> But the issue that I am having is that the ConjugateGradients method doesn't > actually change any coordinates, it seems not to be doing any actual > minimization. The file I am using is a completely unminimized geometry so it > cannot be that it is converging quickly I think.
The OBForceField class makes a copy of the molecule internally. You have to explicitly tell it when you want to update the coordinates, so: for i in range(20): obff.ConjugateGradientsTakeNSteps(1) obff.GetCoordinates(mol) obc.WriteFile(mol, 'filename.%d.out' % i) Hope that helps, -Geoff ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
