Dear Jean-Marc, On Mon, Feb 8, 2010 at 6:06 PM, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> wrote: > Hello, > > After a successful installation of RDKit (Ubuntu 9.10, 32 bits) > I am starting to learn to use it. > > I started with $(RDBASE)/Code/Demos/RDKit/GettingStarted/sample.cpp. > "GettingStarted": that's for me ;-) > I wrote a Makefile of my own, being unfamiliar with the use of a Jamfile. > I finally succeeded to built the "sample" executable.
Yes, this is more difficult than it needs to be. I will do an example Makefile that is compatible with the way the new build system sets up the code and put that into svn tomorrow. > Running "sample" led to the following output: > [21:53:30] non-ring atom 3 marked aromatic > terminate called after throwing an instance of 'RDKit::MolSanitizeException' > what(): std::exception > Abandon > > A quick search showed me that the function call to CleanupMolecule() > was responsible of the error message. > What is wrong with this function? > If I comment out its call, everything is OK. I will take a look at that tomorrow as well. > The MinimizeCLI.cpp file in Minimize has a few "mol" instead of "*mol" as > function parameter that prevent it to be compiled right out of the box. Yes, the MinimizeCLI stuff has not been maintained for rather a long time; I'm not surprised that it doesn't work. It really shouldn't be there in the Demo directory any more. I just moved that (along with a couple of other obsolete demos) to the $RDBASE/Code/Demos/RDKit/Basement directory. > > By the way, is there a bibliographic reference for > the 2D coordinates generator? I'm afraid not. -greg ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
