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 monatomic.)
This would matter from the point of view of RMSD if binding conformations
were being compared to each other or to free molecules, or when free
molecules were being compared to each other in a situation where steric
hindrance affects some tri-something group differently among different
conformations. Considering the tri-anything groups would factor in
significant deviations from the local equilibrium geometry
It would also matter in atomic mappings if you really wanted to know which
hydrogen (or anything else) in a conformer alligns to a particular
tri-anything bond in a reference structure. For example, you might have a
methyl group in the reference structure where one H points into a pocket in
an active site and, in a series of analogs, you want to try substituting
the corresponding H some R group or groups.
-P.
On Dec 22, 2016 11:38 AM, "Brian Cole" <col...@gmail.com> 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 dramatically increase the cost of the computation with
> little added value.
>
> On Thu, Dec 22, 2016 at 10:27 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>>
>> On Thu, Dec 22, 2016 at 4:06 PM, JW Feng <f...@dnli.com> 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 available
>> in C++ (Peter Gedeck is working on this), we'll add that option too.
>>
>> -greg
>>
>>
>>
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