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Orbital Development Kit


                               Egon Willighagen


Bioclipse & Proteochemometric Group (Prof. Wik...
Representation Types



Background

Data Model      Quantum Chemistry
Examples
                      Detailed, accurate
I/...
Representation Types



Background

Data Model      Quantum Chemistry
Examples
                      Detailed, accurate
I/...
Orbital Development Kit



Background

Data Model      Why?
Examples              More in line with how we
I/O            ...
Orbital Development Kit



Background

Data Model      Why?
Examples              More in line with how we
I/O            ...
Methane I
                sp3 hybridization

Background

Data Model

Examples

I/O

Conclusions




 2010-08-25   Bioclips...
Counting electrons

                Oxidation states and filled orbitals

Background

Data Model

Examples

I/O

Conclusion...
Lone Pairs

                Oxidation states and filled orbitals

Background

Data Model

Examples

I/O

Conclusions




 2...
Atom types: from the CDK


                Web Ontology Language
Background

Data Model

Examples

I/O
                <at...
Atom types


                Osp3.getOrbitalTypes()
Background

Data Model

Examples
                public List<IOrbitalT...
Water

                Oxidation states and filled orbitals

Background

Data Model

Examples

I/O

Conclusions




 2010-0...
Water


                MoleculeFactory factory = new MoleculeFactory();
Background

Data Model      IAtom oxygen = factor...
Water


                MoleculeFactory factory = new MoleculeFactory();
Background

Data Model      IAtom oxygen = factor...
Water


                MoleculeFactory factory = new MoleculeFactory();
Background

Data Model      IAtom oxygen = factor...
Zeise’s Salt

                Beyond the Chemical Graph
Background

Data Model

Examples

I/O

Conclusions




 2010-08-25...
Zeise’s Salt



Background      IMolecularOrbital piBond = factory.bind(
Data Model         carbons[0].getFreeSingleElectr...
I/O: Resource Description Framework

                 Molecules
                :mol1 a odk:Molecule ;
Background        o...
Conclusions



Background

Data Model

Examples

I/O
                      Atom types are expressed in more detail
Conclus...
Whereto?



Background

Data Model

Examples

I/O
                      descriptor calculation (QSAR)
Conclusions         ...
The Details



Background

Data Model

Examples
                       http://www.citeulike.org/user/
I/O
                ...
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Orbital Development Kit

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My ideas presented at ACS 2010 Boston on 'beyond the chemical graph'.

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Transcript of "Orbital Development Kit"

  1. 1. Orbital Development Kit Egon Willighagen Bioclipse & Proteochemometric Group (Prof. Wikberg) (Until 2010-09-30) Department of Pharmaceutical Biosciences Uppsala University 2010-08-25
  2. 2. 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-
  3. 3. 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-
  4. 4. 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-
  5. 5. 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-
  6. 6. Methane I sp3 hybridization Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -6-
  7. 7. Counting electrons Oxidation states and filled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -7-
  8. 8. Lone Pairs Oxidation states and filled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group -8-
  9. 9. 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-
  10. 10. 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 -
  11. 11. Water Oxidation states and filled orbitals Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group - 11 -
  12. 12. 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 -
  13. 13. 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 - 13 -
  14. 14. 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 - 14 -
  15. 15. Zeise’s Salt Beyond the Chemical Graph Background Data Model Examples I/O Conclusions 2010-08-25 Bioclipse & Proteochemometric Group - 15 -
  16. 16. 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 -
  17. 17. 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 -
  18. 18. 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 -
  19. 19. 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 -
  20. 20. 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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