Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IMoleculeSet

38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
            HoseCodeGenerator.generateHoseCode(theFile.toString(), theResultDir.toString() + theFile.getName(), theLevelOfHoseCode);
        }
    }
   
    public static void generateHoseCode(String theInputFilePath, String theResultFilePath, int theLevelOfHoseCode) {
        IMoleculeSet theMoleculeSet = SDFReader.openMoleculeFile(new File(theInputFilePath));
        IMoleculeSet theResultMoleculeSet = new MoleculeSet();

        for (int mi = 0, mEnd = theMoleculeSet.getMoleculeCount(); mi < mEnd; mi++) {
            try {
                generateFunctionalGroup(theMoleculeSet.getMolecule(mi), theLevelOfHoseCode);
            } catch (CDKException e) {
                continue;
            }
            theResultMoleculeSet.addMolecule(theMoleculeSet.getMolecule(mi));
        }

        SDFWriter.writeSDFile(theResultMoleculeSet, new File(theResultFilePath));
    }
View Full Code Here
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
        final int FIRST_INDEX = 0;
        final String HOSE_CODE_DESCRIPTOR = "HOSE_CODE";
        final String TEMPLATE_FILE = "Template.sdf";
        final String MOLECULE_NAME_DESCRIPTOR = "cdk:Title";

        IMoleculeSet theMoleculeSet = new MoleculeSet();
        String theDescriptorValue = new String();

        Ring_Perception.setAromaticityBond(theMolecule);
        theMoleculeSet.addMolecule(theMolecule);

        for (int li = 1; li <= theLevelOfHoseCode; li++) {
            IMoleculeSet theTemplateMolecule = new MoleculeSet();
            StringBuilder theDescriptorName = new StringBuilder();

            try {
                runProgram(theMoleculeSet, li);
            } catch (Exception ex) {
                StringBuilder theErrorMessage = new StringBuilder();

                theErrorMessage.append(theMolecule.getProperty(MOLECULE_NAME_DESCRIPTOR).toString()).append(" ").append("Error!!");
                JOptionPane.showMessageDialog(null, theErrorMessage.toString(), "Error", JOptionPane.ERROR_MESSAGE);
            }

            theTemplateMolecule = SDFReader.openMoleculeFile(new File(TEMPLATE_FILE));
            theDescriptorName.append(HOSE_CODE_DESCRIPTOR).append("_").append(li);
            theDescriptorValue = theTemplateMolecule.getMolecule(FIRST_INDEX).getProperty(HOSE_CODE_DESCRIPTOR).toString();
            theMolecule.setProperty(theDescriptorName.toString(), theDescriptorValue);
        }
        File theFile = new File(TEMPLATE_FILE);
        theFile.delete();
    }
View Full Code Here
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
        }

        for (int ai = 0, aEnd = theCheckingFunctionalGroupList.size(); ai < aEnd; ai++) {
            String theOutlierFilePath = theResultDir + theCheckingFunctionalGroupList.get(ai) +"_F" + this.SD_FILE_SUFFIX;
            String theMatchedFilePath = theResultDir + theCheckingFunctionalGroupList.get(ai) +"_T" + this.SD_FILE_SUFFIX;
            IMoleculeSet theOutlierMoleculeSet = this.__getOutlierMoleculeSetInOneFunctionalGroup(theCheckingFunctionalGroupList.get(ai));
            IMoleculeSet theMatchedMoleculeSet = this.__getMatchedMoleculeSetInOneFunctionalGroup(theCheckingFunctionalGroupList.get(ai));

            if (!theOutlierMoleculeSet.isEmpty()) {
                List<Double> theMaximumAndMinimumShift = this.__getMaximumAndMinimumShift(theOutlierMoleculeSet);
               
                System.out.println(theCheckingFunctionalGroupList.get(ai) + " : " + theOutlierMoleculeSet.getMoleculeCount() + "\t[Min , Max] : [" +
                        theMaximumAndMinimumShift.get(this.MINIMUM_VALUE_INDEX) + " , " + theMaximumAndMinimumShift.get(this.MAXIMUM_VALUE_INDEX) + "] / Correlation Table : [" +
                        this.getReferenceCorrelationTable().get(theCheckingFunctionalGroupList.get(ai)).getMinOfRange() + " , " +
                        this.getReferenceCorrelationTable().get(theCheckingFunctionalGroupList.get(ai)).getMaxOfRange() + "]");
               
