Package org.bmdrc.nmr

Examples of org.bmdrc.nmr.Nmr1dUnit

534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
    private Nmr1dUnit __getPeakInACDFormat(String theFileInformation) {

        String[] theSplitedString = theFileInformation.split(this.TAB_STRING);
        String[] theRangeArray = null;
        Nmr1dUnit thePeak = new Nmr1dUnit();

        if (theSplitedString.length == 6) {
            theRangeArray = theSplitedString[5].substring(1, theSplitedString[5].length() - 1).split(this.SPACE_STRING);
        } else {
            for (int theIndexOfRange = 6; !theSplitedString[theIndexOfRange].contains("["); theIndexOfRange++) {
                theRangeArray = theSplitedString[theIndexOfRange].substring(1, theSplitedString[theIndexOfRange].length() - 1).split(this.SPACE_STRING);
            }
        }

        thePeak.setChemicalShift(Double.parseDouble(theSplitedString[this.CHEMICAL_SHIFT_1D_INDEX_IN_ACD]));
        thePeak.setMinOfRange(Double.parseDouble(theRangeArray[this.MIN_CHEMICAL_SHIFT_1D_IN_ACD]));
        thePeak.setMaxOfRange(Double.parseDouble(theRangeArray[this.MAX_CHEMICAL_SHIFT_1D_IN_ACD]));
        thePeak.setIntensity(Double.parseDouble(theSplitedString[this.INTENSITY_1D_INDEX_IN_ACD]));

        return thePeak;
    }
View Full Code Here
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
        return Integer.toString(this.INCORRECT_ATOM_NUMBER);
    }

    private Nmr1dUnit __generatePeakInformation(String[] thePeakInformationArray, List<String> theExperimentEnvironmentList) {
        Nmr1dUnit thePeak = new Nmr1dUnit();

        thePeak.setChemicalShift(Double.parseDouble(thePeakInformationArray[this.CHEMICAL_SHIFT_INDEX]));
        thePeak.setIntensity(this.__convertIntensityValue(thePeakInformationArray[this.INTENSITY_INDEX]));
        thePeak.setAnnotatedAtomNumber(Integer.parseInt(thePeakInformationArray[this.ANNOTATED_ATOM_NUMBER_INDEX]));
        thePeak.setTemperature(theExperimentEnvironmentList.get(this.TEMPERATURE_INDEX));
        thePeak.setFieldStrength(theExperimentEnvironmentList.get(this.FIELD_STRENGTH_INDEX));
        thePeak.setSolvent(theExperimentEnvironmentList.get(this.SOLVENT_INDEX).trim());

        return thePeak;
    }
View Full Code Here
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
    private int __getIndexOfPeakDistribution(double theChemicalShift) {
        return (int) (theChemicalShift / this.getInterval());
    }

    private void __generateReferenceCorrlationTable() {
        Nmr1dUnit the1dPeak = new Nmr1dUnit();

        this.setReferenceCorrelationTable(new HashMap<String, Nmr1dUnit>());

        the1dPeak.setRange(0.8, 1.0);
        this.setReferenceCorrelationTable().put("PrimaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.2, 1.4);
        this.setReferenceCorrelationTable().put("SecondaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.4, 1.7);
        this.setReferenceCorrelationTable().put("TertiaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.2, 2.5);
        this.setReferenceCorrelationTable().put("AromaticAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.0, 4.0);
        this.setReferenceCorrelationTable().put("AlkylChloride", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.5, 4.0);
        this.setReferenceCorrelationTable().put("AlkylBromide", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.5, 4.0);
        this.setReferenceCorrelationTable().put("AlkylIoidide", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.0, 4.5);
        this.setReferenceCorrelationTable().put("AlkylFluoride", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.9);
        this.setReferenceCorrelationTable().put("Ether", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.9);
        this.setReferenceCorrelationTable().put("EsterROOCH2R", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(0.5, 6.0);
        this.setReferenceCorrelationTable().put("Alchol", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 4.0);
        this.setReferenceCorrelationTable().put("CarbonBoundAlchol", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.1, 2.6);
        this.setReferenceCorrelationTable().put("Ketone", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.1, 2.6);
        this.setReferenceCorrelationTable().put("EsterRCH2COOR", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(9.0, 10.0);
        this.setReferenceCorrelationTable().put("Aldehyde", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.6, 5.0);
        this.setReferenceCorrelationTable().put("Alkene", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(6.0, 9.5);
        this.setReferenceCorrelationTable().put("Benzyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(10.0, 13.0);
        this.setReferenceCorrelationTable().put("Carboxylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.0, 7.7);
        this.setReferenceCorrelationTable().put("Phenyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.0, 5.0);
        this.setReferenceCorrelationTable().put("Amine", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(5.0, 9.0);
        this.setReferenceCorrelationTable().put("Amide", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.4, 3.1);
        this.setReferenceCorrelationTable().put("Alkynyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(5.2, 5.7);
        this.setReferenceCorrelationTable().put("Vinylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.6, 1.9);
        this.setReferenceCorrelationTable().put("Allylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.3);
        this.setReferenceCorrelationTable().put("Methoxy", new Nmr1dUnit(the1dPeak));
    }
View Full Code Here
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
        List<Integer> theSolventIndexList = this.__getSolventIndexList(theMolecule);
        Nmr1dUnitList thePeakList = new Nmr1dUnitList();

