Dear Marshall, A quick (and partial) reply.
On Mon, Mar 30, 2009 at 7:22 PM, Marshall Levesque <[email protected]> wrote: > Greg- > > Here is how I fixed the nickel and copper (found this later) organomettalic > compounds within 'atomtyper.cpp': > > ######### addAtomChargeFlags ##### > case 28: // Ni > switch(totalValence){ > case 2: > atomKey += "+2"; > break; > default: > if(tolerateChargeMismatch) atomKey += "+2"; > BOOST_LOG(rdErrorLog) << "UFFTYPER: Unrecognized charge state for > atom: "<< atom->getIdx() << std::endl; > } > break; > case 29: // Cu > switch(totalValence){ > case 1: > atomKey += "+1"; > break; > case 2: > atomKey += "+2"; > break; > default: > if(tolerateChargeMismatch) atomKey += "+1"; > BOOST_LOG(rdErrorLog) << "UFFTYPER: Unrecognized charge state for > atom: "<< atom->getIdx() << std::endl; > } > break; > > ####################### > > ######## getAtomLabel ######## > case 28: > atomKey += '4'; > if(atom->getHybridization()!=Atom::SP3D){ > BOOST_LOG(rdWarningLog) << "UFFTYPER: Warning: hybridization > set to Square Planar for atom "<< atom->getIdx() << std::endl; > } > break; > case 29: > atomKey += '3'; > if(atom->getHybridization()!=Atom::SP3){ > BOOST_LOG(rdWarningLog) << "UFFTYPER: Warning: hybridization > set to Square Planar for atom "<< atom->getIdx() << std::endl; > } > break; > ########################## Thanks. I'll have to go through this a bit more and think about it. > > Now I have found a problem with lead tetraoxide (aka minium or Pb3O4) > > http://www.emolecules.com/cgi-bin/more?vid=474486 The problem here goes far, far beyond UFF parameters and hybridization. Pb3O4 is not a molecular species, it forms a continuous crystalline network connected by covalent bonds. In the language of solid-state chemistry, it's an extended system, not a molecule. Pb3O4 isn't a molecular formula per se, it's just telling you the ratio of the components in the crystal. Take a look at the wikipedia page for minium (http://en.wikipedia.org/wiki/Minium) to see a picture of the crystal structure. Basically, you can't represent this substance as a SMILES at all and can't even do a reasonable approximation without including a *lot* of atoms. Even if you could, the distance geometry code and force field in the RDKit aren't likely to be able to do anything sensible with it. > > The initial error was similar to the previous Ni and Cu problems but I have > not found a fix using the same solution strategy: > > [15:46:23] UFFTYPER: Unrecognized atom type: Pb3+3 (0) > [15:46:23] UFFTYPER: Unrecognized charge state for atom: 2 > [15:46:23] UFFTYPER: Unrecognized atom type: Pb3+3 (2) > [15:46:23] UFFTYPER: Unrecognized charge state for atom: 4 > [15:46:23] UFFTYPER: Unrecognized atom type: Pb3+3 (4) > [15:46:23] > > **** > Pre-condition Violation > bad params pointer > Violation occurred on line 21 in file ForceField/UFF/BondStretch.cpp > Failed Expression: end1Params > **** > > If there isn't an easy fix, can you suggest a strategy for preventing RDKit > from terminating when encountering these hybridization errors and just > moving to the next molecule, while making a note of the molecules name to be > logged as an error? Sure, just put the embedding step in a try/except block and catch the failure. > For the Ni and Cu additions to AtomTyper.cpp, you told me to come up with > some test cases in $RDBASE/Code/GraphMol/ForceFieldHelpers/testHelpers.cpp > Do you want me to follow the examples in that file and also submit a bug to > sourceforge.net to connect the test case to? > Please. That would be very helpful. -greg
