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
compiler directive was documented, e.g. with a comment near the top of
PMI.h, at least until a better solution is in place.
Good to know that the expensive calculation is only done once. Hope it
won't be difficult to sort out the strange PMI & NPR values - please let me
kbow if you need any more information from me.
Chris Earnshaw
On 8 Jan 2017 18:17, "Brian Kelley" <fustiga...@gmail.com> wrote:
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 postponed that we should
probably resurrect. Basically it is an rdkit.h header file that has these
flags built in so you won't have to include them yourself.
----
Brian Kelley
On Jan 8, 2017, at 11:31 AM, Greg Landrum <greg.land...@gmail.com> wrote:
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 documentation, but something seems to have gone wrong when
I ran doxygen. I'll look into this. That documentation is generated from
the header file, so you can just look there:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Descriptors/PMI.h
not that there's a huge amount of documentation available.
W.r.t. efficiency: you do need to call the functions individually, but the
expensive calculation of the moments will only be done once, so it doesn't
end up doing repeated work.
And, finally, on the values themselves: I will have to take a look at that.
-greg
On Sun, Jan 8, 2017 at 11:17 AM, Chris Earnshaw <cgearns...@gmail.com>
wrote:
> 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 available in the main RDKit distrubution I thought I'd
> rewrite my code to use the official version.
>
> Building the new RDKit was no problem, but things went downhill shortly
> after that. There's every chance that I've missed the relevant
> documentation (I hope someone can point me in the right direction if so)
> and done something stupid!
>
> The issues are -
> 1) I can't find any documentation of the C++ API - the only reference to
> PMI in the online RDKit documentation appears to be to the PMI.h file
> 2) Having written a program using the PMI[123] and/or NPR[12] functions, I
> couldn't get it to compile until I added the -DRDK_BUILD_DESCRIPTORS3D
> directive -
> g++ -o sdf_pmi_blob sdf_pmi.cpp -I/packages/rdkit/include/rdkit
> -L/packages/rdkit/lib -lDescriptors -lGraphMol -lFileParsers
> -Wno-deprecated -O2 -DRDK_BUILD_DESCRIPTORS3D
> This seems a bit odd...
> 3) Is it necessary to make separate calls to the individual PMI() and/or
> NPR() functions? Surely this results in duplication of some of the heavier
> calculations? I can't find any equivalent of calcPMIDescriptors() which
> returned a 'Moments' struct containing all the PMI and NPR values in one go.
> 4) The big one! The returned results look very odd. They appear to relate
> more to the dimensions of the molecule than the moments of inertia. For a
> rod-like molecule (dimethylacetylene) I'd expect two large and one small
> PMI (e.g. PMI1: 6.61651 PMI2: 150.434 PMI3: 150.434 NPR1: 0.0439828
> NPR2: 0.999998) but actually get PMI1: 0.061647 PMI2: 0.061652 PMI3:
> 25.3699 NPR1: 0.002430 NPR2: 0.002430.
> For disk-like (benzene) the result should be one large and two medium
> (e.g. PMI1: 89.1448 PMI2: 89.1495 PMI3: 178.294 NPR1: 0.499987 NPR2:
> 0.500013) but get PMI1: 2.37457e-10 PMI2: 11.0844 PMI3: 11.0851 NPR1:
> 2.14213e-11 NPR2: 0.999933.
> Finally for a roughly spherical molecule (neopentane) the NPR values look
> reasonable (no great surprise) but the absolute PMI values may be too
> small: old program - PMI1: 114.795 PMI2: 114.797 PMI3: 114.799
> NPR1: 0.999966 NPR2: 0.999988, new program - PMI1: 6.59466 PMI2:
> 6.59488 PMI3: 6.59531 NPR1: 0.999902 NPR2: 0.999935
>
> As I say, it's entirely likely that I'm doing something stupid here so any
> pointers will be gratefully received. FWIW, the core of my program is -
> mol = MolBlockToMol(ctab, true, false);
> double pmi1 = RDKit::Descriptors::PMI1(*mol);
> double pmi2 = RDKit::Descriptors::PMI2(*mol);
> double pmi3 = RDKit::Descriptors::PMI3(*mol);
> double npr1 = RDKit::Descriptors::NPR1(*mol);
> double npr2 = RDKit::Descriptors::NPR2(*mol);
>
> Thanks for any help!
> Chris
>
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