[Rdkit-discuss] If someone has build problems using conda currently ...
... I just suffered this: https://github.com/conda/conda/issues/4309 Going back to a previous conda version (4.2.12) helps. Other than that: Happy New Year (a late one :-) -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PMI API
On Mon, Jan 16, 2017 at 10:22 AM, Chris Earnshaw wrote: > > Either way, it makes it rather hard to trust their derivations generally - > especially as there appear to be other errors (e.g. the denominator in eq. > 16 should be the square root of the given sum of squares, according to > their reference). > Indeed. Given the problems encountered, I went back and checked some additional references to find definitions of the descriptors. The results are in this PR, which I'd love feedback on if you have time to take a look: https://github.com/rdkit/rdkit/pull/1265 I didn't manage to find any information about "inertial shape factor" and don't have access to the references cited in the Todeschini paper, but I think the others are now reasonably reliable. -greg -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PMI API
Dear Guillaume Thanks - looks like we agree about reality (good!) and that Todeschini et al. are wrong in their discussion about planar molecules. Whether this is a simple mistaken assertion, or if they've mixed up another quantity (e.g. the eigenvalues of the covariance matrix) with the PMIs is impossible to say. Either way, it makes it rather hard to trust their derivations generally - especially as there appear to be other errors (e.g. the denominator in eq. 16 should be the square root of the given sum of squares, according to their reference). Best regards, Chris Dr Chris Earnshaw CGE Computational Chemistry Phone: +44(0) 1223 426000 Mobile: 07944 707773 E-mail: ch...@cge-compchem.co.uk On 16 January 2017 at 08:54, Guillaume GODIN wrote: > Dear Chris, > > > No prob let me explain: > > > I Aggree on monoatomics center of mass is the atom so (for all x axis: > Ix= 0) > > > > Now I consider the mathematics only not the physics. > > > I suggest that they (Todeschini) are not really computing the "real > physical" PMi on the 3 axis but arbitrary said that for 2D molecules the > 3nd axis PMi is zero. > > > BR > > > > *Dr. Guillaume GODIN* > Principal Scientist > Chemoinformatic & Datamining > Innovation > CORPORATE R&D DIVISION > DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045> > MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039> > Firmenich SA > RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 > > -- > *De :* Chris Earnshaw > *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 < > guillaume.go...@firmenich.com> wrote: > >> reading carefully the Todeschini article, them said that Ic,Ib,Ia are >> determine as max & min values of I other all 3D axis passing throught the >> center of mass! >> > I don't quite understand this comment. The inequality Ia <= Ib <= Ic is > one of the errors in the Todeschini article pointed out by Greg yesterday. > By definition, the Principal Moment of Inertia axes pass through the centre > of mass. > > The "global PM" is never zero (sum of mi*ri*ri) idem for PMi even for >> planar molecule. >> > The global Moment of Inertia is only zero for monatomics. > > >> But When you have a planar molecule, the matrix is no more 3D but 2D! so >> it's normal to consider that the 3nd PM is zero. >> > I really don't understand this - it's simply wrong. The molecule may be 2D > but the three principal moments of inertia are most definitely non-zero for > a planar structure. For a fully symmetrical molecule like benzene the > largest PMI is around the axis perpendicular to the plane of the molecule > and there are two equivalent, smaller, PMIs perpendicular to each other in > the plane of the molecule. For a less symmetrical molecule like > naphthalene, the largest PMI is again around the axis perpendicular to the > plane, the intermediate PMI is along the fusion bond between the rings and > the smallest PMI is around the long axis of the molecule. There's no way it > can be correct to consider the 3rd PMI as zero in any planar molecule - > it's never equal to zero and is only degenerate with the 2nd PMI for fully > symmetric molecules. Only in the special case of a completely linear > molecule (e.g. acetylene, HCN) is the 3rd PMI (along the axis of the > molecule) equal to zero. > > Apologies - I appear to have opened a can of worms here... > > Chris > >> -- >> *De :* Greg Landrum >> *Envoyé :* dimanche 15 janvier 2017 17:42 >> *À :* Guillaume GODIN; RDKit Discuss >> >> *Objet :* Re: [Rdkit-discuss] PMI API >> >> Thanks Guillaume! >> >> On Sun, Jan 15, 2017 at 5:01 PM, Guillaume GODIN < >> guillaume.go...@firmenich.com> wrote: >> >>> Here, Dragon results for the 3 molecules: I've included both Whim and >>> 3D descriptors but I don't have access to PMi! >>> >>> >>> I found the second document in agreement with Peter answer... >>> >>> >>> BR, >>> >>> *Dr. Guillaume GODIN* >>> Principal Scientist >>> Chemoinformatic & Datamining >>> Innovation >>> CORPORATE R&D DIVISION >>> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045> >>> MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039> >>> Firmenich SA >>> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 >>> >>> -- >>> *De :* Peter Gedeck >>> *Envoyé :* dimanche 15 janvier 2017 15:07 >>> *À :* Greg Landrum; RDKit 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 >>> molecule (e.g. C#C) is zero. >>> >>> Best, >>> >>> Peter >>> >>> >>> >>> On Sun, Jan 15,
