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| 1 | +/* |
| 2 | + * ------------------------------------------------------------------ |
| 3 | + * This source code, its documentation and all appendant files |
| 4 | + * are protected by copyright law. All rights reserved. |
| 5 | + * |
| 6 | + * Copyright (C) 2021 |
| 7 | + * Novartis Institutes for BioMedical Research |
| 8 | + * |
| 9 | + * |
| 10 | + * This program is free software; you can redistribute it and/or modify |
| 11 | + * it under the terms of the GNU General Public License, Version 3, as |
| 12 | + * published by the Free Software Foundation. |
| 13 | + * |
| 14 | + * This program is distributed in the hope that it will be useful, but |
| 15 | + * WITHOUT ANY WARRANTY; without even the implied warranty of |
| 16 | + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 17 | + * GNU General Public License for more details. |
| 18 | + * |
| 19 | + * You should have received a copy of the GNU General Public License |
| 20 | + * along with this program; if not, see <http://www.gnu.org/licenses>. |
| 21 | + * |
| 22 | + * Additional permission under GNU GPL version 3 section 7: |
| 23 | + * |
| 24 | + * KNIME interoperates with ECLIPSE solely via ECLIPSE's plug-in APIs. |
| 25 | + * Hence, KNIME and ECLIPSE are both independent programs and are not |
| 26 | + * derived from each other. Should, however, the interpretation of the |
| 27 | + * GNU GPL Version 3 ("License") under any applicable laws result in |
| 28 | + * KNIME and ECLIPSE being a combined program, KNIME GMBH herewith grants |
| 29 | + * you the additional permission to use and propagate KNIME together with |
| 30 | + * ECLIPSE with only the license terms in place for ECLIPSE applying to |
| 31 | + * ECLIPSE and the GNU GPL Version 3 applying for KNIME, provided the |
| 32 | + * license terms of ECLIPSE themselves allow for the respective use and |
| 33 | + * propagation of ECLIPSE together with KNIME. |
| 34 | + * |
| 35 | + * Additional permission relating to nodes for KNIME that extend the Node |
| 36 | + * Extension (and in particular that are based on subclasses of NodeModel, |
| 37 | + * NodeDialog, and NodeView) and that only interoperate with KNIME through |
| 38 | + * standard APIs ("Nodes"): |
| 39 | + * Nodes are deemed to be separate and independent programs and to not be |
| 40 | + * covered works. Notwithstanding anything to the contrary in the |
| 41 | + * License, the License does not apply to Nodes, you are not required to |
| 42 | + * license Nodes under the License, and you are granted a license to |
| 43 | + * prepare and propagate Nodes, in each case even if such Nodes are |
| 44 | + * propagated with or for interoperation with KNIME. The owner of a Node |
| 45 | + * may freely choose the license terms applicable to such Node, including |
| 46 | + * when such Node is propagated with or for interoperation with KNIME. |
| 47 | + * --------------------------------------------------------------------- |
| 48 | + */ |
| 49 | +package org.rdkit.knime.nodes.rdkit2svg; |
| 50 | + |
| 51 | +import java.awt.Color; |
| 52 | +import java.awt.Component; |
| 53 | +import java.awt.Dimension; |
| 54 | +import java.awt.event.ActionEvent; |
| 55 | +import java.awt.event.ActionListener; |
| 56 | + |
| 57 | +import javax.swing.BorderFactory; |
| 58 | +import javax.swing.DefaultCellEditor; |
| 59 | +import javax.swing.DefaultListCellRenderer; |
| 60 | +import javax.swing.JComboBox; |
| 61 | +import javax.swing.JLabel; |
| 62 | +import javax.swing.JMenuItem; |
| 63 | +import javax.swing.JPopupMenu; |
| 64 | +import javax.swing.JTable; |
| 65 | +import javax.swing.SwingConstants; |
| 66 | +import javax.swing.table.DefaultTableCellRenderer; |
| 67 | +import javax.swing.table.TableCellEditor; |
| 68 | +import javax.swing.table.TableCellRenderer; |
| 69 | + |
| 70 | +import org.RDKit.EmbedParameters; |
| 71 | +import org.RDKit.MolDrawOptions; |
| 72 | +import org.RDKit.RDKFuncs; |
| 73 | +import org.knime.base.data.aggregation.dialogutil.DataColumnSpecTableCellRenderer; |
| 74 | +import org.knime.core.data.DataColumnSpec; |
| 75 | +import org.knime.core.data.DataTableSpec; |
