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Fixed #716 - Libraries *.msl, *.msp - parse mol file (*.MOL)
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156 changes: 156 additions & 0 deletions
156
.../src/org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/misc/ConverterMOL.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,156 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2021 Lablicate GmbH. | ||
| * | ||
| * All rights reserved. This program and the accompanying materials | ||
| * are made available under the terms of the Eclipse Public License v1.0 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Philip Wenig - initial API and implementation | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.amdis.converter.misc; | ||
|
|
||
| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.FileReader; | ||
| import java.io.IOException; | ||
| import java.util.HashMap; | ||
| import java.util.Map; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
|
|
||
| import org.apache.commons.io.FilenameUtils; | ||
| import org.eclipse.chemclipse.logging.core.Logger; | ||
| import org.eclipse.chemclipse.model.cas.CasSupport; | ||
| import org.eclipse.chemclipse.model.identifier.ILibraryInformation; | ||
| import org.eclipse.chemclipse.msd.model.core.IMassSpectra; | ||
| import org.eclipse.chemclipse.msd.model.core.IRegularLibraryMassSpectrum; | ||
| import org.eclipse.chemclipse.msd.model.core.IScanMSD; | ||
|
|
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| public class ConverterMOL { | ||
|
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| private static final Logger logger = Logger.getLogger(ConverterMOL.class); | ||
| // | ||
| private static final String MARKER_END = "M END"; | ||
| private static final Pattern patternCAS = Pattern.compile("(CAS)(\\s+)(rn)(\\s+)(=)(\\s+)((\\d+)(-?)(\\d+)(-?)(\\d+))"); | ||
|
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| public static Map<String, String> convert(File file) { | ||
|
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| Map<String, String> moleculeStructureMap = new HashMap<>(); | ||
| try (BufferedReader bufferedReader = new BufferedReader(new FileReader(file))) { | ||
| /* | ||
| * Header | ||
| */ | ||
| String line = null; | ||
| String name = null; | ||
| StringBuilder builder = new StringBuilder(); | ||
| // | ||
| while((line = bufferedReader.readLine()) != null) { | ||
| if(line.trim().isEmpty()) { | ||
| continue; | ||
| } else if(line.trim().equals(MARKER_END)) { | ||
| if(name != null) { | ||
| moleculeStructureMap.put(name.toUpperCase(), builder.toString().trim()); | ||
| } | ||
| name = null; | ||
| builder = new StringBuilder(); | ||
| } else { | ||
| if(name == null) { | ||
| name = line.trim(); | ||
| } | ||
| builder.append(line); | ||
| builder.append("\n"); | ||
| } | ||
| } | ||
| } catch(IOException e) { | ||
| logger.warn(e); | ||
| } | ||
| // | ||
| return moleculeStructureMap; | ||
| } | ||
|
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||
| /** | ||
| * Converts e.g. the file | ||
| * --- | ||
| * /home/.../library.msl | ||
| * to | ||
| * /home/.../library.mol | ||
| * --- | ||
| * If the file doesn't exist, null is returned. | ||
| * | ||
| * @param file | ||
| * @return File | ||
| */ | ||
| public static File getFileMOL(File file) { | ||
|
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| File fileMOL = null; | ||
| if(file.isFile()) { | ||
| String path = file.getParentFile().getAbsolutePath(); | ||
| String fileBaseName = FilenameUtils.getBaseName(file.getName()); | ||
| // | ||
| fileMOL = new File(path + File.separator + fileBaseName + ".MOL"); | ||
| if(!fileMOL.exists()) { | ||
| fileMOL = new File(path + File.separator + fileBaseName + ".mol"); | ||
| if(!fileMOL.exists()) { | ||
| fileMOL = null; | ||
| } | ||
| } | ||
| } | ||
| // | ||
| return fileMOL; | ||
| } | ||
|
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| public static void transfer(Map<String, String> moleculeStructureMap, IMassSpectra massSpectra) { | ||
|
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| Map<String, String> casNumberMap = new HashMap<>(); | ||
| for(String moleculeStructure : moleculeStructureMap.values()) { | ||
| String casNumber = extractCASNumber(moleculeStructure); | ||
| if(!casNumber.isEmpty()) { | ||
| casNumberMap.put(CasSupport.format(casNumber), moleculeStructure); | ||
| } | ||
| } | ||
| // | ||
| for(IScanMSD massSpectrum : massSpectra.getList()) { | ||
| if(massSpectrum instanceof IRegularLibraryMassSpectrum) { | ||
| IRegularLibraryMassSpectrum libraryMassSpectrum = (IRegularLibraryMassSpectrum)massSpectrum; | ||
| ILibraryInformation libraryInformation = libraryMassSpectrum.getLibraryInformation(); | ||
| /* | ||
| * Get the molecule structure. | ||
| */ | ||
| String moleculeStructure = moleculeStructureMap.get(libraryInformation.getName().toUpperCase()); | ||
| if(moleculeStructure == null) { | ||
| /* | ||
| * Use the CAS# instead. | ||
| */ | ||
| moleculeStructure = casNumberMap.get(CasSupport.format(libraryInformation.getCasNumber())); | ||
| } | ||
| /* | ||
| * Set if not null or empty. | ||
| */ | ||
| if(moleculeStructure != null && !moleculeStructure.isEmpty()) { | ||
| libraryInformation.setMoleculeStructure(moleculeStructure); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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| /** | ||
| * Returns the CAS# or "" if none is available. | ||
| * ... CAS rn = 19906720, ... | ||
| * ... CAS rn = 19906-72-0, ... | ||
| * | ||
| * @return String | ||
| */ | ||
| public static String extractCASNumber(String moleculeStructure) { | ||
|
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| if(moleculeStructure != null && !moleculeStructure.isEmpty()) { | ||
| Matcher matcher = patternCAS.matcher(moleculeStructure); | ||
| if(matcher.find()) { | ||
| return matcher.group(7); | ||
| } | ||
| } | ||
| // | ||
| return ""; | ||
| } | ||
| } |
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42 changes: 42 additions & 0 deletions
42
...org/eclipse/chemclipse/msd/converter/supplier/amdis/converter/misc/ConverterMOL_Test.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| /******************************************************************************* | ||
| * Copyright (c) 2021 Lablicate GmbH. | ||
| * | ||
| * All rights reserved. This program and the accompanying materials | ||
| * are made available under the terms of the Eclipse Public License v1.0 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contributors: | ||
| * Philip Wenig - initial API and implementation | ||
| *******************************************************************************/ | ||
| package org.eclipse.chemclipse.msd.converter.supplier.amdis.converter.misc; | ||
|
|
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| import junit.framework.TestCase; | ||
|
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| public class ConverterMOL_Test extends TestCase { | ||
|
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| public void test1() { | ||
|
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| assertEquals("19906720", ConverterMOL.extractCASNumber(" CAS rn = 19906720, ")); | ||
| } | ||
|
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| public void test2() { | ||
|
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| assertEquals("19906-72-0", ConverterMOL.extractCASNumber(" CAS rn = 19906-72-0, ")); | ||
| } | ||
|
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| public void test3() { | ||
|
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| assertEquals("", ConverterMOL.extractCASNumber("")); | ||
| } | ||
|
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| public void test4() { | ||
|
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| assertEquals("", ConverterMOL.extractCASNumber(null)); | ||
| } | ||
|
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| public void test5() { | ||
|
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| assertEquals("", ConverterMOL.extractCASNumber(" CAS rn = ABC, ")); | ||
| } | ||
| } |