Cite CDK and OPSIN

openchrom/plugins/net.openchrom.xxd.identifier.supplier.cdk/src/net/openchrom/xxd/identifier/supplier/cdk/settings/IdentifierSettings.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2024 Lablicate GmbH.
+ * Copyright (c) 2014, 2025 Lablicate GmbH.
  * 
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -11,23 +11,35 @@
  *******************************************************************************/
 package net.openchrom.xxd.identifier.supplier.cdk.settings;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
 import org.eclipse.chemclipse.chromatogram.xxd.identifier.settings.IChromatogramIdentifierSettings;
+import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.model.identifier.AbstractIdentifierSettings;
+import org.eclipse.chemclipse.support.literature.LiteratureReference;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 import net.openchrom.xxd.identifier.supplier.cdk.preferences.PreferenceSupplier;
 
 public class IdentifierSettings extends AbstractIdentifierSettings implements IChromatogramIdentifierSettings {
 
+	private static final Logger logger = Logger.getLogger(IdentifierSettings.class);
+
 	@JsonProperty(value = "Allow Radicals", defaultValue = "false")
 	private boolean allowRadicals = PreferenceSupplier.DEF_ALLOW_RADICALS;
+
 	@JsonProperty(value = "Detailed Failure Analysis", defaultValue = "false")
 	private boolean detailedFailureAnalysis = PreferenceSupplier.DEF_DETAILED_FAILURE_ANALYSIS;
+
 	@JsonProperty(value = "Interpret Acids Without The Word Acid", defaultValue = "false")
 	private boolean interpretAcidsWithoutTheWordAcid = PreferenceSupplier.DEF_INTERPRET_ACIDS_WITHOUT_THE_WORD_ACID;
+
 	@JsonProperty(value = "Output Radicals As WildCard Atoms", defaultValue = "false")
 	private boolean outputRadicalsAsWildCardAtoms = PreferenceSupplier.DEF_OUTPUT_RADICALS_AS_WILD_CARD_ATOMS;
+
 	@JsonProperty(value = "Warn Rather Than Fail On Uninterpretable Stereochemistry", defaultValue = "false")
 	private boolean warnRatherThanFailOnUninterpretableStereochemistry = PreferenceSupplier.DEF_WARN_RATHER_THAN_FAIL;
 
@@ -80,4 +92,25 @@ public void setWarnRatherThanFailOnUninterpretableStereochemistry(boolean warnRa
 
 		this.warnRatherThanFailOnUninterpretableStereochemistry = warnRatherThanFailOnUninterpretableStereochemistry;
 	}
+
+	@Override
+	public List<LiteratureReference> getLiteratureReferences() {
+
+		List<LiteratureReference> literatureReferences = new ArrayList<>();
+		literatureReferences.add(createLiteratureReference("ci025584y.ris", "10.1021/ci025584y"));
+		literatureReferences.add(createLiteratureReference("ci100384d.ris", "10.1021/ci100384d"));
+		return literatureReferences;
+	}
+
+	private static LiteratureReference createLiteratureReference(String file, String doi) {
+
+		String content;
+		try {
+			content = new String(IdentifierSettings.class.getResourceAsStream(file).readAllBytes());
+		} catch(IOException | NullPointerException e) {
+			content = doi;
+			logger.warn(e);
+		}
+		return new LiteratureReference(content);
+	}
 }

openchrom/plugins/net.openchrom.xxd.identifier.supplier.cdk/src/net/openchrom/xxd/identifier/supplier/cdk/settings/ci025584y.ris

@@ -0,0 +1,25 @@
+TY  - JOUR
+T1  - The Chemistry Development Kit (CDK):  An Open-Source Java Library for Chemo- and Bioinformatics
+AU  - Steinbeck, Christoph
+AU  - Han, Yongquan
+AU  - Kuhn, Stefan
+AU  - Horlacher, Oliver
+AU  - Luttmann, Edgar
+AU  - Willighagen, Egon
+Y1  - 2003/03/01
+PY  - 2003
+DA  - 2003/03/01
+N1  - doi: 10.1021/ci025584y
+DO  - 10.1021/ci025584y
+T2  - Journal of Chemical Information and Computer Sciences
+JF  - Journal of Chemical Information and Computer Sciences
+JO  - J. Chem. Inf. Comput. Sci.
+SP  - 493
+EP  - 500
+VL  - 43
+IS  - 2
+PB  - American Chemical Society
+SN  - 0095-2338
+M3  - doi: 10.1021/ci025584y
+UR  - https://doi.org/10.1021/ci025584y
+ER  - 

openchrom/plugins/net.openchrom.xxd.identifier.supplier.cdk/src/net/openchrom/xxd/identifier/supplier/cdk/settings/ci100384d.ris

@@ -0,0 +1,23 @@
+TY  - JOUR
+T1  - Chemical Name to Structure: OPSIN, an Open Source Solution
+AU  - Lowe, Daniel M.
+AU  - Corbett, Peter T.
+AU  - Murray-Rust, Peter
+AU  - Glen, Robert C.
+Y1  - 2011/03/28
+PY  - 2011
+DA  - 2011/03/28
+N1  - doi: 10.1021/ci100384d
+DO  - 10.1021/ci100384d
+T2  - Journal of Chemical Information and Modeling
+JF  - Journal of Chemical Information and Modeling
+JO  - J. Chem. Inf. Model.
+SP  - 739
+EP  - 753
+VL  - 51
+IS  - 3
+PB  - American Chemical Society
+SN  - 1549-9596
+M3  - doi: 10.1021/ci100384d
+UR  - https://doi.org/10.1021/ci100384d
+ER  -