Re: [Rdkit-discuss] RDKit in C++
Hi Leon, Sorry for the slow reply. Greg has just merged in an updated C+ document which will be available in the new release. If you've used the old methods for iterating over atoms, you might want to take a look at that bit at least. It is now vastly simpler. It seems the RMS routines in C++ are still waiting for someone to be stirred enough to do them. I'm not sure they will make your life much faster in any case, as it is an inherently expensive process and the basic comparison of 2 conformers is compiled C++ code wrapped up for Python. What the Python wrapper has that isn't in C++ is just a higher-level function that does all conformers vs all conformers for a molecule. The overhead for those extra loops in Python is unlikely to be huge, I wouldn't think. Best, Dave On Wed, Feb 26, 2020 at 5:41 PM topgunhaides . wrote: > Hey Paolo and David, > > Thanks a lot! > This is probably the most helpful resource I can use. It is great that you > are planning to add new stuff in there and update things. > > One reason for me to transform my python code to c++ is to improve > efficiency. > (need to do a series of RDKit works like embedding confromers, RMS between > confs, Shape Tanimoto distances, etc., with a lot of my own programming > logic) > In addition, profiling my python code showed the RMS (bestrms) step is the > bottleneck, is the C++ version of RMS code coming soon? > > I will keep tracking the changes you make in the near future. Really > appreciate it! > > Best, > Leon > > > > > On Wed, Feb 26, 2020 at 11:17 AM David Cosgrove < > davidacosgrov...@gmail.com> wrote: > >> Hi Leon, >> There is indeed such a thing. It's not as complete as the Python one, as >> it was rather more work than I anticipated. Also, I haven't been keeping >> the examples uptodate, especially the newer ways of iterating over atoms >> and bonds, and the CMakeLists.txt. It should give you some useful pointers, >> however. You can find it here: >> https://github.com/rdkit/rdkit/blob/master/Docs/Book/GettingStartedInC%2B%2B.md, >> which should be in $RDBASE/Docs/Book if you have cloned the repo. The >> examples are in C++Examples in that directory also. >> I will try and find time over the next few weeks to make the examples >> current. Also, underneath $RDBASE/Code there are lots of files called >> test*cpp which are the unit tests for the various parts, and they have >> useful stuff in them as well. >> Cheers, >> Dave >> >> >> On Wed, Feb 26, 2020 at 3:53 PM topgunhaides . >> wrote: >> >>> Hi guys, >>> >>> I noticed that someone asked such question some years ago. >>> Since it is now 2020, do we now have anything like "Getting Started with >>> the RDKit in C++"? >>> >>> I am planning to transfer my RDKit python code to C++. >>> Can anyone give me some resources? I found some, but just in case that I >>> missed important ones. Any suggestions are very welcome. Thanks! >>> >>> Best, >>> Leon >>> >>> >>> ___ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> >> >> -- >> David Cosgrove >> Freelance computational chemistry and chemoinformatics developer >> http://cozchemix.co.uk >> >> -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit in C++
Hey Paolo and David, Thanks a lot! This is probably the most helpful resource I can use. It is great that you are planning to add new stuff in there and update things. One reason for me to transform my python code to c++ is to improve efficiency. (need to do a series of RDKit works like embedding confromers, RMS between confs, Shape Tanimoto distances, etc., with a lot of my own programming logic) In addition, profiling my python code showed the RMS (bestrms) step is the bottleneck, is the C++ version of RMS code coming soon? I will keep tracking the changes you make in the near future. Really appreciate it! Best, Leon On Wed, Feb 26, 2020 at 11:17 AM David Cosgrove wrote: > Hi Leon, > There is indeed such a thing. It's not as complete as the Python one, as > it was rather more work than I anticipated. Also, I haven't been keeping > the examples uptodate, especially the newer ways of iterating over atoms > and bonds, and the CMakeLists.txt. It should give you some useful pointers, > however. You can find it here: > https://github.com/rdkit/rdkit/blob/master/Docs/Book/GettingStartedInC%2B%2B.md, > which should be in $RDBASE/Docs/Book if you have cloned the repo. The > examples are in C++Examples in that directory also. > I will try and find time over the next few weeks to make the examples > current. Also, underneath $RDBASE/Code there are lots of files called > test*cpp which are the unit tests for the various parts, and they have > useful stuff in them as well. > Cheers, > Dave > > > On Wed, Feb 26, 2020 at 3:53 PM topgunhaides . > wrote: > >> Hi guys, >> >> I noticed that someone asked such question some years ago. >> Since it is now 2020, do we now have anything like "Getting Started with >> the RDKit in C++"? >> >> I am planning to transfer my RDKit python code to C++. >> Can anyone give me some resources? I found some, but just in case that I >> missed important ones. Any suggestions are very welcome. Thanks! >> >> Best, >> Leon >> >> >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > > > -- > David Cosgrove > Freelance computational chemistry and chemoinformatics developer > http://cozchemix.co.uk > > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit in C++
Hi Leon, There is indeed such a thing. It's not as complete as the Python one, as it was rather more work than I anticipated. Also, I haven't been keeping the examples uptodate, especially the newer ways of iterating over atoms and bonds, and the CMakeLists.txt. It should give you some useful pointers, however. You can find it here: https://github.com/rdkit/rdkit/blob/master/Docs/Book/GettingStartedInC%2B%2B.md, which should be in $RDBASE/Docs/Book if you have cloned the repo. The examples are in C++Examples in that directory also. I will try and find time over the next few weeks to make the examples current. Also, underneath $RDBASE/Code there are lots of files called test*cpp which are the unit tests for the various parts, and they have useful stuff in them as well. Cheers, Dave On Wed, Feb 26, 2020 at 3:53 PM topgunhaides . wrote: > Hi guys, > > I noticed that someone asked such question some years ago. > Since it is now 2020, do we now have anything like "Getting Started with > the RDKit in C++"? > > I am planning to transfer my RDKit python code to C++. > Can anyone give me some resources? I found some, but just in case that I > missed important ones. Any suggestions are very welcome. Thanks! > > Best, > Leon > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit in C++
Hi Leon, there is nice document produced by David Cosgrove and Greg Landrum: https://github.com/rdkit/rdkit/blob/master/Docs/Book/GettingStartedInC%2B%2B.md RDKit C++ unit tests, RDKit C++ API documentations and headers are also very helpful. Cheers, p. On 26/02/2020 15:51, topgunhaides . wrote: Hi guys, I noticed that someone asked such question some years ago. Since it is now 2020, do we now have anything like "Getting Started with the RDKit in C++"? I am planning to transfer my RDKit python code to C++. Can anyone give me some resources? I found some, but just in case that I missed important ones. Any suggestions are very welcome. Thanks! Best, Leon ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit in C++
Hi guys, I noticed that someone asked such question some years ago. Since it is now 2020, do we now have anything like "Getting Started with the RDKit in C++"? I am planning to transfer my RDKit python code to C++. Can anyone give me some resources? I found some, but just in case that I missed important ones. Any suggestions are very welcome. Thanks! Best, Leon ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
