Orbital Development Kit

Orbital Development Kit Egon Willighagen Bioclipse & Proteochemometric Group (Prof. Wikberg) (Until 2010-09-30) Department of Pharmaceutical Biosciences Uppsala University 2010-08-25

Representation Types Background Data Model Quantum Chemistry Examples Detailed, accurate I/O Conclusions Scales badly Chemical Graph Scales OK No electrons 2010-08-25 Bioclipse & Proteochemometric Group -2-

Representation Types Background Data Model Quantum Chemistry Examples Detailed, accurate I/O Conclusions Scales badly Orbital Development Kit Chemical Graph Scales OK No electrons 2010-08-25 Bioclipse & Proteochemometric Group -3-

Orbital Development Kit Background Data Model Why? Examples More in line with how we I/O think about molecules Conclusions Organometallics Stereochemistry at an atomic level Explicit information 2010-08-25 Bioclipse & Proteochemometric Group -4-

Orbital Development Kit Background Data Model Why? Examples More in line with how we I/O think about molecules Conclusions Organometallics Worst of both worlds? Stereochemistry at an atomic level Explicit information 2010-08-25 Bioclipse & Proteochemometric Group -5-

Methane I sp3 hybridization Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -6-

Counting electrons Oxidation states and ﬁlled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -7-

Lone Pairs Oxidation states and ﬁlled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -8-

Atom types: from the CDK Web Ontology Language Background Data Model Examples I/O <at:AtomType rdf:ID="C.minus.sp3"> Conclusions <at:formalCharge>-1</at:formalCharge> <at:hasElement rdf:resource="&elem;C"/> <at:formalNeighbourCount>3</at:formalNeighbourCount> <at:lonePairCount>1</at:lonePairCount> <at:piBondCount>0</at:piBondCount> <at:hybridization rdf:resource="&at;sp3"/> </at:AtomType> 2010-08-25 Bioclipse & Proteochemometric Group -9-

Atom types Osp3.getOrbitalTypes() Background Data Model Examples public List<IOrbitalType> getOrbitalTypes() { I/O List<IOrbitalType> orbitals = Conclusions new ArrayList<IOrbitalType>(); orbitals.add(LonePair.getInstance(Sp3.getInstance())); orbitals.add(LonePair.getInstance(Sp3.getInstance())); orbitals.add(SingleElectron.getInstance(Sp3.getInstance())); orbitals.add(SingleElectron.getInstance(Sp3.getInstance())); return orbitals; } 2010-08-25 Bioclipse & Proteochemometric Group - 10 -

Water Oxidation states and ﬁlled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group - 11 -

Water MoleculeFactory factory = new MoleculeFactory(); Background Data Model IAtom oxygen = factory.addAtom(Osp3.getInstance()); Examples I/O for (int i=1; i<=2; i++) { Conclusions IAtom hydrogen = factory.addAtom(Hs.getInstance()); factory.bind( oxygen.getFreeSingleElectron(Sp3.getInstance()), hydrogen.getFreeSingleElectron(S.getInstance()) ); } IMolecule immutable = factory.getImmutable(); 2010-08-25 Bioclipse & Proteochemometric Group - 12 -

Zeise’s Salt Beyond the Chemical Graph Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group - 15 -

Zeise’s Salt Background IMolecularOrbital piBond = factory.bind( Data Model carbons[0].getFreeSingleElectron(Pz.getInstance()), Examples carbons[1].getFreeSingleElectron(Pz.getInstance()) I/O ); Conclusions IAtom platinum = factory.addAtom(Ptsp.getInstance()); factory.bind( platinum.getFreeEmpty(Dsp.getInstance()), piBond ); 2010-08-25 Bioclipse & Proteochemometric Group - 16 -

I/O: Resource Description Framework Molecules :mol1 a odk:Molecule ; Background odk:hasAtom :atom4 , :atom3 , :atom1 , :atom5 , :atom2 ; Data Model odk:hasOverlap :overlap4 , :overlap1 , :overlap3 , :overlap2 . Examples Atoms I/O :atom3 a odk:Atom ; Conclusions odk:hasAtomType at:Hs ; odk:hasOrbital :orbital6 . Orbitals :orbital8 a odk:Orbital ; odk:hasElectronCount "1" ; odk:hasOrbitalType ot:S . Overlaps :overlap10 a odk:Overlap ; odk:binds :overlap6 , :orbital16 . 2010-08-25 Bioclipse & Proteochemometric Group - 17 -

Conclusions Background Data Model Examples I/O Atom types are expressed in more detail Conclusions Electron counting is explicit We can represent organometallics (De)serialization from/into RDF 2010-08-25 Bioclipse & Proteochemometric Group - 18 -

Whereto? Background Data Model Examples I/O descriptor calculation (QSAR) Conclusions ﬁngerprints (database searching) bridge to the CDK ... 2010-08-25 Bioclipse & Proteochemometric Group - 19 -

The Details Background Data Model Examples http://www.citeulike.org/user/ I/O egonw/tag/papers Conclusions http: //chem-bla-ics.blogspot.com http://egonw.github.com waveto: egon.willighagen@googlewave.com 2010-08-25 Bioclipse & Proteochemometric Group - 20 -

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Orbital Development Kit

by Egon Willighagen

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