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 particularly why the numbers produced by the current
implementation don't appear to match expected values for particular shapes
of molecule, but also the lack of information about the PMI-related
functions in the main RDKit C++ API documentation and the apparently odd
requirement for the -DRDK_BUILD_DESCRIPTORS3D flag (looks more like a cmake
directive) when compiling a program which uses GraphMol/Descriptors3D
functions.
Cheers,
Chris
On 8 January 2017 at 12:13, David Cosgrove <davidacosgrov...@gmail.com>
wrote:
> 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
>>
>>
>> ------------------------------------------------------------
>> ------------------
>>
>> 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
>>
>>
------------------------------------------------------------------------------
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
