VFilter analyzes multiple conformations of a molecule and removes conformations that are identical to within user-specified tolerances. Both global and local chemical symmetries are accounted for when comparing a pair of conformations. For example, if two conformations differ only by a 180º rotation of a benzene ring, the local symmetry of the benzene is detected and applied so that the two conformations are recognized as identical. Alternate resonance forms, but not tautomers, are also accounted for when identifying symmetries.
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Command-line options provide detailed user control, including:
- energy cutoff for filtering out high energy structures (for SDfiles that contain an <energy> block)
- distance tolerance for filtering repeat structures
The MS Windows version of Vfilter includes a convenient graphical user interface that facilitates assigning parameters, running Vfilter, and viewing its results. The interface brings together Vfilter, our molecular display program Vdisplay, and helpful Vfilter support utilities, as shown in the following screen-shots. (Click images for full-sized views.)
VFilter version 1.0 for MS Window2000/XP including a graphical user interface and linux.
Chen, W., J. Huang, and M. K. Gilson (2004). “Identification of symmetries in molecules and complexes.” Journal of Chemical Information and Computer Sciences 44(4): 1301-1313. DOI: 10.1021/ci049966a
Gilson, M. K., H. S. R. Gilson, and M. J. Potter (2003). “Fast assignment of accurate partial atomic charges: An electronegativity equalization method that accounts for alternate resonance forms.” J. Chem. Inf. Comput. Sci. 43: 1982-1997. DOI: 10.1021/ci034148o