Package org.openscience.cdk

Examples of org.openscience.cdk.Molecule

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    private IMolecule itsMolecule;
    private TwoDimensionList<Integer> itsDistanceMatrix;

    public TopologicalDistanceMatrix() {
        this.setMolecule(new Molecule());
        this.setDistanceMatrix(new TwoDimensionList<Integer>());
    }
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        return theMoleculeSet;
    }

    private IMolecule __getChemicalShiftAndMpeoeAndCdeapBySDFormat(Nmr1dUnit thePeak, int theMoleculeIndex) {
        IMolecule theMolecule = new Molecule();
        int theAnnotatedAtomNumber = thePeak.getAnnotatedAtomNumber();

        theMolecule.setProperty(this.CHEMICAL_SHIFT_COLUMN_NAME_IN_RESULT_FILE, thePeak.getChemicalShift());
        theMolecule.setProperty(this.MPEOE_COLUMN_NAME_IN_RESULT_FILE, this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
        theMolecule.setProperty(this.CDEAP_COLUMN_NAME_IN_RESULT_FILE, this.getCDEAPListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));

        return theMolecule;
    }
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        return theMoleculeSet;
    }

    private IMolecule __getHoseCodeDescriptorBySDFormat(Nmr1dUnit thePeak, int theHoseCodeLevel, int theMoleculeIndex) {
        IMolecule theMolecule = new Molecule();
        int theAnnotatedAtomNumber = thePeak.getAnnotatedAtomNumber();

        if (this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber) != this.NOT_CONTAIN_PROPERTY_VALUE
                && !this.getSFEList().get(theMoleculeIndex).equals(this.INCORRECT_VALUE)) {
            HoseCodeDescriptor theHoseCodeDescriptor = new HoseCodeDescriptor(this.getMoleculeSet().getMolecule(theMoleculeIndex), theHoseCodeLevel);

            theMolecule.setProperty(this.CHEMICAL_SHIFT_COLUMN_NAME_IN_RESULT_FILE, thePeak.getChemicalShift());
            theMolecule.setProperty(this.MPEOE_COLUMN_NAME_IN_RESULT_FILE, this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
            theMolecule.setProperty(this.CDEAP_COLUMN_NAME_IN_RESULT_FILE, this.getCDEAPListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
            theMolecule.setProperty(this.SFE_COULUMN_NAME_IN_RESULT_FILE, this.getSFEList().get(theMoleculeIndex));
            theMolecule.setProperties(this.__getHoseCodeDescriptorBySDFormat(this.getMoleculeSet().getMolecule(theMoleculeIndex), theAnnotatedAtomNumber, theHoseCodeLevel));
        }

        return theMolecule;
    }
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        return theMolecule;
    }

    private Map<Object, Object> __getHoseCodeDescriptorBySDFormat(IMolecule theMolecule, int theAnnotatedAtomNumber, int theHoseCodeLevel) {
        HoseCodeDescriptor theHoseCodeDescriptor = new HoseCodeDescriptor(theMolecule, theHoseCodeLevel);
        IMolecule theDataMolecule = new Molecule();

        for (int pi = 0, pEnd = theHoseCodeDescriptor.getHoseCodeNameList().size(); pi < pEnd; pi++) {
            theDataMolecule.setProperty(theHoseCodeDescriptor.getHoseCodeNameList().get(pi), theHoseCodeDescriptor.getHoseCodeValue2dList().get(theAnnotatedAtomNumber).get(pi));
        }

        return theDataMolecule.getProperties();
    }
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    private final int NITROGEN_SYMBOL_INDEX = 14;
    private final int PHOSPHATE_SYMBOL_INDEX = 15;
    private final int SULFUR_SYMBOL_INDEX = 16;

    public HoseCodeDescriptor() {
        this.setMolecule(new Molecule());
        this.setHoseCodeNameList(new ArrayList<String>());
        this.setHoseCodeValue2dList(new TwoDimensionList<Integer>());
        this.setHoseCodeLevel(-1);
    }
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Related Classes of org.openscience.cdk.Molecule

  • org.bmdrc.chemistry.util.DistanceMatrix
  • org.bmdrc.chemistry.util.TopologicalDistanceMatrix
  • org.bmdrc.nmr.tool.HoseCodeDescriptor
  • org.bmdrc.nmr.tool.NMRShiftDB
  • uk.ac.cam.ch.wwmm.oscar3.indexersearcher.LuceneChemicalIndex
  • uk.ac.cam.ch.wwmm.oscar3.resolver.extension.HTTPExtensionNameResolver
  • uk.ac.cam.ch.wwmm.oscar3server.ViewMolServlet
  • uk.ac.cam.ch.wwmm.ptc.experimental.MakeImages
  • uk.ac.cam.ch.wwmm.ptc.experimental.RingDigester
  • uk.ac.cam.ch.wwmm.ptclib.cdk.ConverterToInChI
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