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A couple of minor improvements #96

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Sep 26, 2021
Merged

A couple of minor improvements #96

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2 changes: 1 addition & 1 deletion org.rdkit.knime.feature/feature.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<feature
id="org.rdkit.knime.feature"
label="RDKit Nodes Feature"
version="4.3.0.qualifier"
version="4.3.1.qualifier"
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If you merge this as planned with the RDKit binaries changes, you may just increment the version number together with the binaries change as discussed there. All version numbers should be in sync at the end.

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@greglandrum greglandrum Sep 24, 2021 •
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yeah, these changes were made as part of the RDKit binaries merge, so they are in sync now

provider-name="NIBR"
plugin="org.rdkit.knime.nodes">

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2 changes: 1 addition & 1 deletion org.rdkit.knime.nodes/META-INF/MANIFEST.MF
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Expand Up @@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
Bundle-Name: RDKit Nodes
Bundle-SymbolicName: org.rdkit.knime.nodes;singleton:=true
Automatic-Module-Name: org.rdkit.knime.nodes
Bundle-Version: 4.3.0.qualifier
Bundle-Version: 4.3.1.qualifier
Bundle-Vendor: NIBR
Bundle-RequiredExecutionEnvironment: JavaSE-1.8
Require-Bundle: org.eclipse.ui;bundle-version="[3.109.0,4.0.0)",
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3 changes: 3 additions & 0 deletions org.rdkit.knime.nodes/src/org/rdkit/knime/nodes/highlighting/RDKitHighlightingNodeModel.java
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Expand Up @@ -60,6 +60,7 @@
import org.RDKit.DrawColour;
import org.RDKit.Int_Vect;
import org.RDKit.MolDraw2DSVG;
import org.RDKit.MolDrawOptions;
import org.RDKit.ROMol;
import org.knime.base.data.xml.SvgCell;
import org.knime.base.data.xml.SvgCellFactory;
Expand Down Expand Up @@ -417,6 +418,8 @@ public DataCell[] process(final InputDataInfo[] arrInputDataInfo, final DataRow
}

final MolDraw2DSVG molDrawing = markForCleanup(new MolDraw2DSVG(300, 300), lUniqueWaveId);
MolDrawOptions opts = molDrawing.drawOptions();
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Shouldn't this also be wrapped in markForCleanup(..., lUniqueWaveId) ? There is a chance that it gets cleaned up with its parent object MolDraw2DSVG, but if in doubt (and I usually am, because you cannot look into that type of code) I would always call the delete() function at the end. The cleanup code handles it properly, if marked for cleanup.

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That's a good question, but that object doesn't own any memory of its own... it's just a reference to memory that the MolDraw2DSVG owns, so it should not cause a leak.

opts.setAddStereoAnnotation(true);
molDrawing.drawMolecule(mol, "", ivAtoms, ivBonds, mapRdkitAtomColors, mapRdkitBondColors);
molDrawing.finishDrawing();

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3 changes: 2 additions & 1 deletion org.rdkit.knime.nodes/src/org/rdkit/knime/nodes/preferences/RDKitNodesPreferencePage.java
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Expand Up @@ -54,6 +54,7 @@
import java.lang.reflect.Field;
import java.lang.reflect.Method;

import org.RDKit.RDKFuncs;
import org.eclipse.core.runtime.IConfigurationElement;
import org.eclipse.core.runtime.IExtension;
import org.eclipse.core.runtime.IExtensionPoint;
Expand Down Expand Up @@ -137,7 +138,7 @@ public ImageData getImageData() {

// We use the pref store of the UI plugin
setPreferenceStore(RDKitNodePlugin.getDefault().getPreferenceStore());
setDescription("This section contains sub sections to control preferences for RDKit Nodes.");
setDescription("This section contains sub sections to control preferences for the RDKit Nodes.\nThe nodes are using version "+RDKFuncs.getRdkitVersion()+" of the RDKit backend.");
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Very nice.

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yeah, I think this will be quite useful

}

/** {@inheritDoc} */
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1 change: 1 addition & 0 deletions org.rdkit.knime.types/rdkit-chemsrc/org/rdkit/knime/types/RDKitMolValueRenderer.java
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Expand Up @@ -275,6 +275,7 @@ else if (value instanceof SmartsValue) {
MolDrawOptions opts = molDrawing.drawOptions();
// we've already prepared the molecule appropriately, so don't try again:
opts.setPrepareMolsBeforeDrawing(false);
opts.setAddStereoAnnotation(true);
molDrawing.drawMolecule((ROMol)mol);
molDrawing.finishDrawing();

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