| 76 | +import org.knime.core.data.IntValue; |
| 77 | +import org.knime.core.data.LongValue; |
| 78 | +import org.knime.core.node.NodeSettingsRO; |
| 79 | +import org.knime.core.node.NotConfigurableException; |
| 80 | +import org.knime.core.node.defaultnodesettings.DefaultNodeSettingsPane; |
| 81 | +import org.knime.core.node.defaultnodesettings.DialogComponentBoolean; |
| 82 | +import org.knime.core.node.defaultnodesettings.DialogComponentButton; |
| 83 | +import org.knime.core.node.defaultnodesettings.DialogComponentDoubleRange; |
| 84 | +import org.knime.core.node.defaultnodesettings.DialogComponentLabel; |
| 85 | +import org.knime.core.node.defaultnodesettings.DialogComponentNumber; |
| 86 | +import org.knime.core.node.defaultnodesettings.DialogComponentString; |
| 87 | +import org.knime.core.node.defaultnodesettings.SettingsModelBoolean; |
| 88 | +import org.knime.core.node.defaultnodesettings.SettingsModelDouble; |
| 89 | +import org.knime.core.node.defaultnodesettings.SettingsModelDoubleBounded; |
| 90 | +import org.knime.core.node.defaultnodesettings.SettingsModelInteger; |
| 91 | +import org.knime.core.node.defaultnodesettings.SettingsModelIntegerBounded; |
| 92 | +import org.knime.core.node.defaultnodesettings.SettingsModelString; |
| 93 | +import org.knime.core.node.util.ColumnFilter; |
| 94 | +import org.knime.core.node.util.ColumnSelectionPanel; |
| 95 | +import org.rdkit.knime.nodes.highlighting.HighlightingDefinition.Type; |
| 96 | +import org.rdkit.knime.types.RDKitMolValue; |
| 97 | +import org.rdkit.knime.util.DialogComponentColumnNameSelection; |
| 98 | +import org.rdkit.knime.util.DialogComponentSeparator; |
| 99 | +import org.rdkit.knime.util.DialogComponentTable; |
| 100 | +import org.rdkit.knime.util.LayoutUtils; |
| 101 | +import org.rdkit.knime.util.TableCellAction; |
| 102 | +import org.rdkit.knime.util.TableColorCellEditor; |
| 103 | + |
| 104 | +/** |
| 105 | + * <code>NodeDialog</code> for the "RDKit2SVG" Node. Creates a SVG column |
| 106 | + * showing a molecule. |
| 107 | + * |
| 108 | + * This node dialog derives from {@link DefaultNodeSettingsPane} which allows |
| 109 | + * creation of a simple dialog with standard components. If you need a more |
| 110 | + * complex dialog please derive directly from |
| 111 | + * {@link org.knime.core.node.NodeDialogPane}. |
| 112 | + * |
| 113 | + * @author Greg Landrum |
| 114 | + */ |
| 115 | +public class RDKit2SVGNodeDialog extends DefaultNodeSettingsPane { |
| 116 | + |
| 117 | + // |
| 118 | + // Constants |
| 119 | + // |
| 120 | + |
| 121 | + /** Default values, directly taken from RDKit binaries. */ |
| 122 | + public static final MolDrawOptions RDKIT_DEFAULT_PARAMETERS = new MolDrawOptions(); |
| 123 | + |
| 124 | + // |
| 125 | + // Constructor |
| 126 | + // |
| 127 | + |
| 128 | + /** |
| 129 | + * Create a new dialog pane with default components to configure an input |
| 130 | + * column, the name of a new column, which will contain the calculation results, |
| 131 | + * an option to tell, if the source column shall be removed from the result |
| 132 | + * table. |
| 133 | + */ |
| 134 | + RDKit2SVGNodeDialog() { |
| 135 | + super.addDialogComponent(new DialogComponentColumnNameSelection(createInputColumnNameModel(), |
| 136 | + "RDKit Mol column: ", 0, RDKitMolValue.class)); |
| 137 | + super.addDialogComponent(new DialogComponentString(createNewColumnNameModel(), "New column name: ")); |
| 138 | + super.addDialogComponent( |
| 139 | + new DialogComponentBoolean(createRemoveSourceColumnsOptionModel(), "Remove source column")); |
| 140 | + |
| 141 | + super.createNewTab("Drawing Options"); |
| 142 | + super.addDialogComponent( |
| 143 | + new DialogComponentBoolean(createPrepareBeforeDrawingOptionModel(), "Prepare before drawing")); |
| 144 | + super.addDialogComponent( |
| 145 | + new DialogComponentBoolean(createCenterBeforeDrawingOptionModel(), "Center before drawing")); |
| 146 | + super.addDialogComponent(new DialogComponentBoolean(createClearBackgroundOptionModel(), "Clear background")); |
| 147 | + super.addDialogComponent(new DialogComponentBoolean(createAddAtomIndicesOptionModel(), "Add atom indices")); |
