Marshall, On Tue, Mar 31, 2009 at 6:56 AM, Marshall Levesque <[email protected]> wrote: > I found there are a few molecules that have undergone a crazy transformation > from 2D to 3D with RDKit in my batch conversion due to having a long carbon > chain. > Here is one example molecules on eMolecules.com: > http://www.emolecules.com/cgi-bin/more?vid=600149 > I've attached the input (2D) and output (3D) SDFs. > Here are other examples that result in the same "messy" 3D structures: > http://www.emolecules.com/cgi-bin/more?vid=479405 > http://www.emolecules.com/cgi-bin/more?vid=445711 > Has anyone seen this type of problem before? Is there a way to fix the > "messy" conversion? Or a way to detect when this long carbon chain is > present and tell RDKit to not convert/output these molecules?
looks to me like the UFF optimization just didn't converge. Here's a
better version, generated as follows:
#---------------
[3]>>> m = Chem.MolFromMolFile('crazymol.2D.sdf')
[6]>>> mh = Chem.AddHs(m)
[7]>>> AllChem.EmbedMolecule(mh)
Out[7] 0
[8]>>> AllChem.UFFOptimizeMolecule(mh)
Out[8] 1
[9]>>> AllChem.UFFOptimizeMolecule(mh)
Out[9] 1
[10]>>> AllChem.UFFOptimizeMolecule(mh)
Out[10] 1
[11]>>> AllChem.UFFOptimizeMolecule(mh)
Out[11] 0
[12]>>> print >>file('crazymol.3D.gl.sdf','w+'),Chem.MolToMolBlock(mh)
#---------------
converting that series of calls to UFFOptimizeMolecule to something
general is left as an exercise to the reader. :-)
-greg
crazymol.3D.gl.sdf
Description: StarMath document
