Add enhanced stereochemistry support to SubstructureCounter and RDKit…

…MoleculeSubstructFilter (#89) * version bump * Add enhanced stereo support to SubstructureCounter * Add enhanced stereo support to RDKitMoleculeSubstructFilter
rdkit · Mar 18, 2021 · 5fe11f9 · 5fe11f9
1 parent 575ca0b
commit 5fe11f9
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Showing 21 changed files with 103 additions and 20 deletions.
diff --git a/org.rdkit.knime.bin.linux.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.linux.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit Linux
 Bundle-SymbolicName: org.rdkit.knime.bin.linux.x86_64;singleton:=true
-Bundle-Version: 4.2.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
+Bundle-Version: 4.3.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.3.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=linux)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.bin.macosx.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.macosx.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit MacOSX
 Bundle-SymbolicName: org.rdkit.knime.bin.macosx.x86_64;singleton:=true
-Bundle-Version: 4.2.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
+Bundle-Version: 4.3.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.3.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=macosx)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.bin.win32.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.win32.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit Windows
 Bundle-SymbolicName: org.rdkit.knime.bin.win32.x86_64;singleton:=true
-Bundle-Version: 4.2.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
+Bundle-Version: 4.3.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.3.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=win32)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.binaries.feature/feature.xml b/org.rdkit.knime.binaries.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.binaries.feature"
       label="RDKit Binaries for Java"
-      version="4.2.0.qualifier"
+      version="4.3.0.qualifier"
       provider-name="NIBR">
 
    <description>

diff --git a/org.rdkit.knime.feature/feature.xml b/org.rdkit.knime.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.feature"
       label="RDKit KNIME integration"
-      version="4.2.0.qualifier"
+      version="4.3.0.qualifier"
       provider-name="NIBR"
       plugin="org.rdkit.knime.nodes">
 

diff --git a/org.rdkit.knime.nodes/META-INF/MANIFEST.MF b/org.rdkit.knime.nodes/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes for Knime
 Bundle-SymbolicName: org.rdkit.knime.nodes;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.nodes
-Bundle-Version: 4.2.0.qualifier
+Bundle-Version: 4.3.0.qualifier
 Bundle-Vendor: NIBR
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.eclipse.ui;bundle-version="[3.109.0,4.0.0)",

diff --git a/...org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeDialog.java b/...org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeDialog.java
@@ -102,8 +102,17 @@ protected RDKitMoleculeSubstructFilterNodeDialog() {
 		final DialogComponent compQueryColumn = add(new DialogComponentColumnNameSelection(
 				createQueryColumnNameModel(), "Query Mol column: ", 1,
 				arrClassesQueryType));
-		final DialogComponent compUseChirality = add(new DialogComponentBoolean(createUseChiralityModel(),
+
+
+		final SettingsModelBoolean modelUseChiralityOption = createUseChiralityModel();
+		final DialogComponent compUseChirality = add(new DialogComponentBoolean(modelUseChiralityOption,
 				"Use stereochemistry"));
+		final DialogComponent compUseEnhancedStereo = add(
+				new DialogComponentBoolean(createUseEnhancedStereoModel(modelUseChiralityOption),
+						"Use enhanced stereochemistry when matching"));
+
+
+
 		final SettingsModelEnumeration<MatchingCriteria> modelMatchingCriteria =
 				createMatchingCriteriaModel();
 		final DialogComponent compMatchingCriteria = add(new DialogComponentEnumButtonGroup<MatchingCriteria>(
@@ -136,6 +145,10 @@ protected RDKitMoleculeSubstructFilterNodeDialog() {
 				0, iRow++, LayoutUtils.REMAINDER, 1,
 				LayoutUtils.NONE, LayoutUtils.CENTER, 0.0d, 0.0d,
 				0, 10, 0, 10);
+		LayoutUtils.constrain(panel, compUseEnhancedStereo.getComponentPanel(),
+				0, iRow++, LayoutUtils.REMAINDER, 1,
+				LayoutUtils.NONE, LayoutUtils.CENTER, 0.0d, 0.0d,
+				0, 10, 0, 10);
 		LayoutUtils.constrain(panel, new JLabel("Match:", SwingConstants.RIGHT),
 				0, iRow, 1, 1,
 				LayoutUtils.HORIZONTAL, LayoutUtils.NORTHEAST, 1.0d, 0.0d,
@@ -269,6 +282,32 @@ static final SettingsModelString createNewColumnNameModel() {
 	static final SettingsModelBoolean createUseChiralityModel() {
 		return new SettingsModelBoolean("use_chirality", false);
 	}
+
+	/**
+	 * Creates the settings model to be used to specify the option
+	 * to use enhanced stereo in the matching.
+	 * Added in March 2021.
+	 * 
+	 * @return Settings model for useEnhancedStereo option.
+	 */
+	static final SettingsModelBoolean createUseEnhancedStereoModel(final SettingsModelBoolean modelUseChiralityOption) {
+		final SettingsModelBoolean modelWithDependency = new SettingsModelBoolean("useEnhancedStereo", false);
+
+		// React on any changes
+		modelUseChiralityOption.addChangeListener(new ChangeListener() {
+
+			@Override
+			public void stateChanged(final ChangeEvent e) {
+				// Enable or disable the model
+				modelWithDependency.setEnabled(modelUseChiralityOption.getBooleanValue());
+			}
+		});
+
+		// Enable this model based on the dependent model's state
+		modelWithDependency.setEnabled(modelUseChiralityOption.getBooleanValue());
+
+		return modelWithDependency;
+	}
 
