Interesting point. I had not considered to separate fixed segments. Fixing the rotor bonds explicitly is likely the best option as a more generic approach.
Small question arises as to whether or not to atoms connected to these "fixed rotor bonds" should be allowed to move during the molecular mechanics energy minimization cleanups that occur in the rotor search code. (My vote would be for a true/false option with the default to true.) Somewhat of an aside: The only alternative I can come up with is specifying some sort of "rigid body" constraint which accepts N atoms, all which all must be connected (with associated validation code), and then fixed bonds inferred from these "rigid body" constraints. This may or may not be an easier adaptation of the code base. This whole thread has me thinking of coding some simple monte carlo simulation code in here too. Cheers, Chris. On Wed, Jun 30, 2010 at 3:48 PM, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > 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
