Hi Geoff, I used git bisect and rested to this commit 79000d56e85bd94b1eaebbeb79019e4f26b530fe. Some changes you made, particularly in mol.cpp file disappeared now. But now openbabel uses cc-cd ring conjugated double bond correctly.
For example, you made some changes to recognize 7-membered aromatic ring in the new versions, but probably there are some bugs there. Look forward to hearing you, Mohammad > On Oct 24, 2014, at 3:00 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > > On 2014-10-24 14:20, Mohammad Mehdi Ghahremanpour wrote: >> Hi Geoff, >> >> If you remember my previous emails, the developer version often makes >> mistake in assigning SP2-conjugated double bonds in the ring systems. >> SP2-conjugated double bond should be cc-cd, but the developer version >> sometimes assigns cc-cc that is incorrect. >> >> I compared the mol.cpp file between the developer master version and >> V-2-3-2 version. They are different, particularly in void >> OBMol::PerceiveBondOrders(). I compared these two files for this method >> and saw that the sections of Pass5 and Pass6 are different. Pass 5 >> checks for aromatic rings and assigns bonds, and Pass 6 assings >> remaining bond types ordered by electronegativity. Pass 6 also >> recognizes possible SP2-hybrid atoms. >> >> That would be great if you could have look at the void >> OBMol::PerceiveBondOrders(). It may be useful to debug this problem. >> > > We will try to find the issue which I suspect is in mol.cpp using git > bisect. > > > > >> Cheers! >> Mohammad >> >> >> >>> On Oct 23, 2014, at 1:59 AM, Geoffrey Hutchison >>> <geoff.hutchi...@gmail.com <mailto:geoff.hutchi...@gmail.com> >>> <mailto:geoff.hutchi...@gmail.com <mailto:geoff.hutchi...@gmail.com>>> >>> wrote: >>> >>> Atom typing for force fields is not done through the internal type >>> translation. For fidelity, it is done by the force field code itself. >>> >>> I haven't had time to look at code changes, but I suspect there have >>> been GAFF patches since 2.3.2. >>> >>> Geoff >>> >>> On Wednesday, October 22, 2014, David van der Spoel >>> <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >>> <mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>> wrote: >>> >>> >>> >>> On 22 okt 2014, at 15:21, Geoffrey Hutchison >>> <geoff.hutchi...@gmail.com <mailto:geoff.hutchi...@gmail.com> >>> <javascript:;>> wrote: >>> >>>>> I am using the developer version in my programs, I have to use >>> that, please help me understand why the developer version of >>> openbabel has problem to match cc and cd atom types. >>>> >>>> The difference is that I noticed v2.3.2 was still using the >>> Ghemical force field as the default, which isn't a good thing. You >>> definitely want atom typing and energies from MMFF94, which is >>> what's used in the developer "master" version. >>>> >>>> Hope that helps, >>> >>> We are using Gaff. But openbabel uses an internal type first, right? >>>> -Geoff >>>> >>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>>> Comprehensive Server Monitoring with Site24x7. >>>> Monitor 10 servers for $9/Month. >>>> Get alerted through email, SMS, voice calls or mobile push >>> notifications. >>>> Take corrective actions from your mobile device. >>>> http://p.sf.net/sfu/Zoho >>>> _______________________________________________ >>>> OpenBabel-Devel mailing list >>>> OpenBabel-Devel@lists.sourceforge.net <javascript:;> >>>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >>> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> OpenBabel-Devel mailing list >>> OpenBabel-Devel@lists.sourceforge.net <javascript:;> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> OpenBabel-Devel mailing list >>> OpenBabel-Devel@lists.sourceforge.net >>> <mailto:OpenBabel-Devel@lists.sourceforge.net> >>> <mailto:OpenBabel-Devel@lists.sourceforge.net >>> <mailto:OpenBabel-Devel@lists.sourceforge.net>> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >>> <https://lists.sourceforge.net/lists/listinfo/openbabel-devel> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> > http://folding.bmc.uu.se <http://folding.bmc.uu.se/> > > ------------------------------------------------------------------------------ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > <mailto:OpenBabel-Devel@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > <https://lists.sourceforge.net/lists/listinfo/openbabel-devel>
------------------------------------------------------------------------------
_______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
