Examples of org.openscience.cdk.interfaces.IMoleculeSet

org.openscience.cdk.interfaces.IMoleculeSet


        return theMoleculeSet;
    }


    private IMoleculeSet __getChemicalShiftAndMpeoeAndCdeapBySDFormat(Nmr1dUnitList thePeakList, int theMoleculeIndex, String theFunctionalGroup) {
        IMoleculeSet theMoleculeSet = new MoleculeSet();
        List<String> theFunctionalGroupList = this.__getFunctionalGroupList(this.getMoleculeSet().getMolecule(theMoleculeIndex));


        for (Nmr1dUnit thePeak : thePeakList.getPeakList()) {
            if (thePeak.getAnnotatedAtomNumber() != this.INCORRECT_ATOM_NUMBER) {
                int theFunctionalGroupIndex = this.__getFunctionalGroupIndex(thePeak.getAnnotatedAtomNumber(), theMoleculeIndex);


                if (theFunctionalGroupList.contains(theFunctionalGroup)) {
                    theMoleculeSet.addMolecule(this.__getChemicalShiftAndMpeoeAndCdeapBySDFormat(thePeak, theMoleculeIndex));
                }
            }
        }


        return theMoleculeSet;

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        return theStringBuilder.toString();
    }


    public IMoleculeSet findMatchedMoleculeForChemicalShiftAndMpeoeAndCdeap(double theChemicalShift, double theMpeoe, double theCdeap) {
        IMoleculeSet theMoleculeSet = new MoleculeSet();


        for (int mi = 0, mEnd = this.getMoleculeSet().getMoleculeCount(); mi < mEnd; mi++) {
            if (this.__isMatchedMoleculeForChemicalShiftAndMpeoeAndCdeap(mi, theChemicalShift, theMpeoe, theCdeap)) {
                theMoleculeSet.addMolecule(this.getMoleculeSet().getMolecule(mi));
            }
        }


        return theMoleculeSet;
    }

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        }
    }


    private void __writeHoseCodeDescriptorBySolventForSDFormat(String theResultDir, String theFunctionalGroup, String theSolvent, int theHoseCodeLevel) throws IOException {
        StringBuilder theResultFilePath = new StringBuilder();
        IMoleculeSet theMoleculeSet = this.__getHoseCodeDescriptorBySolventForSDForamt(theFunctionalGroup, theSolvent, theHoseCodeLevel);


        theResultFilePath.append(theResultDir);


        if (!theResultDir.substring(theResultDir.length() - 1).equals("\\")) {
            theResultFilePath.append(this.BACK_SLASH_STRING);

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        theResultFilePath.append(theFunctionalGroup).append(this.UNDER_BAR).append(theSolvent).append(this.MOLECULE_SUFFIX);
        SDFWriter.writeSDFile(theMoleculeSet, new File(theResultFilePath.toString()));
    }


    private IMoleculeSet __getHoseCodeDescriptorBySolventForSDForamt(String theFunctionalGroup, String theSolvent, int theHoseCodeLevel) {
        IMoleculeSet theMoleculeSet = new MoleculeSet();


        for (int mi = 0, mEnd = this.getHydrogenPeakListByMolecules().size(); mi < mEnd; mi++) {
            if (this.__calculateMolecularWeight(this.getMoleculeSet().getMolecule(mi)) > 200) {
                for (Nmr1dUnitList thePeakList : this.getHydrogenPeakListByMolecules().get(mi)) {
                    theMoleculeSet.add(this.__getHoseCodeDescriptorBySolventForSDForamt(thePeakList, theHoseCodeLevel, theFunctionalGroup, mi, theSolvent));
                }
            }
        }


        return theMoleculeSet;

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        return theMoleculeSet;
    }


    private IMoleculeSet __getHoseCodeDescriptorBySolventForSDForamt(Nmr1dUnitList thePeakList, int theHoseCodeLevel, String theFunctionalGroup, int theMoleculeIndex, String theSolvent) {
        IMoleculeSet theMoleculeSet = new MoleculeSet();
        List<String> theFunctionalGroupList = this.__getFunctionalGroupList(this.getMoleculeSet().getMolecule(theMoleculeIndex));
        NMRShiftDBSolventList theSolventList = new NMRShiftDBSolventList();
        List<Integer> theUsedAtomNumberList = new ArrayList<Integer>();


        for (Nmr1dUnit thePeak : thePeakList.getPeakList()) {
            if (!theSolvent.equals(theSolventList.modifyStandardSolventName(thePeak.getSolvent()))) {
                return new MoleculeSet();
            } else if (thePeak.getAnnotatedAtomNumber() != this.INCORRECT_ATOM_NUMBER && !theUsedAtomNumberList.contains(thePeak.getAnnotatedAtomNumber())) {
                int theFunctionalGroupIndex = this.__getFunctionalGroupIndex(thePeak.getAnnotatedAtomNumber(), theMoleculeIndex);


                if (theFunctionalGroupList.get(theFunctionalGroupIndex).equals(theFunctionalGroup)) {
                    theMoleculeSet.addMolecule(this.__getHoseCodeDescriptorBySDFormat(thePeak, theHoseCodeLevel, theMoleculeIndex));
                    theUsedAtomNumberList.add(thePeak.getAnnotatedAtomNumber());
                }
            }
        }

