D. Šakić, V. Vrček, J. Phys. Chem. A 2012, 116(4), 1298-1306.
Although, original script did not have minimal distance value, the same
was added for quick elimination of unfit structures.
Help from Valerije Vrček (discussion), Hendrik Zipse (documentation, suggestions) and Vasily Korotenko (testing) is greatly appreciated. Please report all suggestion, changes, improvements, and usage to dsakic@pharma.hr