Re: [Rdkit-discuss] PMI API
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 appreciated. The fact that I picked a seemingly unreliable source for the definitions of those descriptors and that it's turning out to be difficult than I might like to find reliable definitions for some of them is just the way things are. I'll have an updated version checked in (hopefully) in the next couple hours. It would be great if you could take a look at it and let me know if it looks right. -greg -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PMI API
Dear Chris, No prob let me explain: I Aggree on monoatomics center of mass is the atom so (for all x axis: Ix= 0) Now I consider the mathematics only not the physics. I suggest that they (Todeschini) are not really computing the "real physical" PMi on the 3 axis but arbitrary said that for 2D molecules the 3nd axis PMi is zero. BR Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R&D DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Chris Earnshaw 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 mailto:guillaume.go...@firmenich.com>> wrote: reading carefully the Todeschini article, them said that Ic,Ib,Ia are determine as max & min values of I other all 3D axis passing throught the center of mass! I don't quite understand this comment. The inequality Ia <= Ib <= Ic is one of the errors in the Todeschini article pointed out by Greg yesterday. By definition, the Principal Moment of Inertia axes pass through the centre of mass. The "global PM" is never zero (sum of mi*ri*ri) idem for PMi even for planar molecule. The global Moment of Inertia is only zero for monatomics. But When you have a planar molecule, the matrix is no more 3D but 2D! so it's normal to consider that the 3nd PM is zero. I really don't understand this - it's simply wrong. The molecule may be 2D but the three principal moments of inertia are most definitely non-zero for a planar structure. For a fully symmetrical molecule like benzene the largest PMI is around the axis perpendicular to the plane of the molecule and there are two equivalent, smaller, PMIs perpendicular to each other in the plane of the molecule. For a less symmetrical molecule like naphthalene, the largest PMI is again around the axis perpendicular to the plane, the intermediate PMI is along the fusion bond between the rings and the smallest PMI is around the long axis of the molecule. There's no way it can be correct to consider the 3rd PMI as zero in any planar molecule - it's never equal to zero and is only degenerate with the 2nd PMI for fully symmetric molecules. Only in the special case of a completely linear molecule (e.g. acetylene, HCN) is the 3rd PMI (along the axis of the molecule) equal to zero. Apologies - I appear to have opened a can of worms here... Chris De : Greg Landrum mailto: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, Jan 15, 2017 at 5:01 PM, Guillaume GODIN mailto:guillaume.go...@firmenich.com>> wrote: Here, Dragon results for the 3 molecules: I've included both Whim and 3D descriptors but I don't have access to PMi! I found the second document in agreement with Peter answer... BR, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R&D DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8 De : Peter Gedeck mailto:peter.ged...@gmail.com>> Envoyé : dimanche 15 janvier 2017 15:07 À : Greg Landrum; RDKit 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 molecule (e.g. C#C) is zero. Best, Peter On Sun, Jan 15, 2017 at 8:15 AM Greg Landrum mailto:greg.land...@gmail.com>> wrote: Hi Guillaume, I think it this case it's something else. According to the Todeschini article the smallest moment of inertia of a planar molecule like benzene should be zero. The eigenvalues of the inertia matrix for benzene, however, are definitely not zero (and not close enough that it's likely to be round-off error). It would be very nice if you could run the three files I mention through Dragon and let me know what it calculates for those descriptors. -greg _ From: Guillaume GODIN mailto:guillaume.go...@firmenich.com>> Sent: Sunday, January 15, 2017 1:11 PM Subject: RE: [Rdkit-discuss] PMI API To: Greg Landrum mailto:greg.land...@gmail.com>>, RDKit Discuss mailto:rdkit-discuss@lists.sourceforge.net>>, Chris Earnshaw mailto:cgearns...@gmail.com>> Dear Greg, I suspect that it's a precision error or eigen algorithm shift between rdkit c++ & dragon. To obtain good value, I suggest to try to implement a test on the eigen values like i did in gateway.cpp implementation. JacobiSVD getSVD(MatrixXd
Re: [Rdkit-discuss] PMI API
On 16 January 2017 at 06:25, Guillaume GODIN
wrote:
> reading carefully the Todeschini article, them said that Ic,Ib,Ia are
> determine as max & min values of I other all 3D axis passing throught the
> center of mass!
