> So my question is this: Is there anyway to speed-up this start up time, > or at the very least a way to perform consecutive minimizations without a > startup in between every one?
Keep in mind the "startup" involves assigning the molecular mechanics atom/bond types, assigning aromaticity, detecting rings, etc. Molecules with large numbers of fused aromatic rings are challenging for the current aromaticity code in Open Babel, and so this "startup time" is highly dependent on the size and complexity of the molecule. You can, of course, perform a variety of MM calculations consecutively without penalty using code in Python or C++ -- for example, the "--gen3d" flag for obabel will generate initial coordinates, followed by a steepest-descent search, a conformer search, and a conjugate gradient optimization of the final conformation. All these are done without needing to hit "startup" again. Unless you have an extremely slow disk, or extremely limited RAM, the actual startup of "obminimize" or other programs should be fractions of a second. You can test this by trying to minimize something like benzene. Hope that helps, -Geoff ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
