Update to v1.36.3

Bug Fixes * Fixes error in complexity estimation when a single bond cut is not being made (See #20)
vernalis · May 15, 2023 · 909dc55 · 909dc55
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,9 +6,9 @@ The table shows the latest version of the nodes available in each update site fo
 
 | KNIME AP Desktop Version | Vernalis Plugin Version |
 | :------------------------: | :-----------------------: |
-| Nightly | [v1.36.1](#v1361---11-nov-2022) |
-| 4.7* | [v1.36.1](#v1361---11-nov-2022) |
-| 4.6* | [v1.36.1](#v1361---11-nov-2022) |
+| Nightly | [v1.36.3](#v1363---15-may-2023) |
+| 4.7* | [v1.36.3](#v1363---15-may-2023) |
+| 4.6* | [v1.36.3](#v1363---15-may-2023) |
 | 4.5 | [v1.36.1](#v1361---11-nov-2022) |
 | Nightly* | [v1.36.2](#v1362---13-jan-2023) |
 | 4.7* | [v1.36.2](#v1362---13-jan-2023) |
@@ -38,6 +38,13 @@ The table shows the latest version of the nodes available in each update site fo
 
 Back to [ReadMe](README.md)
 
+## v1.36.3 - 15-May-2023
+
+_Bug Fixes_
+* Fixes error in complexity estimation when a single bond cut is not being made (See #20)
+
+Back to [top](#changelog)
+
 ## v1.36.2 - 13-Jan-2023
 
 _Enhancements_

diff --git a/com.vernalis.knime.bio.core/META-INF/MANIFEST.MF b/com.vernalis.knime.bio.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.bio.core;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-Activator: com.vernalis.knime.bio.core.BioCorePlugin
 Bundle-Vendor: %Bundle-Vendor
 Bundle-ClassPath: .

diff --git a/com.vernalis.knime.bio.speedyseq/META-INF/MANIFEST.MF b/com.vernalis.knime.bio.speedyseq/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.bio.speedyseq;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.bio.speedyseq.SpeedySeqNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.chem.core/META-INF/MANIFEST.MF b/com.vernalis.knime.chem.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.chem.core; singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.chem.core.VernalisChemCoreNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.chem.mmp/META-INF/MANIFEST.MF b/com.vernalis.knime.chem.mmp/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.chem.mmp;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/.../com/vernalis/knime/mmp/nodes/fragutil/fragment/abstrct/AbstractMMPFragmentNodeModel.java b/.../com/vernalis/knime/mmp/nodes/fragutil/fragment/abstrct/AbstractMMPFragmentNodeModel.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2017, 2021 Vernalis (R&D) Ltd
+ * Copyright (c) 2017, 2023 Vernalis (R&D) Ltd
  *  This program is free software; you can redistribute it and/or modify it 
  *  under the terms of the GNU General Public License, Version 3, as 
  *  published by the Free Software Foundation.
@@ -139,6 +139,7 @@
  * </p>
  * 
  * @author s.roughley
+ * 
  * @param <T>
  *            The type of the molecule object
  * @param <U>
@@ -524,6 +525,7 @@ protected int countFragmentationColumns() {
 	 * 
 	 * @param spec
 	 *            The incoming data table spec
+	 * 
 	 * @return The 1st output table spec
 	 */
 	protected DataTableSpec createSpec_0(DataTableSpec spec) {
@@ -614,6 +616,7 @@ protected DataTableSpec createSpec_0(DataTableSpec spec) {
 	 * 
 	 * @param dataTableSpec
 	 *            Incoming DTS
+	 * 
 	 * @return DTS with optional fail reason column
 	 */
 	protected DataTableSpec createSpec_1(DataTableSpec dataTableSpec) {
@@ -993,7 +996,9 @@ protected DataCell[] getCellsForFragmentation(DataCell idCell,
 	 * @param logger
 	 * @param verboseLogging
 	 * @param retVal
+	 * 
 	 * @return
+	 * 
 	 * @throws IllegalArgumentException
 	 * @throws CanceledExecutionException
 	 * @throws ClosedFactoryException
@@ -1050,9 +1055,11 @@ protected DataCell[] getCellsForFragmentation(DataCell idCell,
 						fragFactoryHAdded.getMatchingBonds().size();
 			}
 			final int matchingBondCount = fragFactory.getMatchingBonds().size();
-			numberOfFragmentations += matchingBondCount;
-			// Each 1-bond cut can be either way around...
-			numberOfFragmentations *= 2;
+			if (minNumCuts == 1) {
+				numberOfFragmentations += matchingBondCount;
+				// Each 1-bond cut can be either way around...
+				numberOfFragmentations *= 2;
+			}
 			if (minNumCuts <= 2 && maxNumCuts >= 2 && allowTwoCutsToBondValue) {
 				if (m_limitByComplexity.getBooleanValue()) {
 					numberOfFragmentations += matchingBondCount;