        for (String theSpectrumPeak : thePeakInformationArrayInFile) {
            String[] theSplitedInformation = theSpectrumPeak.split(";");
            Nmr1dUnit thePeak = new Nmr1dUnit();

            thePeak.setAnnotatedAtomNumber(Integer.parseInt(theSplitedInformation[this.INDEX_OF_ATOM_NUMBER_IN_NMRSHIFTDB]));
            thePeak.setChemicalShift(Double.parseDouble(theSplitedInformation[this.INDEX_OF_CHEMICAL_SHIFT_IN_NMRSHIFTDB]));
            try {
                thePeak.setSolvent(theSolventList.get(theSolventIndexList.indexOf(theSpectrumNumber)));
            } catch (ArrayIndexOutOfBoundsException e) {
                e.printStackTrace();
                System.err.println(theKey + " " + theSpectrumNumber + " " + theMolecule.getProperty(this.KEY_VALUE_OF_NMRSHIFTDB2_ID).toString());
            }
            thePeakList.addPeak(thePeak);
View Full Code Here
430
431
432
433
434
435
436
437
438
439
440
    private Nmr1dUnitList __getChemicalShiftRangeList(int theTolerence) {
        Nmr1dUnitList theChemicalShiftRangeList = new Nmr1dUnitList();

        for (int di = 0, dEnd = this.getPeakDistributionList().size(); di < dEnd; di++) {
            if (this.getPeakDistributionList().get(di) <= theTolerence && this.getPeakDistributionList().get(di) != 0) {
                Nmr1dUnit theChemicalShiftRange = this.__setChemicalShiftRange(di);

                theChemicalShiftRangeList.addPeak(theChemicalShiftRange);
            }
        }
View Full Code Here
440
441
442
443
444
445
446
447
448
449
450
451
        return theChemicalShiftRangeList;
    }

    private Nmr1dUnit __setChemicalShiftRange(int theIndex) {
        Nmr1dUnit theChemicalShiftRange = new Nmr1dUnit();

        theChemicalShiftRange.setMinOfRange(this.MINIMUM_CHEMICAL_SHIFT + (this.getInterval() * theIndex));
        theChemicalShiftRange.setMaxOfRange(this.MINIMUM_CHEMICAL_SHIFT + (this.getInterval() * (theIndex + 1)));

        return theChemicalShiftRange;
    }
View Full Code Here
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
    public List<FunctionalGroupList> setFunctionalGroupListInMoleculeSet() {
        return itsFunctionalGroupListInMoleculeSet;
    }

    private void __generateReferenceCorrlationTable() {
        Nmr1dUnit the1dPeak = new Nmr1dUnit();

        this.setReferenceCorrelationTable(new HashMap<String, Nmr1dUnit>());

        the1dPeak.setRange(0.8, 1.0);
        this.setReferenceCorrelationTable().put("PrimaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.2, 1.4);
        this.setReferenceCorrelationTable().put("SecondaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.4, 1.7);
        this.setReferenceCorrelationTable().put("TertiaryAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.2, 2.5);
        this.setReferenceCorrelationTable().put("AromaticAlkyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.0, 4.0);
        this.setReferenceCorrelationTable().put("AlkylChloride", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.5, 4.0);
        this.setReferenceCorrelationTable().put("AlkylBromide", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.5, 4.0);
        this.setReferenceCorrelationTable().put("AlkylIoidide", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.0, 4.5);
        this.setReferenceCorrelationTable().put("AlkylFluoride", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.9);
        this.setReferenceCorrelationTable().put("Ether", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.9);
        this.setReferenceCorrelationTable().put("EsterROOCH2R", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(0.5, 6.0);
        this.setReferenceCorrelationTable().put("Alchol", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 4.0);
        this.setReferenceCorrelationTable().put("CarbonBoundAlchol", new Nmr1dUnit(the1dPeak));
       
        the1dPeak.setRange(2.1, 2.6);
        this.setReferenceCorrelationTable().put("Ketone", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(2.1, 2.6);
        this.setReferenceCorrelationTable().put("EsterRCH2COOR", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(9.0, 10.0);
        this.setReferenceCorrelationTable().put("Aldehyde", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.6, 5.0);
        this.setReferenceCorrelationTable().put("Alkene", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(6.0, 9.5);
        this.setReferenceCorrelationTable().put("Benzyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(10.0, 13.0);
        this.setReferenceCorrelationTable().put("Carboxylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(4.0, 7.7);
        this.setReferenceCorrelationTable().put("Phenyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.0, 5.0);
        this.setReferenceCorrelationTable().put("Amine", new Nmr1dUnit(the1dPeak));

