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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