Up Directory CCL Script which finds rotatable bonds in mol2 file(s)


Short summary: Script which determines the rotatable bonds in mol2 file(s). Usage: file1.mol2 <file2.mol2 file3.mol2 ...> The info about rotatable bonds is output to the screen, and also to file(s) with extension *.aux, one for each molecule. More details: Written by Visvaldas Kairys. Created in about 2000-2001, when I was a postdoc at Center for Advanced Research in Biotechnology / University of Maryland The criteria for prohibited flexible bonds are taken from S. Makino, I. D. Kuntz J. Comput. Chem., vol. 18, p. 1812-1825 (1997). In other words, the script pays attention to the atom types: does not rotate double bonds, etc. Also finds terminal bonds and considers them non-rotatable (example: C-H bond). In addition, considers methyls as non-rotatable. After little editing, some of the restrictions could be removed. If you want this behavior to be modified, drop me a line, The scheme is not perfect (for example, -NH3 groups are rotatable, actually this could be added to the script, but I didn't get to that), but hopefully is usable. Of course, bonds inside the rings are not rotatable. Ring detection algorithm taken from: Th. Hanser, Ph. Jauffret, G. Kaufmann J. Chem. Inf. Comput. Sci. 1996, vol 36, p. 1146-1152. In principle, could be edited to get quite thourough information about rings, which can be useful for condensed rings, etc, but that wasn't what interested me at that time. Appreciation to Mike Potter for tips and Mike Gilson for guidance. Covered by General Public License.

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  • [18kB] : The script which finds rotatable bonds in a mol2 file
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Modified: Mon Jul 3 13:54:42 2006 GMT
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