Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Tri-anything groups can be considered one by one after the remaining heavy atoms have been aligned. This turns a combinatorial explosion into a linear algorithm for these groups. (Well, it would be linear in number of tri-anything groups, but it gets more complicated if the anythings are more than

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Missed the swap == swap with same type. There probably is some moment based heuristic you use to check for bad outliers. Brian Kelley > On Dec 22, 2016, at 11:49 AM, Greg Landrum wrote: > > >> On Thu, Dec 22, 2016 at 5:37 PM, Brian Cole wrote:

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

On Thu, Dec 22, 2016 at 5:37 PM, Brian Cole wrote: > RMSD with auto-morph symmetries with hydrogens are crazy expensive to > calculate. Symmetry should be on by default, but without hydrogens. Would > even love to see the RMSD auto-morph symmetry code ignore trifluro type of >

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

RMSD with auto-morph symmetries with hydrogens are crazy expensive to calculate. Symmetry should be on by default, but without hydrogens. Would even love to see the RMSD auto-morph symmetry code ignore trifluro type of groups too as they dramatically increase the cost of the computation with

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Hi Greg and Sereina, Thanks for confirming the bug. I also vote for changing the code to use only heavy atoms. Is symmetry taken into consideration when calculating RMS during the pruning step? Best, JW ___ JW Feng, Ph.D. Denali Therapeutics Inc. 151 Oyster Point Blvd, 2nd

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

On Thu, Dec 22, 2016 at 4:06 PM, JW Feng wrote: > > Thanks for confirming the bug. I also vote for changing the code to use > only heavy atoms. Is symmetry taken into consideration when calculating > RMS during the pruning step? > Symmetry is not taken into account, once the

Re: [Rdkit-discuss] Bug in AllChem.EmbedMultipleConfs pruning?

Hi JW, On Wed, Dec 21, 2016 at 11:57 PM, JW Feng wrote: > > I am using AllChem.EmbedMultipleConfs to generate conformers. I noticed > that conformers in the result set are very similar to each other. I wrote > a test script to calculate RMS for the conformers and may have found