Greg- I gotta say that the "RDKit Tech Support Team" is phenomenal at getting questions answered!
The previous spiderweb of a 3D structure made it not at all obvious to me that a little more optimization would do the trick. I will look into adding the additional UFFOptimizeMolecule calls. Is there a rough estimate you have for the MAX number of attempts one would make with a 'screening compound' sized molecule in Optimizing via RDKit? As always... Thanks a lot! -Marshall On Mon, Mar 30, 2009 at 10:13 PM, Greg Landrum <[email protected]> wrote: > 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 >
