Add RDKit renderers for SMILES/SMARTS/MOL/SDF (#85)

greglandrum · web-flow · commit 3a14e5496d1d · 2021-02-12T05:54:21.000+01:00
* version bump

* initial pass at adding an RDKit renderer for mol, SDF, SMILES, and SMARTS
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: 4.1.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.1.0"
+Bundle-Version: 4.2.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
 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: 4.1.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.1.0"
+Bundle-Version: 4.2.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
 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: 4.1.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.1.0"
+Bundle-Version: 4.2.0.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.2.0"
 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="4.1.0.qualifier"
+      version="4.2.0.qualifier"
       provider-name="NIBR">
 
    <description>
@@ -14,7 +14,7 @@
    </copyright>
 
    <license url="http://www.gnu.org/licenses/gpl-3.0.html">
-GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
+      GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007
 
  Copyright (C) 2007 Free Software Foundation, Inc. &lt;https://fsf.org/&gt;
  Everyone is permitted to copy and distribute verbatim copies
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="4.1.0.qualifier"
+      version="4.2.0.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: 4.1.0.qualifier
+Bundle-Version: 4.2.0.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.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="4.1.0.qualifier"
+      version="4.2.0.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: 4.1.0.qualifier
-Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.1.0"
+Bundle-Version: 4.2.0.qualifier
+Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.2.0"
 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/org.rdkit.knime.testing/regression-tests/zips/Tests for Molecule Renderer.zip b/org.rdkit.knime.testing/regression-tests/zips/Tests for Molecule Renderer.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: 4.1.0.qualifier
+Bundle-Version: 4.2.0.qualifier
 Bundle-Name: RDKit Chemistry Type Definition Plugin
 Bundle-Activator: org.rdkit.knime.RDKitTypesPluginActivator
 Bundle-ManifestVersion: 2
diff --git a/org.rdkit.knime.types/plugin.xml b/org.rdkit.knime.types/plugin.xml
@@ -41,6 +41,27 @@
                suggestAsDefault="true">
          </renderer>
       </dataValue>
+      <dataValue
+            valueClass="org.knime.chem.types.SmilesValue">
+         <renderer
+               rendererFactoryClass="org.rdkit.knime.types.RDKitMolValueRenderer$Factory"
+               suggestAsDefault="false">
+         </renderer>
+      </dataValue>
+      <dataValue
+            valueClass="org.knime.chem.types.SdfValue">
+         <renderer
+               rendererFactoryClass="org.rdkit.knime.types.RDKitMolValueRenderer$Factory"
+               suggestAsDefault="false">
+         </renderer>
+      </dataValue>
+      <dataValue
+            valueClass="org.knime.chem.types.SmartsValue">
+         <renderer
+               rendererFactoryClass="org.rdkit.knime.types.RDKitMolValueRenderer$Factory"
+               suggestAsDefault="false">
+         </renderer>
+      </dataValue>
    </extension>
    
    <extension point="org.knime.workbench.ui.startupMessages">
diff --git a/org.rdkit.knime.types/rdkit-chemsrc/org/rdkit/knime/types/RDKitMolValueRenderer.java b/org.rdkit.knime.types/rdkit-chemsrc/org/rdkit/knime/types/RDKitMolValueRenderer.java
@@ -57,7 +57,9 @@
 import java.awt.Graphics2D;
 import java.io.StringReader;
 
+import org.RDKit.GenericRDKitException;
 import org.RDKit.MolDraw2DSVG;
+import org.RDKit.MolDrawOptions;
 import org.RDKit.MolSanitizeException;
 import org.RDKit.RDKFuncs;
 import org.RDKit.ROMol;
@@ -75,6 +77,12 @@
 import org.knime.core.data.renderer.DataValueRenderer;
 import org.w3c.dom.svg.SVGDocument;
 
+import org.knime.chem.types.MolValue;
+import org.knime.chem.types.SdfValue;
+import org.knime.chem.types.SmartsValue;
+import org.knime.chem.types.SmilesValue;
+
+
 /**
  * This a renderer that draws nice 2D depictions of RDKit molecules.
  *
@@ -152,60 +160,125 @@ protected void setValue(final Object value) {
 		m_bIsMissingCell = (value instanceof DataCell && ((DataCell)value).isMissing());
 
 		RDKitMolValue molCell = null;
-
-		// We have an old plain RDKit Mol Value
-		if (value instanceof RDKitMolValue) {
-			molCell = (RDKitMolValue)value;
-		}
-
-		// We have a wrapped RDKit Mol Value (or an error)
-		else if (value instanceof AdapterValue) {
-			final AdapterValue adapter = (AdapterValue)value;
-
-			if (adapter.getAdapterError(RDKitMolValue.class) != null) {
-				m_bIsMissingCell = true;
-				m_strError = adapter.getAdapterError(RDKitMolValue.class).getError();
+		ROMol omol = null;
+		boolean trySanitizing = true;
+		try {
+			// We have an old plain RDKit Mol Value
+			if (value instanceof RDKitMolValue) {
+				molCell = (RDKitMolValue)value;
 			}
+	
+			// We have a wrapped RDKit Mol Value (or an error)
+			else if (value instanceof AdapterValue) {
+				final AdapterValue adapter = (AdapterValue)value;
+	
+				try {
+					if (adapter.getAdapterError(RDKitMolValue.class) != null) {
+						m_bIsMissingCell = true;
+						m_strError = adapter.getAdapterError(RDKitMolValue.class).getError();
+					}
+					else {
+						molCell = adapter.getAdapter(RDKitMolValue.class);
+					}
+				} catch (final IllegalArgumentException ex) {
+					// we land here if there's no adapter in place
+					molCell = null;
+				}
+			}
+			// We just have a missing cell (which might be caused by some error)
 			else {
-				molCell = adapter.getAdapter(RDKitMolValue.class);
+				m_bIsMissingCell = (value instanceof DataCell && ((DataCell)value).isMissing());
+				if (value instanceof MissingCell) {
+					m_strError = ((MissingCell)value).getError();
+				}
 			}
-		}
+		} catch (final Exception ex) {
+			// If conversion fails we set a null value, which will show up as error messgae
+			omol = null;
+			// Logging something here may swamp the log files - not desired.
 