>
I don't quite understand this comment. The inequality Ia <= Ib <= Ic is one
of the errors in the Todeschini article pointed out by Greg yesterday. By
definition, the Principal Moment of Inertia axes pass through the centre of
mass.
The "global PM" is never zero (sum of mi*ri*ri) idem for PMi even for
> planar molecule.
>
The global Moment of Inertia is only zero for monatomics.
> But When you have a planar molecule, the matrix is no more 3D but 2D! so
> it's normal to consider that the 3nd PM is zero.
>
I really don't understand this - it's simply wrong. The molecule may be 2D
but the three principal moments of inertia are most definitely non-zero for
a planar structure. For a fully symmetrical molecule like benzene the
largest PMI is around the axis perpendicular to the plane of the molecule
and there are two equivalent, smaller, PMIs perpendicular to each other in
the plane of the molecule. For a less symmetrical molecule like
naphthalene, the largest PMI is again around the axis perpendicular to the
plane, the intermediate PMI is along the fusion bond between the rings and
the smallest PMI is around the long axis of the molecule. There's no way it
can be correct to consider the 3rd PMI as zero in any planar molecule -
it's never equal to zero and is only degenerate with the 2nd PMI for fully
symmetric molecules. Only in the special case of a completely linear
molecule (e.g. acetylene, HCN) is the 3rd PMI (along the axis of the
molecule) equal to zero.
Apologies - I appear to have opened a can of worms here...
Chris
> --
> *De :* Greg Landrum
> *Envoyé :* dimanche 15 janvier 2017 17:42
> *À :* Guillaume GODIN; RDKit Discuss
>
> *Objet :* Re: [Rdkit-discuss] PMI API
>
> Thanks Guillaume!
>
> On Sun, Jan 15, 2017 at 5:01 PM, Guillaume GODIN <
> guillaume.go...@firmenich.com> wrote:
>
>> Here, Dragon results for the 3 molecules: I've included both Whim and 3D
>> descriptors but I don't have access to PMi!
>>
>>
>> I found the second document in agreement with Peter answer...
>>
>>
>> BR,
>>
>> *Dr. Guillaume GODIN*
>> Principal Scientist
>> Chemoinformatic & Datamining
>> Innovation
>> CORPORATE R&D DIVISION
>> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045>
>> MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039>
>> Firmenich SA
>> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>>
>> --
>> *De :* Peter Gedeck
>> *Envoyé :* dimanche 15 janvier 2017 15:07
>> *À :* Greg Landrum; RDKit 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
>> molecule (e.g. C#C) is zero.
>>
>> Best,
>>
>> Peter
>>
>>
>>
>> On Sun, Jan 15, 2017 at 8:15 AM Greg Landrum
>> wrote:
>>
>>> Hi Guillaume,
>>>
>>> I think it this case it's something else. According to the Todeschini
>>> article the smallest moment of inertia of a planar molecule like benzene
>>> should be zero. The eigenvalues of the inertia matrix for benzene, however,
>>> are definitely not zero (and not close enough that it's likely to be
>>> round-off error).
>>> It would be very nice if you could run the three files I mention through
>>> Dragon and let me know what it calculates for those descriptors.
>>>
>>> -greg
>>>
>>>
>>> _
>>> From: Guillaume GODIN
>>> Sent: Sunday, January 15, 2017 1:11 PM
>>> Subject: RE: [Rdkit-discuss] PMI API
>>> To: Greg Landrum , 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 between
>>> rdkit c++ & dragon.
>>>
>>>
>>> To obtain good value, I suggest to try to implement a test on the eigen
>>> values like i did in gateway.cpp implementation.
>>>
>>>
>>>
>>> JacobiSVD getSVD(MatrixXd A) {
>>>
>>> JacobiSVD mysvd(A, ComputeThinU | ComputeThinV);
>>>
>>> return mysvd;
>>>
>>> }
>>>
>>>
>>> // get the A-1 matrix using
>>>
>>> MatrixXd GetPinv(MatrixXd A){
>>>
>>> JacobiSVD svd = getSVD(A);
>>>
>>> double pinvtoler=1.e-2;// choose your tolerance wisely!
>>>
>>> VectorXd vs=svd.singularValues();
>>>
>>> VectorXd vsinv=svd.singularValues();
>>>
>>>
>>> for (unsignedint i=0; i>>
>>> if ( vs(i) > pinvtoler )
>>>
>>>vsinv(i)=1.0/vs(i);
>>>
>>>else vsinv(i)=0.0;
>>>
>>> }
>>>
>>>
>>> MatrixXd S = vsinv.asDiagonal();
>>>
>>> MatrixXd Ap = svd.matrixV() * S * svd.matrixU().transpose();
>>>
>>> ret
