Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

I have a fix for this in the conda recipes I can submit, it boils down to something like the following ( setting the CXXFLAGS for c++11 ) if otool -L "$PYROOT/lib/libboost_python.dylib" | grep libc++ ; then FLAGS="-std=c++11 -stdlib=libc++" else FLAGS="-stdlib=libstdc++" fi

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

On Tue, Feb 23, 2016 at 3:50 PM, Paul Emsley wrote: > > This seems to be the relevant difference in the cmake output: > > > > [ 3%] Linking CXX shared library ../../lib/libRDBoost.dylib > Undefined symbols for architecture x86_64: >

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

Hi Greg, I tried to investigate this further with github rdkit but I am as yet unable to configure/cmake it yet on this Mac (something related to boost python has changed) :-/ :-) - will keep poking at it and/or abstracting it... Thanks, Paul. On 19/02/2016 09:19, Greg Landrum wrote: > > >

Re: [Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

Hi Paul, That is indeed very strange behavior and I can't think of what would cause it. I'm not able to reproduce it with either the current github master, the 2015_09_2, or the 2015_03_1 release. Can you please send me a small test program that reproduces the problem? -greg On Wed, Feb 17,

[Rdkit-discuss] Atoms with strange positions/bonds when drawer makes PNG

Dear RDKitters, I have the following test code: std::string smiles="Clc1c1"; RDKit::ROMol *m_local = RDKit::SmilesToMol(smiles); RDDepict::compute2DCoords(*m_local); RDKit::Conformer conf = m_local->getConformer(); WedgeMolBonds(*m_local, ); bool includeStereo = true;