-		// We just have a missing cell (which might be caused by some error)
-		else {
-			m_bIsMissingCell = (value instanceof DataCell && ((DataCell)value).isMissing());
-			if (value instanceof MissingCell) {
-				m_strError = ((MissingCell)value).getError();
-			}
 		}
-
 		if (molCell != null) {
-			// Try to render the cell
 			m_strSmiles = molCell.getSmilesValue();
-			ROMol omol = null;
+			omol = molCell.readMoleculeValue();
+		} else {
+			// see if we have a value that we can understand
+			try {
+				RWMol tmol = null;
+				if (value instanceof SmilesValue) {
+		            String val = ((SmilesValue) value).getSmilesValue();
+		            tmol = RWMol.MolFromSmiles(val,0,false);
+		        }
+				else if (value instanceof SdfValue) {
+		            String val = ((SdfValue) value).getSdfValue();
+		            tmol = RWMol.MolFromMolBlock(val,false);
+		        }
+				else if (value instanceof MolValue) {
+		            String val = ((MolValue) value).getMolValue();
+		            tmol = RWMol.MolFromMolBlock(val,false);
+		        }
+				else if (value instanceof SmartsValue) {
+		            String val = ((SmartsValue) value).getSmartsValue();
+		            tmol = RWMol.MolFromSmarts(val);
+		            trySanitizing=false;
+		        }
+				if(tmol != null) {
+					// save a copy in case something goes badly wrong in the sanitization
+					omol = new ROMol(tmol);
+					if(trySanitizing) {
+						try {
+							RDKFuncs.sanitizeMol(tmol);
+							omol.delete();
+							omol = tmol;
+						} catch (final Exception ex) {
+							trySanitizing=false;					
+							tmol.delete();
+							tmol = null;
+						}
+					}
+					// don't put this in an "else", we want to execute it if sanitization fails above.
+					if(!trySanitizing) {
+						// do a minimal amount of sanitization so that we can draw things properly
+						omol.updatePropertyCache(false);
+						RDKFuncs.symmetrizeSSSR(omol);
+						RDKFuncs.setHybridization(omol);
+						tmol.delete();
+					}
+				}
+			} catch (final Exception ex) {
+				omol = null;
+			}
+		}
+		if(omol != null) {
+			// Try to render the cell
 			final Thread t = Thread.currentThread();
 			final ClassLoader contextClassLoader = t.getContextClassLoader();
 			t.setContextClassLoader(getClass().getClassLoader());
 
 			try {
-				omol = molCell.readMoleculeValue();
-
 				RWMol mol;
 				mol = new RWMol(omol);
-				try {
-					RDKFuncs.prepareMolForDrawing(mol);
-				} catch(final MolSanitizeException ex) {
-					mol.delete();
-					mol = new RWMol(omol);
-					// skip kekulization. If this still fails we throw up our hands
+				if(trySanitizing) {
+					try {
+						RDKFuncs.prepareMolForDrawing(mol);
+					} catch(final MolSanitizeException ex) {
+						mol.delete();
+						mol = new RWMol(omol);
+						// skip kekulization. If this still fails we throw up our hands
+						RDKFuncs.prepareMolForDrawing(mol,false);
+					}
+				} else {
+					// skip kekulization
 					RDKFuncs.prepareMolForDrawing(mol,false);
 				}
 				final MolDraw2DSVG molDrawing = new MolDraw2DSVG(300, 300);
+				MolDrawOptions opts = molDrawing.drawOptions();
+				// we've already prepared the molecule appropriately, so don't try again:
+				opts.setPrepareMolsBeforeDrawing(false);
 				molDrawing.drawMolecule((ROMol)mol);
 				molDrawing.finishDrawing();
 
-				// the svg namespace causes problems with the javascript table (github #29)
-				final String svg = molDrawing.getDrawingText().replaceAll("svg:", "").replaceAll("xmlns:svg=", "xmlns=");
+				final String svg = molDrawing.getDrawingText();
 				if(mol != omol){
 					mol.delete();
 				}
@@ -228,8 +301,7 @@ else if (value instanceof AdapterValue) {
 				// labels to be printed off their places
 				m_svgDocument.getRootElement().removeAttributeNS(
 						"http://www.w3.org/XML/1998/namespace", "space");
-			}
-			catch (final Exception ex) {
+			}catch (final Exception ex) {
 				// If conversion fails we set a null value, which will show up as error messgae
 				m_svgDocument = null;
 				// Logging something here may swam the log files - not desired.
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="4.1.0.qualifier">
+      version="4.2.0.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="4.1.0.qualifier"
+      version="4.2.0.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: 4.1.0.qualifier
+Bundle-Version: 4.2.0.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: 4.1.0.qualifier
+Bundle-Version: 4.2.0.qualifier
 Bundle-Activator: org.rdkit.knime.wizards.RDKitNodesWizardsPlugin
 Bundle-Vendor: NIBR
 Require-Bundle: org.knime.base;bundle-version="[3.6.2,5.0.0)",