        //---------------------------------------------------- Start
        the1dPeak.setRange(1.0, 5.0);
        this.setReferenceCorrelationTable().put("PrimaryAmine", new Nmr1dUnit(the1dPeak));
       
        the1dPeak.setRange(1.0, 5.0);
        this.setReferenceCorrelationTable().put("SecondaryAmine", new Nmr1dUnit(the1dPeak));
        //---------------------------------------------------- End
        the1dPeak.setRange(5.0, 9.0);
        this.setReferenceCorrelationTable().put("Amide", new Nmr1dUnit(the1dPeak));
        //---------------------------------------------------- Start
        the1dPeak.setRange(5.0, 9.0);
        this.setReferenceCorrelationTable().put("Primary_Amide_N", new Nmr1dUnit(the1dPeak));
       
        the1dPeak.setRange(5.0, 9.0);
        this.setReferenceCorrelationTable().put("Secondary_Amide_N", new Nmr1dUnit(the1dPeak));
        //---------------------------------------------------- End
        the1dPeak.setRange(2.4, 3.1);
        this.setReferenceCorrelationTable().put("Alkynyl", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(5.2, 5.7);
        this.setReferenceCorrelationTable().put("Vinylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(1.6, 1.9);
        this.setReferenceCorrelationTable().put("Allylic", new Nmr1dUnit(the1dPeak));

        the1dPeak.setRange(3.3, 3.3);
        this.setReferenceCorrelationTable().put("Methoxy", new Nmr1dUnit(the1dPeak));
    }
View Full Code Here
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
        List<Integer> theSolventIndexList = this.__getSolventIndexList(theMolecule);
        Nmr1dUnitList thePeakList = new Nmr1dUnitList();

        for (String theSpectrumPeak : thePeakInformationArrayInFile) {
            String[] theSplitedInformation = theSpectrumPeak.split(";");
            Nmr1dUnit thePeak = new Nmr1dUnit();

            thePeak.setAnnotatedAtomNumber(Integer.parseInt(theSplitedInformation[this.INDEX_OF_ATOM_NUMBER_IN_NMRSHIFTDB]));
            thePeak.setChemicalShift(Double.parseDouble(theSplitedInformation[this.INDEX_OF_CHEMICAL_SHIFT_IN_NMRSHIFTDB]));
            try {
                thePeak.setSolvent(theSolventList.get(theSolventIndexList.indexOf(theSpectrumNumber)));
            } catch (ArrayIndexOutOfBoundsException e) {
                e.printStackTrace();
                System.err.println(theKey + " " + theSpectrumNumber + " " + theMolecule.getProperty(this.KEY_VALUE_OF_NMRSHIFTDB2_ID).toString());
            }
            thePeakList.addPeak(thePeak);
View Full Code Here
463
464
465
466
467
468
469
470
471
472
473
        return theOutlierMoleculeSet;
    }

    private boolean __isOutlierMolecule(int theMoleculeIndex, String theFunctionalGroup) {
        Nmr1dUnitList theCheckPeakList = this.__getPeakListInMoleculeContainFunctionalGroup(theMoleculeIndex, theFunctionalGroup);
        Nmr1dUnit theShiftRangeInReferenceCorrelationTable = this.getReferenceCorrelationTable().get(theFunctionalGroup);

        for (int li = 0, lEnd = theCheckPeakList.getPeakList().size(); li < lEnd; li++) {
            if (!this.__isShiftInRange(theCheckPeakList.getPeak(li), theFunctionalGroup)) {
                return true;
            }
View Full Code Here
476
477
478
479
480
481
482
483
484
485
486
        return false;
    }

    private boolean __isMatchedMolecule(int theMoleculeIndex, String theFunctionalGroup) {
        Nmr1dUnitList theCheckPeakList = this.__getPeakListInMoleculeContainFunctionalGroup(theMoleculeIndex, theFunctionalGroup);
        Nmr1dUnit theShiftRangeInReferenceCorrelationTable = this.getReferenceCorrelationTable().get(theFunctionalGroup);

        for (int li = 0, lEnd = theCheckPeakList.getPeakList().size(); li < lEnd; li++) {
            if (this.__isShiftInRange(theCheckPeakList.getPeak(li), theFunctionalGroup)) {
                return true;
            }
View Full Code Here
TOP

Related Classes of org.bmdrc.nmr.Nmr1dUnit

  • modify_file.HydrogenQueryGeneratorInNmr2d
  • org.bmdrc.nmr.tool.CorrelationTableManipulator
  • org.bmdrc.nmr.tool.NMRShiftDB
  • org.bmdrc.nmr.tool.PeakDistributionCalculator
    • 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.