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My ideas presented at ACS 2010 Boston on 'beyond the chemical graph'.
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Orbital Development Kit
Egon Willighagen
Bioclipse & Proteochemometric Group (Prof. Wikberg)(Until 2010-09-30)
Department of Pharmaceutical Biosciences
Uppsala University
2010-08-25
Background
Data Model
Examples
I/O
Conclusions
Representation Types
Quantum ChemistryDetailed, accurateScales badly
Chemical GraphScales OKNo electrons
2010-08-25 Bioclipse & Proteochemometric Group - 2 -
Background
Data Model
Examples
I/O
Conclusions
Representation Types
Quantum ChemistryDetailed, accurateScales badly
Chemical GraphScales OKNo electrons
Orbital Development Kit
2010-08-25 Bioclipse & Proteochemometric Group - 3 -
Background
Data Model
Examples
I/O
Conclusions
Orbital Development Kit
Why?More in line with how wethink about moleculesOrganometallicsStereochemistry at anatomic levelExplicit information
2010-08-25 Bioclipse & Proteochemometric Group - 4 -
Background
Data Model
Examples
I/O
Conclusions
Orbital Development Kit
Why?More in line with how wethink about moleculesOrganometallicsStereochemistry at anatomic levelExplicit information
Worst of both worlds?
2010-08-25 Bioclipse & Proteochemometric Group - 5 -
Background
Data Model
Examples
I/O
Conclusions
Methane I
sp3 hybridization
2010-08-25 Bioclipse & Proteochemometric Group - 6 -
Background
Data Model
Examples
I/O
Conclusions
Counting electrons
Oxidation states and filled orbitals
2010-08-25 Bioclipse & Proteochemometric Group - 7 -
Background
Data Model
Examples
I/O
Conclusions
Lone Pairs
Oxidation states and filled orbitals
2010-08-25 Bioclipse & Proteochemometric Group - 8 -
Background
Data Model
Examples
I/O
Conclusions
Atom types: from the CDK
Web Ontology Language
<at:AtomType rdf:ID="C.minus.sp3"><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 -
Background
Data Model
Examples
I/O
Conclusions
Atom types
Osp3.getOrbitalTypes()
public List<IOrbitalType> getOrbitalTypes() {List<IOrbitalType> orbitals =
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 -
Background
Data Model
Examples
I/O
Conclusions
Water
Oxidation states and filled orbitals
2010-08-25 Bioclipse & Proteochemometric Group - 11 -
Background
Data Model
Examples
I/O
Conclusions
Water
MoleculeFactory factory = new MoleculeFactory();
IAtom oxygen = factory.addAtom(Osp3.getInstance());
for (int i=1; i<=2; i++) {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 -
Background
Data Model
Examples
I/O
Conclusions
Water
MoleculeFactory factory = new MoleculeFactory();
IAtom oxygen = factory.addAtom(Osp3.getInstance());
for (int i=1; i<=2; i++) {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 -
Background
Data Model
Examples
I/O
Conclusions
Water
MoleculeFactory factory = new MoleculeFactory();
IAtom oxygen = factory.addAtom(Osp3.getInstance());
for (int i=1; i<=2; i++) {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 -
Background
Data Model
Examples
I/O
Conclusions
Zeise’s Salt
Beyond the Chemical Graph
2010-08-25 Bioclipse & Proteochemometric Group - 15 -
Background
Data Model
Examples
I/O
Conclusions
Zeise’s Salt
IMolecularOrbital piBond = factory.bind(carbons[0].getFreeSingleElectron(Pz.getInstance()),carbons[1].getFreeSingleElectron(Pz.getInstance())
);IAtom platinum = factory.addAtom(Ptsp.getInstance());
factory.bind(platinum.getFreeEmpty(Dsp.getInstance()),piBond
);
2010-08-25 Bioclipse & Proteochemometric Group - 16 -
Background
Data Model
Examples
I/O
Conclusions
I/O: Resource Description Framework
Molecules:mol1 a odk:Molecule ;
odk:hasAtom :atom4 , :atom3 , :atom1 , :atom5 , :atom2 ;odk:hasOverlap :overlap4 , :overlap1 , :overlap3 , :overlap2 .
Atoms:atom3 a odk:Atom ;
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 -
Background
Data Model
Examples
I/O
Conclusions
Conclusions
Atom types are expressed in more detailElectron counting is explicitWe can represent organometallics(De)serialization from/into RDF
2010-08-25 Bioclipse & Proteochemometric Group - 18 -
Background
Data Model
Examples
I/O
Conclusions
Whereto?
descriptor calculation (QSAR)fingerprints (database searching)bridge to the CDK...
2010-08-25 Bioclipse & Proteochemometric Group - 19 -
Background
Data Model
Examples
I/O
Conclusions
The Details
http://www.citeulike.org/user/
egonw/tag/papers
http:
//chem-bla-ics.blogspot.com
http://egonw.github.com
waveto:
2010-08-25 Bioclipse & Proteochemometric Group - 20 -