 	/**
 	 * Creates the settings model to be used to specify the option

diff --git a/...org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeFactory.xml b/...org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeFactory.xml
@@ -18,6 +18,7 @@
             <option name="Query Mol column">Select the column from the second input table that contains the query molecules.
                 Acceptable types are SMARTS, SMILES, SDF and RDKit Mol.</option>
             <option name="Use chirality">If this is set, information about stereochemistry will be used in the substructure search.</option>
+            <option name="Use enhanced stereochemistry">If this is set, information about enhanced stereochemistry will be used in the substructure search.</option>
             <option name="Matches">Select the minimum number of patterns that must match for each molecule so that it is
                 included in the first output table</option>
             <option name="New column name for matching substructures">Enter here the name of the new column that will contain

diff --git a/.../org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeModel.java b/.../org/rdkit/knime/nodes/moleculesubstructfilter/RDKitMoleculeSubstructFilterNodeModel.java
@@ -91,6 +91,7 @@
 import org.rdkit.knime.nodes.rdkfingerprint.DefaultFingerprintSettings;
 import org.rdkit.knime.nodes.rdkfingerprint.FingerprintSettings;
 import org.rdkit.knime.nodes.rdkfingerprint.FingerprintType;
+import org.rdkit.knime.nodes.substructfilter.RDKitSubstructFilterNodeDialog;
 import org.rdkit.knime.nodes.substructfilter.RDKitSubstructFilterNodeModel;
 import org.rdkit.knime.types.RDKitAdapterCell;
 import org.rdkit.knime.types.RDKitMolValue;
@@ -193,6 +194,10 @@ public String toString() {
 	protected final SettingsModelBoolean m_modelUseChirality =
 			registerSettings(RDKitMoleculeSubstructFilterNodeDialog.createUseChiralityModel(), true);
 
+	/** Settings model for the option to use enhanced stereo in the match. Added in March 2021. */
+	private final SettingsModelBoolean m_modelUseEnhancedStereo =
+			registerSettings(RDKitMoleculeSubstructFilterNodeDialog.createUseEnhancedStereoModel(m_modelUseChirality), true);
+
 	/** Settings model for the matching criteria. */
 	protected final SettingsModelEnumeration<MatchingCriteria> m_modelMatchingCriteria =
 			registerSettings(RDKitMoleculeSubstructFilterNodeDialog.createMatchingCriteriaModel(), true);
@@ -456,6 +461,7 @@ public DataCell[] process(final InputDataInfo[] arrInputDataInfo, final DataRow
 
 				final SubstructMatchParameters ps = new SubstructMatchParameters();
 				ps.setUseChirality(m_modelUseChirality.getBooleanValue());
+				ps.setUseEnhancedStereo(m_modelUseEnhancedStereo.getBooleanValue());
 
 				for (int i = 0; i < m_arrQueryMols.length; i++) {
 					final ROMol molPattern = m_arrQueryMols[i];

