Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread Greg Landrum
On Tuesday, April 5, 2011, Geoffrey Hutchison wrote: >> That'll leave you with a couple of options: >> 1) read the code and figure it out yourself >> 2) get a satellite dish installed on Bouvet Island. > 3) Clone Greg. > If someone could please do this now I would be most grateful! -greg > Chee

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread Geoffrey Hutchison
> That'll leave you with a couple of options: > 1) read the code and figure it out yourself > 2) get a satellite dish installed on Bouvet Island. 3) Clone Greg. Cheers, -Geoff -- Xperia(TM) PLAY It's a major breakthrough.

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread Greg Landrum
On Tue, Apr 5, 2011 at 1:57 PM, JP wrote: > So many tricks 'n' tips!  What will we do if you ever opt for a life > of solitude, without satellite connection, on Bouvet Island? That'll leave you with a couple of options: 1) read the code and figure it out yourself 2) get a satellite dish installed

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread JP
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 wrote: > On Tue, Apr 5, 2011 at 11:07 AM, JP wrote: >> Greg - there is an inherent subtlety in here - check

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread Greg Landrum
On Tue, Apr 5, 2011 at 11:07 AM, JP 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) filt

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-05 Thread JP
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 wrote: > Dear JP, > > On Mon, Apr 4,

Re: [Rdkit-discuss] Question based on some code... RMS

2011-04-04 Thread Greg Landrum
Dear JP, On Mon, Apr 4, 2011 at 6:53 PM, JP 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

[Rdkit-discuss] Question based on some code... RMS

2011-04-04 Thread JP
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