So many tricks 'n' tips! What will we do if you ever opt for a life
of solitude, without satellite connection, on Bouvet Island?
Thanks ... Got it...
On 5 April 2011 12:43, Greg Landrum <greg.land...@gmail.com> wrote:
> On Tue, Apr 5, 2011 at 11:07 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
>> 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.
>
> No. If you use the RMS(D) filter on conformer generation, it applies
> to all conformers.
> Here's a modified version of the script that shows this:
> #-------------------------------------
> # 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)
>
> confIds = [x.GetId() for x in mol_h.GetConformers()]
> for i in range(len(confIds)):
> for j in range(i+1,len(confIds)):
> # match the first (original) conformer to the rest
> rms = AllChem.AlignMol(mol_h, mol_h, confIds[i], confIds[j])
> bestrms = AllChem.GetBestRMS(mol_h, mol_h, confIds[i],confIds[j])
> print(i,j,rms,bestrms)
> #-------------------------------------
>
> The output I get is:
> ~ > python script.py
> (0, 1, 1.3379167659438251, 0.60362436042913781)
> (0, 2, 1.1782030519271491, 0.59622250108410513)
> (0, 3, 1.2243862716355547, 0.30392328812710107)
> (0, 4, 1.1984592787586832, 0.55143501013497065)
> (0, 5, 1.0641915526094818, 0.68902440786534314)
> (1, 2, 1.0255947054908345, 0.59258704355875447)
> (1, 3, 1.0951734935453765, 0.44791337584830399)
> (1, 4, 1.0543889914981652, 0.9168070962596423)
> (1, 5, 1.1385762625965217, 0.43605179946798073)
> (2, 3, 1.5373690362549735, 0.53769968087304854)
> (2, 4, 1.2293196779352933, 0.81799884353238672)
> (2, 5, 1.0825253214349586, 0.34237739827222707)
> (3, 4, 1.1332931410059917, 0.68575442529906516)
> (3, 5, 1.0079860535928928, 0.65467761705027916)
> (4, 5, 1.4641765048256545, 1.0142361289438402)
>
>
> The sample script above has another correction to the original one:
> It's not safe to assume that conformers are labelled sequentially.
> They often are, but there's no guarantee of this. To correct for this,
> I modified the script so that it loops over the conformer ids that are
> actually present.
>
> Best,
> -greg
>
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
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