Package org.openscience.cdk.interfaces

Examples of org.openscience.cdk.interfaces.IMoleculeSet

84
85
86
87
88
89
90
91
92
93
94
95
96
97
    }
  }
 
  private IMolecule getMoleculeStructure(IMolecule inputMol) throws Exception {
    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    IMoleculeSet originalMols = ConnectivityChecker.partitionIntoMolecules(inputMol);
    MoleculeSet mols = new MoleculeSet();
    for(int i=0;i<originalMols.getMoleculeCount();i++) {
      IMolecule mol = originalMols.getMolecule(i);
      sdg.setMolecule(mol);
      //sdg.setMolecule(new Molecule(th.getTemplateAt(6)));
      sdg.setTemplateHandler(th);
      sdg.generateCoordinates();
      mols.addMolecule(sdg.getMolecule());
View Full Code Here
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
    public void setTolerence(double theTolerance) {
        this.itsTolerance = theTolerance;
    }

    public IMoleculeSet matchBetweenMoleculeSetAndPeakList() {
        IMoleculeSet theMoleculeSet = new MoleculeSet();

        for (IAtomContainer theSingleMolecule : this.getMoleculeSet().molecules()) {
            if (this.__ismatchedBetweenMoleculeAndPeakList(theSingleMolecule)) {
                theMoleculeSet.addMolecule((IMolecule) theSingleMolecule);
            }
        }

        return theMoleculeSet;
    }
View Full Code Here
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
        String pklDir = "E:\\FG\\FTICRDATA\\140815";
        ArrayList<String> theBSPropertyNames = new ArrayList<>();
        theBSPropertyNames.add("SciName");
        theBSPropertyNames.add("Biological_Source");

        IMoleculeSet theResultMoleculeSet = new MoleculeSet();
        double theTolerance = 0.0005;
        IMoleculeSet inputMolSet = new MoleculeSet();
       
        inputMolSet.add(ModifyClass.readFolderWithTag(theGinsengMoleculeFolder, "SciName", "Panax ginseng"));
        inputMolSet.add(ModifyClass.readFolderWithTag(theLamMoleculeFolder, "SciName", "Laminaria japonica"));
        inputMolSet.add(ModifyClass.readFolderWithTag(theScutellariaMoleculeFolder, "SciName", "Scutellaria baicalensis"));
        inputMolSet.add(ModifyClass.readFolderWithTag(thePoriaMoleculeFolder, "SciName", "Poria cocos"));
        inputMolSet.add(ModifyClass.readFolderWithTag(theOphiopogonMoleculeFolder, "SciName", "Ophiopogon japonicus"));
       
       
       
       
        for (File[] theInputMoleculeFolder : theFileLists) {
            String theDBSourceText = theInputMoleculeFolder[0].getParent().split("\\\\")[3];
            for (File inputSDF : theInputMoleculeFolder) {
                try {
                    IteratingMDLReader reader = new IteratingMDLReader(new FileInputStream(inputSDF), DefaultChemObjectBuilder.getInstance());
                    while (reader.hasNext()) {
                        inputMolSet.addMolecule((IMolecule) reader.next());
                        //inputMolSet.getAtomContainer(inputMolSet.getMoleculeCount()).setProperty("DBSourceText", theDBSourceText);
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        }
       
       
        /*
         try {
         IteratingMDLReader reader = new IteratingMDLReader(new FileInputStream(theInputMoleculeFile), DefaultChemObjectBuilder.getInstance());
         while (reader.hasNext()) {
         inputMolSet.addMolecule((IMolecule) reader.next());
         }
         } catch (Exception e) {
         e.printStackTrace();
         }
       

