I don't disagree about having a calcrmsd, but the executable provided as part of confab is not an all-purpose RMSD calculator. It's pretty specific for the Confab output, hence the 'rename' to confabreport format.
I would argue for a separate calcrmsd executable that covered the common use cases (first against rest, all-against-all, include hydrogens, include symmetry, perform least-squares alignment). In the end, do you want me to revert my changes to IsSetupNeeded code? I realise that there is an interaction with Avogadro that might be upset. - Noel On 6 June 2013 15:50, Geoffrey Hutchison <geo...@pitt.edu> wrote: > Hi Noel, > > Sorry for the long delay. I've started reviewing the confab branch. > >> and calcrmsd executables in there, but I plan to remove them as they >> are replaced by the --confab op and -oconfabreport format. > > I think we definitely need a rmsd command-line tool. There seems to be an > unmet need based on a wide range of comments I've seen. > >> One possible bone of contention is that I have changed IsSetupNeeded() >> for forcefields to always return true. > > I think the current code is much better, but you do have a point that the > client code probably knows better whether the molecule has been chemically > changed (as opposed to coordinate changes). > >> I don't think there's not much else there that people might disagree >> with. There were some changes to reduce torsions based on graph >> symmetry. There actually was code in rotor.cpp and friends to do this >> but it was disabled. Furthermore it detected graph symmetry by >> applying the torsion and checking the RMSDs, rather than, well, using >> graph symmetry. > > This is good too. > > So I need to finish code review, but it looks generally fine to merge. > > -Geoff ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
