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
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
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
Hi All,
I used obenergy command from two different version of openbabel on the same
molecule, but I got two different output. The atom type is different.
The molecule is 4-methyloxazole. I once used the developer version and once
openbabel-2.3.2. Please have a look at the results presented
On 22 okt 2014, at 15:21, Geoffrey Hutchison geoff.hutchi...@gmail.com 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
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
