I was wondering what would be the best way in RDKit to represent molecules with a metal complex in SMILES, for instance heme. Apparently different programs use different approaches, CACTVS uses a non-standard notation CC1=C(CCC(O)=O)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(CCC(O)=O)c7C)C(=C(C=C)C6=Cc8n5c(C=C13)c(C=C)c8C)C, some represent coordinate bonds as standard bonds and others use a disconnected notation CC1=C(C2=CC3=NC(=CC4=C(C(=C([N-]4)C=C5C(=C(C(=N5)C=C1[N-]2)C=C)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C=C.[Fe+2]. Will there be any openSMILES standard for this?
MSDchem: http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?FUNCTION=record&ENTITY=CHEM_COMP&PRIMARYKEY=1804&PARENTINDEX=-1&APPLICATION=1 pubChem: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=444098 Adrian