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        theFileWriter.close();
    }


    public void writeMoleculeFileHavingNumberUnderTolerence(int theTolerence, File theResultFile) {
        Nmr1dUnitList theChemicalShiftRangeList = this.__getChemicalShiftRangeList(theTolerence);
        IMoleculeSet theMoleculeSet = this.__getMoleculeSetHavingNumberUnderTolerenceInPeakDistribution(theChemicalShiftRangeList);


        SDFWriter.writeSDFile(theMoleculeSet, theResultFile);
    }

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        return theChemicalShiftRange;
    }


    private IMoleculeSet __getMoleculeSetHavingNumberUnderTolerenceInPeakDistribution(Nmr1dUnitList theChemicalShiftRangeList) {
        IMoleculeSet theMoleculeSet = new MoleculeSet();


        for (int hi = 0, hEnd = this.getHydrogenChemicalShiftDataInMoleculeSet().size(); hi < hEnd; hi++) {
            if (this.__isMoleculeInRange(theChemicalShiftRangeList, hi)) {
                this.getMoleculeSet().getMolecule(hi).setProperty(this.KEY_VALUE_OF_MOLECULE_IN_TOLERENCE, this.__getPropertyValueInMatchedShift(theChemicalShiftRangeList, hi));
                theMoleculeSet.addMolecule(this.getMoleculeSet().getMolecule(hi));
            }
        }


        return theMoleculeSet;
    }

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        return itsMainFrame;
    }


    public void mergeMoleculeFile(String theInputDir, String theResultFilePath) {
        List<File> theFileList = Module.getFileList(theInputDir);
        IMoleculeSet theResultMoleculeSet = new MoleculeSet();
        int theNumberOfFile = theFileList.size();


        this.setMainFrame().setLogTextArea().append("Merge Molecule File Start!!\n");
        for (File theFile : theFileList) {
            try {
                IMoleculeSet theMoleculeSet = SDFReader.openMoleculeFile(theFile);


                theResultMoleculeSet.addMolecule(theMoleculeSet.getMolecule(0));
            } catch (NullPointerException e) {
                this.setMainFrame().setLogTextArea().append(theFile.toString() + " ---> Error!!\n");
                theNumberOfFile--;
            }
        }

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        theFrame.setInputArea().add(Box.createVerticalStrut(theInputBoxVerticalMargin));
        theFrame.setInputArea().add(theFrame.generateInputBox(new JLabel("Result File : "), new JTextField(20), new JButton("select")));
    }


    public void splitedMoleculeFile(String theMoleculeFilePath, String theResultDir) {
        IMoleculeSet theMoleculeSet = SDFReader.openMoleculeFile(new File(theMoleculeFilePath));
        
        this.setMainFrame().setLogTextArea().append("Split Molecule File Start!!\n");
        if (!theResultDir.substring(theResultDir.length() - 1, theResultDir.length() - 1).equals("\\")) {
            theResultDir = theResultDir + "\\";
        }


        for (int mi = 0, mEnd = theMoleculeSet.getMoleculeCount(); mi < mEnd; mi++) {
            IMoleculeSet theResultMoleculeSet = new MoleculeSet();


            theResultMoleculeSet.addMolecule(theMoleculeSet.getMolecule(mi));
            SDFWriter.writeSDFile(theResultMoleculeSet, new File(theResultDir + String.format("%04d", mi) + ".sdf"));
        }
        this.setMainFrame().setLogTextArea().append("Split Molecule End!!\n");
        this.setMainFrame().setLogTextArea().append("Total Number of File : " + theMoleculeSet.getMoleculeCount() + "\n");
    }

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            theFileWriter.flush();
            theFileWriter.write(theResultString);
            theFileWriter.close();


            IMoleculeSet theMoleculeSet = SDFReader.openMoleculeFile(new File(theResultFilePath.toString()));
            SDFWriter.writeSDFile(theMoleculeSet, new File(theResultFilePath.toString()));
        }


        theFileReader.close();
    }

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Related Classes of org.openscience.cdk.interfaces.IMoleculeSet

modify_file.MassMatcher

modify_file.ModifyClass

modify_file.MoleculeSetFilter

modify_file.TestClass

org.bmdrc.chemistry.tool.HoseCodeGenerator

org.bmdrc.chemistry.tool.MoleculeModifier

org.bmdrc.chemistry.tool.MpeoeAndCdeapCalculator

org.bmdrc.mass.tool.PeakMatcher

org.bmdrc.nmr.tool.CorrelationTableManipulator

org.bmdrc.nmr.tool.NMRShiftDB

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