Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Guillaume GODIN
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Brian Kelley <fustiga...@gmail.com> Envoyé : mardi 17 janvier 2017 14:06 À : Guillaume GODIN Cc : cgearns...@gmail.com; Rdkit-discuss@lists.sourceforge.net; Greg Landrum Objet : Re: [Rdkit-discuss] P

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Brian Kelley
4 > *À :* Chris Earnshaw > *Cc :* Rdkit-discuss@lists.sourceforge.net; Greg Landrum > *Objet :* Re: [Rdkit-discuss] PMI API > > I think we agree here. Here I was talking about the raw Moment (M1z) not > the moment of interia (MI1), I should have made the disctinction more > expli

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Guillaume GODIN
gt; Envoyé : mardi 17 janvier 2017 13:44 À : Chris Earnshaw Cc : Rdkit-discuss@lists.sourceforge.net; Greg Landrum Objet : Re: [Rdkit-discuss] PMI API I think we agree here. Here I was talking about the raw Moment (M1z) not the moment of interia (MI1), I should have made the disctinction mor

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Brian Kelley
I think we agree here. Here I was talking about the raw Moment (M1z) not the moment of interia (MI1), I should have made the disctinction more explicit. Moments are not necessarily Moments of inertia. The terminology gets confusing. After a brief discussion with Greg, the Moments.py does the

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Chris Earnshaw
The dimensions along one of the axes of a planar molecule in its inertial frame will be zero, but the principal moments of inertia will all be non-zero. The moment of inertia about an axis can only be zero if all the atoms in the molecule are precisely aligned on that axis. That's only possible

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Brian Kelley
Looks like I'm late to the game. I don't know about the PMI descriptors per-se, but if a planar molecule is in it's inertial frame, one of the axes should be zero (whether it is x, y or z) which means that the one of the M1x, M1y or M1z should be zero. We had some good experimentation with

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Chris Earnshaw
The new version looks good to me as far as I can test it. PMI and NPR are still fine, the radius of gyration is right (for an extremely artificial test system) and the asphericity index also seems right (despite my best efforts to confuse things further - sorry about that!). Also highlights even

Re: [Rdkit-discuss] PMI API

2017-01-16 Thread Chris Earnshaw
9 <+41%2079%20536%2010%2039> > Firmenich SA > RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 > > -- > *De :* Chris Earnshaw <cgearns...@gmail.com> > *Envoyé :* lundi 16 janvier 2017 09:36 > *À :* Guillaume GODIN

Re: [Rdkit-discuss] PMI API

2017-01-16 Thread Greg Landrum
On Mon, Jan 16, 2017 at 9:36 AM, Chris Earnshaw wrote: > > Apologies - I appear to have opened a can of worms here... > No need whatsoever to apologize. You identified and pointed out a bug in the implementation of the new 3D descriptors, which is something very much

Re: [Rdkit-discuss] PMI API

2017-01-16 Thread Guillaume GODIN
CH-1211 GENEVE 8 De : Chris Earnshaw <cgearns...@gmail.com> Envoyé : lundi 16 janvier 2017 09:36 À : Guillaume GODIN Cc : Greg Landrum; RDKit Discuss Objet : Re: [Rdkit-discuss] PMI API On 16 January 2017 at 06:25, Guillaume GODIN <guilla

Re: [Rdkit-discuss] PMI API

2017-01-16 Thread Chris Earnshaw
ologies - I appear to have opened a can of worms here... Chris > -- > *De :* Greg Landrum <greg.land...@gmail.com> > *Envoyé :* dimanche 15 janvier 2017 17:42 > *À :* Guillaume GODIN; RDKit Discuss > > *Objet :* Re: [Rdkit-discuss] PMI A

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Guillaume GODIN
Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Greg Landrum <greg.land...@gmail.com> Envoyé : dimanche 15 janvier 2017 17:42 À : Guillaume GODIN; RDKit Discuss Objet : Re: [Rdkit-discuss] PMI API Thanks Guillaume! On Sun,

