On Aug 11, 2010, at 8:49 AM, David Lonie wrote: >> The comment in the declaration (and the API documentation) for >> OBMol::GetEnergy()) is >> "return the heat of formation for this molecule (in kcal/mol)" ... > Another point that came up is what to do with other thermodynamic > quantities. I use enthalpies frequently, as well as semiempirical/MM > "energies" that have little to no physical meaning.
I would be fine if we simply mark this as deprecated and agree on putting energetic and thermodynamic quantities into generic pairs with some set of agreed-upon identifiers. The GetEnergy() bits are holdovers from Open Eye -- I believe the documentation stems from that period as well. Some QM programs (notably MOPAC) do give heats of formation. Some MM methods (e.g., MMFF94) attempt to parameterize so that the energy roughly corresponds to a heats of formation. Chris is correct that in many cases, the QM format uses the total energy, which is only related if we had the corresponding energy of each element in that particular calculation method. Then you could calculate a heat of formation by taking the difference of the total energy and the sum of all atomic contributions. (Alas, this is basically impossible to do in OB.) So I would vote +1 for deprecating _energy and pushing towards paired identifiers. -Geoff ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