diff --git a/...me.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeDialog.java b/...me.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeDialog.java
@@ -100,9 +100,14 @@ public class SubstructureCounterNodeDialog extends DefaultNodeSettingsPane {
 		super.addDialogComponent(
 				new DialogComponentBoolean(createUniqueMatchesOnlyModel(),
 						"Count unique matches only"));
+		final SettingsModelBoolean modelUseChiralityOption = createUseChiralityModel();
 		super.addDialogComponent(
-				new DialogComponentBoolean(createUseChiralityModel(),
+				new DialogComponentBoolean(modelUseChiralityOption,
 						"Use chirality when matching"));
+		super.addDialogComponent(
+				new DialogComponentBoolean(createUseEnhancedStereoModel(modelUseChiralityOption),
+						"Use enhanced stereochemistry when matching"));
+
 
 		createNewGroup("Output");
 		// Add query name option settings
@@ -177,6 +182,32 @@ static final SettingsModelBoolean createUseChiralityModel() {
 		return new SettingsModelBoolean("useChirality", false);
 	}
 
+	/**
+	 * Creates the settings model to be used to specify the option
+	 * to use enhanced stereo in the matching.
+	 * Added in March 2021.
+	 * 
+	 * @return Settings model for useEnhancedStereo option.
+	 */
+	static final SettingsModelBoolean createUseEnhancedStereoModel(final SettingsModelBoolean modelUseChiralityOption) {
+		final SettingsModelBoolean modelWithDependency = new SettingsModelBoolean("useEnhancedStereo", false);
+
+		// React on any changes
+		modelUseChiralityOption.addChangeListener(new ChangeListener() {
+
+			@Override
+			public void stateChanged(final ChangeEvent e) {
+				// Enable or disable the model
+				modelWithDependency.setEnabled(modelUseChiralityOption.getBooleanValue());
+			}
+		});
+
+		// Enable this model based on the dependent model's state
+		modelWithDependency.setEnabled(modelUseChiralityOption.getBooleanValue());
+
+		return modelWithDependency;
+	}
+
 	/**
 	 * Creates the settings model to be used to specify the option
 	 * to use data of specific input table column as column names

diff --git a/...me.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeFactory.xml b/...me.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeFactory.xml
@@ -20,6 +20,7 @@
         <tab name="Search">
             <option name="Count Unique Matches Only?">This option is selected if user requires unique matches of the query molecule in an input molecule.</option>
             <option name="Use chirality">If this is set, information about stereochemistry will be used in the substructure search.</option>
+            <option name="Use enhanced stereochemistry">If this is set, information about enhanced stereochemistry will be used in the substructure search.</option>
         </tab>
         <tab name="Output">
             <option name="Instead of query molecules use names as result header titles (and tags)">

diff --git a/...ime.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeModel.java b/...ime.nodes/src/org/rdkit/knime/nodes/substructurecounter/SubstructureCounterNodeModel.java
@@ -142,6 +142,10 @@ public class SubstructureCounterNodeModel extends AbstractRDKitCalculatorNodeMod
 	private final SettingsModelBoolean m_modelUseChirality =
 			registerSettings(SubstructureCounterNodeDialog.createUseChiralityModel(), true);
 
+	/** Settings model for the option to use enhanced stereo in the match. Added in March 2021. */
+	private final SettingsModelBoolean m_modelUseEnhancedStereo =
+			registerSettings(SubstructureCounterNodeDialog.createUseEnhancedStereoModel(m_modelUseChirality), true);
+
 	/** Settings model for the option to use a query name column. */
 	private final SettingsModelBoolean m_modelUseQueryNameColumn =
 			registerSettings(SubstructureCounterNodeDialog.createUseQueryNameColumnModel(), true);
@@ -522,6 +526,7 @@ protected AbstractRDKitCellFactory[] createOutputFactories(final int outPort, fi
 
 			final SubstructMatchParameters ps = markForCleanup(new SubstructMatchParameters());
 			ps.setUseChirality(m_modelUseChirality.getBooleanValue());
+    		ps.setUseEnhancedStereo(m_modelUseEnhancedStereo.getBooleanValue());
 			ps.setUniquify(m_modelUniqueMatchesOnly.getBooleanValue());
 
