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 what I've managed so far (
https://github.com/DavidACosgrove/rdkit/blob/GetStartedC%2B%2B/Docs/Book/GettingStartedInC%2B%2B.md).
It's pretty basic stuff that you may already be beyond, but there are some
examples and a CMakeLists.txt file that builds them which might be helpful.
It's probably time I tidied it up (having just looked at it to get the link
above, I see there's a typo on the first sentence, for example!) and sent
in an interim Pull Request as for people starting out it might already be
of value.
Cheers,
Dave
On Sun, 8 Jan 2017 at 10:19, 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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