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Greg Landrum
%20536%2010%2039> > Firmenich SA > RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 > > -- > *De :* Peter Gedeck <peter.ged...@gmail.com> > *Envoyé :* dimanche 15 janvier 2017 15:07 > *À :* Greg Landrum; RDKit

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Greg Landrum
On Sun, Jan 15, 2017 at 5:15 PM, Chris Earnshaw wrote: > > I've built a version of RDKit with fixes from https://github.com/ > greglandrum/rdkit/tree/fix/github1262 and can confirm that it gives > exactly the same values of PMI and NPR that I got with the RDKit fork by >

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Chris Earnshaw
Thanks Greg I've built a version of RDKit with fixes from https://github.com/ greglandrum/rdkit/tree/fix/github1262 and can confirm that it gives exactly the same values of PMI and NPR that I got with the RDKit fork by 'hahnda6'. I can't say for certain that the PMI values are correct in absolute

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Guillaume GODIN
it Discuss; Guillaume GODIN Objet : Re: [Rdkit-discuss] PMI API According to this: https://en.wikipedia.org/wiki/List_of_moments_of_inertia The moments of inertia of a disk (something like benzene) are: Iz = mr^2/2 Ix = Iy = mr^2/4 None of them is zero. The smallest moment of inertia of a rod-like molecul

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Peter Gedeck
; > > _ > From: Guillaume GODIN <guillaume.go...@firmenich.com> > Sent: Sunday, January 15, 2017 1:11 PM > Subject: RE: [Rdkit-discuss] PMI API > To: Greg Landrum <greg.land...@gmail.com>, RDKit Discuss < > rdkit-discuss@lists.sourceforge.net&

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Greg Landrum
ary 15, 2017 1:11 PM Subject: RE: [Rdkit-discuss] PMI API To: Greg Landrum <greg.land...@gmail.com>, RDKit Discuss <rdkit-discuss@lists.sourceforge.net>, Chris Earnshaw <cgearns...@gmail.com> Dear Greg, I  suspect that it's a precision error or eigen algorithm shift bet

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Guillaume GODIN
(0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Greg Landrum <greg.land...@gmail.com> Envoyé : dimanche 15 janvier 2017 11:50 À : Chris Earnshaw; RDKit Discuss Objet : Re: [Rdkit-discuss] PMI API I manag

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Greg Landrum
I managed to make some time to look into this this weekend and I've found a bug and something I don't understand. Hopefully the community can help out here. On Sun, Jan 8, 2017 at 11:17 AM, Chris Earnshaw wrote: > 4) The big one! The returned results look very odd. They

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Greg Landrum
A more straightforward solution to this one, and what I probably should have done in the first place, would be to not include the conditional compilation directives in the PMI.h header file. It should be fine to have the declarations in the header even if there is no corresponding definition, and

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Chris Earnshaw
Hi Brian & Greg Many thanks for the replies. I built RDKit with Descriptors3D enabled without any problems, it was working out how to tell the compiler to process my source code using the new functions which was troublesome. It would be very helpful if the need for the -DRDK_BUILD_DESCRIPTORS3D

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Brian Kelley
I think the relevant issue is that if you are using an existing build, we don't yet have the capability for you to know what was built and what was not. I.e. You need to add the compiler flag to indicate that the 3D stuff was actually built. I had a PR to fix this a while ago that was

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Greg Landrum
Hi Chris, The RDKit should automatically build with the new descriptors enabled if eigen3 can be found when cmake is run. When you run cmake you should see a message if/when the build is disabled. If you want to call the functions, the best documentation available is the standard C++ API

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Chris Earnshaw
Hi David Thanks for the rapid reply! Looks like a very useful document for people getting started with the RDKit C++ API. As you suspected, I'm slightly beyond that stage having been an RDKit user for a number of years. My queries are specifically to do with using the PMI functionality; most

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread David Cosgrove
Hi Chris, I can help a bit with the first point - I am currently 'porting' the getting started in Python bit of the documentation to c++. There's a long way to go, but if you go to my fork of RDKit at https://github.com/DavidACosgrove and check out the GetStartedC++ branch, you can at least use