> I've tried looking into it to propose a possible solution, but I couldn't pin
> exactly where this happens in the code.
...
> I suspect the problem might be in builder.cpp, where the math for the bond
> angles is computed, but where exactly I have no idea.
It's most likely here in GetNewBondVector()
https://github.com/openbabel/openbabel/blob/master/src/builder.cpp#L150
<https://github.com/openbabel/openbabel/blob/master/src/builder.cpp#L150>
I suspect that the code that attempts to place alkyl chains correctly is the
culprit - can't find the exact line.
I've been playing with the DG and knowledge-based DG methods in RDKit more and
would love to have an OB equivalent. Greg's code is definitely better for 3D
structure generation of organics. (Not sure if they've handled all the square
planar, octahedral, etc. cases that are in OB, though.)
-Geoff
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