                SDFWriter.writeSDFile(theOutlierMoleculeSet, new File(theOutlierFilePath));
            }
           
            if(!theMatchedMoleculeSet.isEmpty()) {
                SDFWriter.writeSDFile(theMatchedMoleculeSet, new File(theMatchedFilePath));
            }
           
            this.__removeOutlierAndMatchedProperty();
        }
View Full Code Here
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
            }
        }
    }
   
    private IMoleculeSet __getMatchedMoleculeSetInOneFunctionalGroup(String theFunctionalGroup) {
        IMoleculeSet theMatchedMoleculeSet = new MoleculeSet();
       
        for (int mi = 0, mEnd = this.getMoleculeSet().getMoleculeCount(); mi < mEnd; mi++) {
            if (this.__isMatchedMolecule(mi, theFunctionalGroup)) {
                this.__setMatchedProperty(mi, theFunctionalGroup);
                theMatchedMoleculeSet.addMolecule(this.getMoleculeSet().getMolecule(mi));
            }
        }
       
        return theMatchedMoleculeSet;
    }
View Full Code Here
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
       
        return Double.parseDouble(theSplitedString[this.CHEMICAL_SHIFT_INDEX_IN_OUTLIER_PROPERTY].substring(this.STARTING_STRING_VALUE_OF_OUTLIER_PROPERTY_IN_ONE_GROUP.length()));
    }
   
    private IMoleculeSet __getOutlierMoleculeSetInOneFunctionalGroup(String theFunctionalGroup) {
        IMoleculeSet theOutlierMoleculeSet = new MoleculeSet();
       
        for (int mi = 0, mEnd = this.getMoleculeSet().getMoleculeCount(); mi < mEnd; mi++) {
            if (this.__isOutlierMolecule(mi, theFunctionalGroup)) {
                this.__setOutlierProperty(mi, theFunctionalGroup);
                theOutlierMoleculeSet.addMolecule(this.getMoleculeSet().getMolecule(mi));
            }
        }

        return theOutlierMoleculeSet;
    }
View Full Code Here
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
            theFrame.setLogTextArea().append(theMolecule.getProperty(MolecularPropertyCalculator.MOLECULAR_FORMULA_PROPERTY_NAME).toString());
        }
    }

    private static IMoleculeSet __readFolderWithTag(File theDir, String tagPropertyName, String theTag) {
        IMoleculeSet theResultMoleculeSet = new MoleculeSet();
        File[] theFileArray = theDir.listFiles();

        for (File theFile : theFileArray) {
            theResultMoleculeSet.add(SDFReader.openMoleculeFile(theFile));
        }

        for (int mi = 0, mEnd = theResultMoleculeSet.getMoleculeCount(); mi < mEnd; mi++) {
            theResultMoleculeSet.getMolecule(mi).setProperty(tagPropertyName, theTag);
        }

        return theResultMoleculeSet;
    }
View Full Code Here
35
36
37
38
39
40
41
42
43
44
45
46
47
        UrlParser theUrlParser = new UrlParser();
       
        new File(theOutputDir).mkdir();
        for (File theInputMoleculeFile : theInputFolder) {
            File theOutputMoleculeFile = new File(theOutputDir + theInputMoleculeFile.getName());
            IMoleculeSet inputMolSet = SDFReader.openMoleculeFile(theInputMoleculeFile);

            for (IAtomContainer eachMol : inputMolSet.molecules()) {
                List<String> cidList = theUrlParser.getCIDList("\"" + (String) eachMol.getProperty(inchiPropertyName) + "\"[INCHI]");
                for (String cid : cidList) {
                    StringBuilder propertyString = new StringBuilder();
                    for (String activityString : theUrlParser.getPubchemCSV(cid, new ArrayList<String>(Arrays.asList("active", activityName)))) {
                        if (!activityString.contains("Nohitsfor:")) {
View Full Code Here
TOP

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
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.