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 a
> bug. Looks
Hi Greg,
I would also vote for changing the code such that only heavy atoms are used in
the RMS calculation.
Best,
Sereina
On 22 Dec 2016, at 13:36, Greg Landrum wrote:
> Hi JW,
>
> On Wed, Dec 21, 2016 at 11:57 PM, JW Feng wrote:
>
> I am using AllChem.EmbedMultipleConfs to generate conf
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 code to do that is
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 Flo
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
little
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
> groups too as they
So no halogens? That seems... wrong.
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:
>> RMSD with auto-morph symmetries with hydrogens are crazy expensive to
>> calculate. Symmetry should be on by default, but
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:
>> RMSD with auto-morph symmetries with hyd
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
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