On Wed, Jun 30, 2010 at 9:28 PM, Christopher Wassman <cwass...@ics.uci.edu> wrote: > Looks like Geoff already committed some changes into svn.
I don't like the way fixed atoms are translated to fixed bonds though. To fix a bond, at least 4 atoms need to be fixed. But even if we changed this to 2, there are still ambiguous cases. For example take a octane molecule with carbon atom indexes 1-8. There are 5 rotor bonds (terminal bonds to methyl are not rotors). If a user wishes to only rotate the middle bond (C4-C5), there is no way to specify this. Perhaps we need to add new constraint type to fix rotor bonds explicitly. C1-C2-C3-C4-C5-C6-C7-C8 Suggestions? Tim > You guys rock. > > Cheers, > Chris. > > On Wed, Jun 30, 2010 at 9:14 AM, Tim Vandermeersch > <tim.vandermeer...@gmail.com> wrote: >> On Wed, Jun 30, 2010 at 6:05 AM, Geoffrey Hutchison >> <ge...@geoffhutchison.net> wrote: >>>> I edited "src/forcefield.cpp", adding this line: >>>> rl.SetFixAtoms(_constraints.GetFixedBitVec()); >>> >>> Well, that's not quite kosher, since the constraints will return a >>> temporary variable, and SetFixAtoms wants a reference. It's easy to fix, >>> though. >> >> Yes, I'll commit a slightly modified version later today. >> >> Thanks for the suggestion, not sure why we haven't done this before. >> >> Tim >> >>>> Hopefully this is an appropriate place to post such modifications. >>> >>> The best place is openbabel-devel or the patch tracker, but we certainly >>> follow openbabel-general too. :-) >>> >>>> Let me know what you think. >>> >>> Thanks, it's good to get the right hand talking to the left hand (as far as >>> freezing atoms goes). >>> >>> Best regards, >>> -Geoff >>> ------------------------------------------------------------------------------ >>> 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-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >> >> > ------------------------------------------------------------------------------ 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-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