 			// Generate factory
@@ -668,7 +673,7 @@ else if (mol.getNumAtoms() > 0 && mol.getAtomWithIdx(0).hasQuery()) {
 
 				// Or a SMILES (or SMARTS conversion failed)
 				if (strQueryMolString == null) {
-					strQueryMolString = mol.MolToSmiles(true);
+					strQueryMolString = RDKFuncs.MolToCXSmiles(mol);					
 				}
 
 				// Fallback, if SMARTS/SMILES conversion failed

diff --git a/org.rdkit.knime.testing.feature/feature.xml b/org.rdkit.knime.testing.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.testing.feature"
       label="RDKit KNIME JUnit Test"
-      version="4.2.0.qualifier"
+      version="4.3.0.qualifier"
       provider-name="NIBR">
 
    <description>

diff --git a/org.rdkit.knime.testing/META-INF/MANIFEST.MF b/org.rdkit.knime.testing/META-INF/MANIFEST.MF
@@ -3,8 +3,8 @@ Bundle-ManifestVersion: 2
 Bundle-Name: Testing
 Bundle-SymbolicName: org.rdkit.knime.testing;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.testing
-Bundle-Version: 4.2.0.qualifier
-Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.2.0"
+Bundle-Version: 4.3.0.qualifier
+Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.3.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.knime.testing;bundle-version="[3.7.0,5.0.0)",
  org.knime.chem.base;bundle-version="[3.6.0,5.0.0)"

diff --git a/...dkit.knime.testing/regression-tests/zips/Tests for RDKit Molecule Substructure Filter.zip b/...dkit.knime.testing/regression-tests/zips/Tests for RDKit Molecule Substructure Filter.zip
diff --git a/org.rdkit.knime.testing/regression-tests/zips/Tests for Substructure Counter.zip b/org.rdkit.knime.testing/regression-tests/zips/Tests for Substructure Counter.zip
diff --git a/org.rdkit.knime.types/META-INF/MANIFEST.MF b/org.rdkit.knime.types/META-INF/MANIFEST.MF
@@ -21,7 +21,7 @@ Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: rdkit-chem.jar,
  lib/org.RDKit.jar,
  lib/org.RDKitDoc.jar
-Bundle-Version: 4.2.0.qualifier
+Bundle-Version: 4.3.0.qualifier
 Bundle-Name: RDKit Chemistry Type Definition Plugin
 Bundle-Activator: org.rdkit.knime.RDKitTypesPluginActivator
 Bundle-ManifestVersion: 2

diff --git a/org.rdkit.knime.update/feature.xml b/org.rdkit.knime.update/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.update"
       label="RDKit Update Site"
-      version="4.2.0.qualifier">
+      version="4.3.0.qualifier">
 
    <description url="http://www.example.com/description">
       [Enter Feature Description here.]

diff --git a/org.rdkit.knime.wizards.feature/feature.xml b/org.rdkit.knime.wizards.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.wizards.feature"
       label="RDKit KNIME Wizards"
-      version="4.2.0.qualifier"
+      version="4.3.0.qualifier"
       provider-name="NIBR"
       plugin="org.rdkit.knime.wizards">
 

diff --git a/org.rdkit.knime.wizards.samples/META-INF/MANIFEST.MF b/org.rdkit.knime.wizards.samples/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Node Wizards Samples
 Bundle-SymbolicName: org.rdkit.knime.wizards.samples;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.wizards.samples
-Bundle-Version: 4.2.0.qualifier
+Bundle-Version: 4.3.0.qualifier
 Bundle-Activator: org.rdkit.knime.wizards.samples.Activator
 Bundle-Vendor: NIBR
 Require-Bundle: org.knime.base;bundle-version="[3.6.2,5.0.0)",

diff --git a/org.rdkit.knime.wizards/META-INF/MANIFEST.MF b/org.rdkit.knime.wizards/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes Wizards
 Bundle-SymbolicName: org.rdkit.knime.wizards;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.wizards
-Bundle-Version: 4.2.0.qualifier
+Bundle-Version: 4.3.0.qualifier
 Bundle-Activator: org.rdkit.knime.wizards.RDKitNodesWizardsPlugin
 Bundle-Vendor: NIBR
 Require-Bundle: org.knime.base;bundle-version="[3.6.2,5.0.0)",