diff --git a/com.vernalis.knime.chem.pmi/META-INF/MANIFEST.MF b/com.vernalis.knime.chem.pmi/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.chem.pmi;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.chem.pmi.PmiNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.chem.rdkit/META-INF/MANIFEST.MF b/com.vernalis.knime.chem.rdkit/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.chem.rdkit;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-Vendor: %Bundle-Vendor
 Bundle-ClassPath: .
 Automatic-Module-Name: com.vernalis.knime.chem.rdkit

diff --git a/com.vernalis.knime.chem.speedysmiles/META-INF/MANIFEST.MF b/com.vernalis.knime.chem.speedysmiles/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.chem.speedysmiles;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.chem.speedysmiles.SpeedySmilesNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.core/META-INF/MANIFEST.MF b/com.vernalis.knime.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.core;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.core.VernalisCoreNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.database.core.tests/META-INF/MANIFEST.MF b/com.vernalis.knime.database.core.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.database.core.tests;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-Vendor: %Bundle-Vendor
 Fragment-Host: com.vernalis.knime.database.core;bundle-version="[1.0.0,2.0.0)"
 Bundle-ClassPath: .

diff --git a/com.vernalis.knime.database.core/META-INF/MANIFEST.MF b/com.vernalis.knime.database.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.database.core;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.database.core.DatabaseCorePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.database/META-INF/MANIFEST.MF b/com.vernalis.knime.database/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.database;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.database.VernalisDatabaseConnectorNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.db.tests/META-INF/MANIFEST.MF b/com.vernalis.knime.db.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.db.tests;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-Vendor: %Bundle-Vendor
 Fragment-Host: com.vernalis.knime.db;bundle-version="[1.0.0,2.0.0)"
 Bundle-ClassPath: .

diff --git a/com.vernalis.knime.db/META-INF/MANIFEST.MF b/com.vernalis.knime.db/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.db;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.db.DBNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.feature/feature.xml b/com.vernalis.knime.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="com.vernalis.knime.feature"
       label="Vernalis KNIME Nodes"
-      version="1.36.2.qualifier"
+      version="1.36.3.qualifier"
       provider-name="Vernalis Research Ltd, Cambridge, UK"
       plugin="com.vernalis.knime.core">
 

diff --git a/com.vernalis.knime.fingerprint/META-INF/MANIFEST.MF b/com.vernalis.knime.fingerprint/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.fingerprint;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.fingerprint.SparseToDenseNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.flowcontrol/META-INF/MANIFEST.MF b/com.vernalis.knime.flowcontrol/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.flowcontrol;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.flowcontrol.FlowControlNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.io/META-INF/MANIFEST.MF b/com.vernalis.knime.io/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.io;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.io.MiscIOPlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.jfcplot.core/META-INF/MANIFEST.MF b/com.vernalis.knime.jfcplot.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.jfcplot.core;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.jfcplot.core.VernalisJFreeChartCorePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.misc.gc/META-INF/MANIFEST.MF b/com.vernalis.knime.misc.gc/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.misc.gc;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.misc.gc.RunGarbageCollectorNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.pdbconnector/META-INF/MANIFEST.MF b/com.vernalis.knime.pdbconnector/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.pdbconnector;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Vendor: %Bundle-Vendor
 Require-Bundle: org.knime.workbench.core;bundle-version="[3.0.0,5.0.0)",

