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
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
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
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
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
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
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
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
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
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
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
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,
%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
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
>
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
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
;
>
> _
> 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&
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
(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
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
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
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
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
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
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
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
Hi
A while ago I had a project which needed PMI descriptors (specifically NPR1
and NPR2) which were not available in the main branch of RDKit at the time.
At the time I used the fork by 'hahnda6' which provided the
calcPMIDescriptors() function, and this worked well. Now that PMI
descriptors are
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