On Thu, 1 Jul 2010 16:36:33 +0200 Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote:
> On Thu, Jul 1, 2010 at 3:56 PM, Konstantin Tokarev > <annu...@yandex.ru> wrote: > > Hi, > > I think geometry optimization steps have slightly different nature > > than set of molecular conformers, and possibility to distinguish > > this data types in software using OB (e.g., Avogadro) will be > > useful. Also, there are relaxed scans consisting of series of > > geometry optimizations, and set of minimal points of scan could be > > interpreted as 'real' conformers. > > > > So IMO new data type is needed (e.g., OBGeometryOptData), and OBMol > > should be able to store arbitrary number of these objects (e.g., in > > vector). Any ideas? > > A generic class for series of coordinates might be better. An enum > with various types could be used (e.g. GeometryOptimization, > MolecularDynamics, MonteCarlo, Docking, ...). Are mentioned types really different? AFAIU, there are no more than three types of coordinate sets: 1) sequential optimizaton steps (geometry optimization, Monte Carlo). They are ordered by step number 2) minimal points of constrained optimization (reaction path, rotation barrier). They are ordered by scan coordinate(s), frozen in any optimization run 3) minimal points of PES (conformations). There is no universal approach to their ordering. Probably molecular dynamics and docking go here too. > Using OBGenericData, per > frame data could be added. The current Data functions allow us to add > an arbitrary number of these objects to an OBMol. Could you explain it a bit more? -- Regards, Konstantin ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