diff --git a/com.vernalis.knime.perfmon/META-INF/MANIFEST.MF b/com.vernalis.knime.perfmon/META-INF/MANIFEST.MF
@@ -2,11 +2,12 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.perfmon;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.perfmon.TimingStartNodePlugin
 Bundle-Vendor: %Bundle-Vendor
 Require-Bundle: org.eclipse.core.runtime;bundle-version="[3.11.0,5.0.0)",
+ org.knime.core;bundle-version="[4.4.0,5.0.0)",
  org.knime.workbench.core;bundle-version="[3.0.0,5.0.0)",
  org.knime.workbench.repository;bundle-version="[3.0.0,5.0.0)",
  org.knime.base;bundle-version="[3.0.0,5.0.0)",

diff --git a/com.vernalis.knime.plot.jfreechart/META-INF/MANIFEST.MF b/com.vernalis.knime.plot.jfreechart/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.plot.jfreechart; singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.plot.jfreechart.VernalisJFreeChartNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.testing.core/META-INF/MANIFEST.MF b/com.vernalis.knime.testing.core/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.testing.core;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.testing.VernalisTestingCoreNodePlugin
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime.testing.feature/feature.xml b/com.vernalis.knime.testing.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="com.vernalis.knime.testing.feature"
       label="Vernalis Testing feature"
-      version="1.36.2.qualifier"
+      version="1.36.3.qualifier"
       provider-name="Vernalis">
 
    <description>

diff --git a/com.vernalis.knime.testing.tests/META-INF/MANIFEST.MF b/com.vernalis.knime.testing.tests/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.testing.tests;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-Vendor: %Bundle-Vendor
 Fragment-Host: com.vernalis.knime.testing;bundle-version="[1.0.0,2.0.0)"
 Bundle-ClassPath: .

diff --git a/com.vernalis.knime.testing/META-INF/MANIFEST.MF b/com.vernalis.knime.testing/META-INF/MANIFEST.MF
@@ -2,11 +2,12 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.testing;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Bundle-Activator: com.vernalis.knime.testing.TestingPlugin
 Bundle-Vendor: %Bundle-Vendor
 Require-Bundle: org.eclipse.core.runtime;bundle-version="[3.12.0,5.0.0)",
+ org.knime.core;bundle-version="[4.4.0,5.0.0)",
  org.knime.workbench.core;bundle-version="[3.0.0,5.0.0]",
  org.knime.workbench.repository;bundle-version="[3.0.0,5.0.0]",
  org.knime.base;bundle-version="[3.0.0,5.0.0)",

diff --git a/com.vernalis.knime.ui/META-INF/MANIFEST.MF b/com.vernalis.knime.ui/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime.ui;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Activator: com.vernalis.knime.ui.VernalisUIPluginActivator
 Bundle-Vendor: %Bundle-Vendor

diff --git a/com.vernalis.knime/META-INF/MANIFEST.MF b/com.vernalis.knime/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Bundle-SymbolicName: com.vernalis.knime;singleton:=true
-Bundle-Version: 1.36.2.qualifier
+Bundle-Version: 1.36.3.qualifier
 Bundle-ClassPath: .
 Bundle-Vendor: %Bundle-Vendor
 Require-Bundle: org.knime.workbench.core;bundle-version="[3.0.0,5.0.0)",

diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     <packaging>pom</packaging>
 
     <properties>
-        <revision>1.36.2</revision>
+        <revision>1.36.3</revision>
         <changelist>-SNAPSHOT</changelist>
         <knime.version>4.7</knime.version>
         <tycho.version>2.7.5</tycho.version>