         String[] drg = {"Platycodon grandiflorum"};
         String[] sbc = {"Saururus chinensis", "Houttuynia cordata"};
         String[] hso = {"Polygonum multiflorum"};
         */
        //Main.calculateExactMass(inputMolSet, "IDE.MF");
        Module.addHydrogen(inputMolSet, "cdkErrors.txt");
        ModifyClass.setMF(inputMolSet);
        ModifyClass.calculateExactMass(inputMolSet, "Molecular_Formula");
        //Main.calculateExactMass(inputMolSet, "Formula");
        //inputMolSet = Main.getMoleculesWithMuchInfo(inputMolSet);
        //inputMolSet = Main.filterMoleculeByBiologicalSource(inputMolSet, "SciName", drg);
        System.out.println("found " + inputMolSet.getMoleculeCount());
        //inputMolSet = Main.filterMoleculeByBiologicalSource(inputMolSet, "Biological_Source", sbc);
        /*
        for (String[] theBSText : Main.readBScsv(theBSInformationFile)){
            ArrayList<String> theFilterString = new ArrayList<>();
            for (int i = 2; i<theBSText.length; i++){
View Full Code Here
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
        for (IAtomContainer theMolecule : molSet.molecules()) {
            theMolecule.setProperty("Molecular_Formula", MolecularFormulaManipulator.getString(MolecularFormulaManipulator.getMolecularFormula(theMolecule)));
        }
    }
    public static IMoleculeSet readFolderWithTag(File folder, String tagPropertyName, String tag){
        IMoleculeSet resultMol = new MoleculeSet();
        for (File inputSDF : folder.listFiles()) {
                try {
                    IteratingMDLReader reader = new IteratingMDLReader(new FileInputStream(inputSDF), DefaultChemObjectBuilder.getInstance());
                    while (reader.hasNext()) {
                        resultMol.addMolecule((IMolecule) reader.next());
                        //inputMolSet.getAtomContainer(inputMolSet.getMoleculeCount()).setProperty("DBSourceText", theDBSourceText);
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        for (int i =0; i<resultMol.getMoleculeCount(); i++){
            resultMol.getMolecule(i).setProperty(tagPropertyName, tag);
        }
        return resultMol;
    }
View Full Code Here
269
270
271
272
273
274
275
276
277
278
279
280
281
            molSet.getAtomContainer(i).setProperty("exact mass", exactMass);
        }
    }

    public static IMoleculeSet getMoleculesWithMuchInfo(IMoleculeSet molSet) {
        IMoleculeSet resultSet = new MoleculeSet();
        for (IAtomContainer eachMol : molSet.molecules()) {
            if (eachMol.getProperties().keySet().size() > 30) {
                resultSet.addMolecule((IMolecule) eachMol);
            }
        }
        return resultSet;
    }
View Full Code Here
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
        }
        return resultSet;
    }

    public static IMoleculeSet filterMoleculeByBiologicalSource(IMoleculeSet molSet, String BSPropertyName, String[] filterString) {
        IMoleculeSet resultSet = new MoleculeSet();
        for (IAtomContainer eachMol : molSet.molecules()) {
            for (int i = 0; i < filterString.length; i++) {
                if (((String) eachMol.getProperty(BSPropertyName)).toLowerCase().contains(filterString[i].toLowerCase())) {
                    resultSet.addMolecule((IMolecule) eachMol);
                }
            }
        }
        return resultSet;
    }
View Full Code Here
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
        }
        return resultSet;
    }

    public static IMoleculeSet filterMoleculeByBiologicalSource(IMoleculeSet molSet, String BSPropertyName, ArrayList<String> filterString) {
        IMoleculeSet resultSet = new MoleculeSet();
        for (IAtomContainer eachMol : molSet.molecules()) {
            if (eachMol.getProperty(BSPropertyName) != null) {
                for (int i = 0; i < filterString.size(); i++) {
                    if (((String) eachMol.getProperty(BSPropertyName)).toLowerCase().contains(filterString.get(i).toLowerCase())) {
                        resultSet.addMolecule((IMolecule) eachMol);
                    }
                }
            }
        }
        return resultSet;
View Full Code Here
304
305
306
307
308
309
310
311
312
313
314
315
316
            }
        }
        return resultSet;
    }
    public static IMoleculeSet filterMoleculeByBiologicalSource(IMoleculeSet molSet, ArrayList<String> BSPropertyName, ArrayList<String> filterString){
        IMoleculeSet resultSet = new MoleculeSet();
        for (String a : BSPropertyName){
            if (resultSet != null){
                resultSet.add(ModifyClass.filterMoleculeByBiologicalSource(molSet, a, filterString));
            }
        }
        return resultSet;
    }
View Full Code Here
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
        }
        return resultSet;
    }

    public static IMoleculeSet filterMoleculeByStringProperty(IMoleculeSet molSet, String propertyName, String filterString) {
        IMoleculeSet resultSet = new MoleculeSet();
        for (IAtomContainer eachMol : molSet.molecules()) {
            for (int i = 0; i < filterString.length(); i++) {
                if (((String) eachMol.getProperty(propertyName)).toLowerCase().contains(filterString.toLowerCase())) {
                    resultSet.addMolecule((IMolecule) eachMol);
                }
            }
        }
        return resultSet;
    }
View Full Code Here
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
        }
        return resultSet;
    }

    public static IMoleculeSet filterMoleculeByDoubleProperty(IMoleculeSet molSet, String propertyName, Double filterThreshold) {
        IMoleculeSet resultSet = new MoleculeSet();
        for (IAtomContainer eachMol : molSet.molecules()) {
            Boolean isRemaining = false;
            for (String eachString : ((String) eachMol.getProperty(propertyName)).split("\n")) {
                if (Double.parseDouble(eachString) >= filterThreshold) {
                    isRemaining = true;
                }
            }
            if (isRemaining) {
                resultSet.addMolecule((IMolecule) eachMol);
            }
        }
        return resultSet;
    }
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.