Greg - there is an inherent subtlety in here - check my thinking...
You might generate a 1,000 conformers which are all at least 1.0A
RMS(D) from the first conformer, but which are all 0.1A RMS(D) from
each other.
Right?
On 5 April 2011 05:36, Greg Landrum <greg.land...@gmail.com> wrote:
> Dear JP,
>
> On Mon, Apr 4, 2011 at 6:53 PM, JP <jeanpaul.ebe...@inhibox.com> wrote:
>> Can anyone explain why the conformer RMS values which are printed out
>> are all smaller than 1.0?
>> I am pruning using the pruneRmsThresh (=1.0) variable in
>> EmbedMultipleConfs method so I was expecting this would not happen.
>> I am expecting to see values > 1.0 since they should be at least this
>> distance from the first conformer so not to be pruned
>
> The difference is that the conformation-generation code isn't using
> the best RMSD, as your code does, instead it's just using the standard
> RMSD. You can see this by printing an additional value in your code:
>
> #-------------------------------------
> # usual imports
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> # generate a mol
> mol = Chem.MolFromSmiles('O=CCC=O')
> # add hydrogens
> mol_h = AllChem.AddHs(mol)
> # notice the prune threshold - set to 1.0 RMS...
> conformation_ids = AllChem.EmbedMultipleConfs(mol_h, numConfs=50,
> pruneRmsThresh=1.0)
>
> for i in range(mol_h.GetNumConformers()):
> # match the first (original) conformer to the rest
> rms = AllChem.AlignMol(mol_h, mol_h, 0, i)
> bestrms = AllChem.GetBestRMS(mol_h, mol_h, 0, i)
> print(rms,bestrms)
> #-------------------------------------
>
> The output from this is:
> $ python script.py
> (0.0, 0.0)
> (1.3379167659438125, 0.60362436042913903)
> (1.1782030519271443, 0.59622250108412145)
> (1.2243862716355582, 0.30392328812710512)
> (1.1984592787588044, 0.55143501013497576)
> (1.0641915526094825, 0.68902440786535935)
>
>
> Best,
> -greg
>
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
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