On Apr 28, 2008, at 2:58 PM, Daniel Russel wrote:
probably some readme should be included somewhere in the imp distribution how to install the necessary libs if there are licensing issues in putting the whole lib into the package (containing the url, for example).if cgal can be installed painlessly, i.e., a normal person (non-bioinformatics person or non-computer scientist) can install itwith few mouse-clicks or commands (<5) on major platforms (linux, mac,windows), i think nothing would speak against it. also the lib should not mess up the harddisk.I have only installed it from the command line, but that is a matter of typing "./install_cgal --prefix=where_to_install". There are binaries for windows (and I'll check on macs).
it'd be probably a good idea to have a non-bonded list dedicated for approximately similar radii. to me it seems a general purpose non- bonded list is still too slow for most atomic calculations. from my limited experience with the old code, it seemed like you need to gain several magnitudes in computational speed to make the non-bonded list usable for atomic applications. you will be the expert on how much can be gained by improvements in the implementation and what the actual limitations of the algorithm are. probably, it will be unavoidable anyway, to have some folder designated for atomic applications anyways. e.g., there will not be a general-particle DOPE.:-) The modeller code doesn't work because it assumes equal sized particles. He also claims he put a fair bit of effort into optimizing it. I don't really feel like spending my time that way. I have looked for good public domain code to steal, but haven't found any.
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