Orbital Development Kit
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1 Orbital Development Kit Egon Willighagen Bioclipse & Proteochemometric Group (Prof. Wikberg) (Until ) Department of Pharmaceutical Biosciences Uppsala University
2 Representation Types Quantum Chemistry Detailed, accurate Scales badly Chemical Graph Scales OK No electrons Bioclipse & Proteochemometric Group - 2 -
3 Representation Types Quantum Chemistry Detailed, accurate Scales badly Chemical Graph Scales OK No electrons Orbital Development Kit Bioclipse & Proteochemometric Group - 3 -
4 Orbital Development Kit Why? More in line with how we think about molecules Organometallics Stereochemistry at an atomic level Explicit information Bioclipse & Proteochemometric Group - 4 -
5 Orbital Development Kit Why? More in line with how we think about molecules Organometallics Stereochemistry at an atomic level Explicit information Worst of both worlds? Bioclipse & Proteochemometric Group - 5 -
6 Methane I sp3 hybridization Bioclipse & Proteochemometric Group - 6 -
7 Counting electrons Oxidation states and filled orbitals Bioclipse & Proteochemometric Group - 7 -
8 Lone Pairs Oxidation states and filled orbitals Bioclipse & Proteochemometric Group - 8 -
9 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> Bioclipse & Proteochemometric Group - 9 -
10 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; } Bioclipse & Proteochemometric Group
11 Water Oxidation states and filled orbitals Bioclipse & Proteochemometric Group
12 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(); Bioclipse & Proteochemometric Group
13 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(); Bioclipse & Proteochemometric Group
14 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(); Bioclipse & Proteochemometric Group
15 Zeise s Salt Beyond the Chemical Graph Bioclipse & Proteochemometric Group
16 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 ); Bioclipse & Proteochemometric Group
17 : 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, :orbital Bioclipse & Proteochemometric Group
18 Atom types are expressed in more detail Electron counting is explicit We can represent organometallics (De)serialization from/into RDF Bioclipse & Proteochemometric Group
19 Whereto? descriptor calculation (QSAR) fingerprints (database searching) bridge to the CDK Bioclipse & Proteochemometric Group
20 The Details egonw/tag/papers http: //chem-bla-ics.blogspot.com waveto: Bioclipse & Proteochemometric Group
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