| 148 | + super.addDialogComponent(new DialogComponentBoolean(createAddBondIndicesOptionModel(), "Add bond indices")); |
| 149 | + super.addDialogComponent( |
| 150 | + new DialogComponentBoolean(createAddStereoAnnotationOptionModel(), "Add stereo annotations")); |
| 151 | + super.addDialogComponent( |
| 152 | + new DialogComponentBoolean(createIncludeChiralFlagOptionModel(), "Include chiral flag")); |
| 153 | + super.addDialogComponent( |
| 154 | + new DialogComponentBoolean(createSimplifiedStereoGroupsOptionModel(), "Use simplified stereo groups")); |
| 155 | + super.addDialogComponent( |
| 156 | + new DialogComponentBoolean(createSingleColorWedgeBondsOptionModel(), "Single color wedge bonds")); |
| 157 | + super.addDialogComponent( |
| 158 | + new DialogComponentBoolean(createExplicitMethylOptionModel(), "Draw explicit methyl groups")); |
| 159 | + super.addDialogComponent( |
| 160 | + new DialogComponentBoolean(createDummiesAreAttachmentsOptionModel(), "Dummies are attachment points")); |
| 161 | + super.addDialogComponent(new DialogComponentBoolean(createIncludeRadicalsOptionModel(), "Draw radicals")); |
| 162 | + super.addDialogComponent(new DialogComponentBoolean(createNoAtomLabelsOptionModel(), "No atom labels")); |
| 163 | + super.addDialogComponent( |
| 164 | + new DialogComponentBoolean(createIsotopeLabelsOptionModel(), "Include isotope labels")); |
| 165 | + super.addDialogComponent( |
| 166 | + new DialogComponentBoolean(createDummyIsotopeLabelsOptionModel(), "Include isotope labels on dummies")); |
| 167 | + super.addDialogComponent(new DialogComponentBoolean(createComicModeOptionModel(), "Comic mode")); |
| 168 | + super.addDialogComponent(new DialogComponentBoolean(createBWModeOptionModel(), "Black&White mode")); |
| 169 | + |
| 170 | + super.addDialogComponent( |
| 171 | + new DialogComponentNumber(createBondLineWidthOptionModel(), "Line width for bonds", 1)); |
| 172 | + |
| 173 | + super.addDialogComponent(new DialogComponentNumber(createMinFontSizeOptionModel(), "Min font size", 1)); |
| 174 | + super.addDialogComponent(new DialogComponentNumber(createMaxFontSizeOptionModel(), "Max font size", 1)); |
| 175 | + super.addDialogComponent( |
| 176 | + new DialogComponentNumber(createAnnotationFontScaleOptionModel(), "Annotation font scale", 0.05)); |
| 177 | + |
| 178 | + } |
| 179 | + |
| 180 | + // |
| 181 | + // Static Methods |
| 182 | + // |
| 183 | + |
| 184 | + /** |
| 185 | + * Creates the settings model to be used for the input column. |
| 186 | + * |
| 187 | + * @return Settings model for input column selection. |
| 188 | + */ |
| 189 | + static final SettingsModelString createInputColumnNameModel() { |
| 190 | + return new SettingsModelString("input_column", null); |
| 191 | + } |
| 192 | + |
| 193 | + /** |
| 194 | + * Creates the settings model to be used to specify the new column name. |
| 195 | + * |
| 196 | + * @return Settings model for result column name. |
| 197 | + */ |
| 198 | + static final SettingsModelString createNewColumnNameModel() { |
| 199 | + return new SettingsModelString("new_column_name", null); |
| 200 | + } |
| 201 | + |
| 202 | + /** |
| 203 | + * Creates the settings model for the boolean flag to determine if the source |
| 204 | + * column shall be removed from the result table. The default is false. |
| 205 | + * |
| 206 | + * @return Settings model for check box whether to remove source columns. |
| 207 | + */ |
| 208 | + static final SettingsModelBoolean createRemoveSourceColumnsOptionModel() { |
| 209 | + return new SettingsModelBoolean("remove_source_columns", false); |
| 210 | + } |
| 211 | + |
| 212 | + static final SettingsModelBoolean createClearBackgroundOptionModel() { |
| 213 | + return new SettingsModelBoolean("clear_background", RDKIT_DEFAULT_PARAMETERS.getClearBackground()); |
| 214 | + } |
| 215 | + |
| 216 | + static final SettingsModelBoolean createDummiesAreAttachmentsOptionModel() { |
| 217 | + return new SettingsModelBoolean("dummies_are_attachments", |
| 218 | + RDKIT_DEFAULT_PARAMETERS.getDummiesAreAttachments()); |
| 219 | + } |
| 220 | + |
| 221 | + static final SettingsModelBoolean createAddAtomIndicesOptionModel() { |
| 222 | + return new SettingsModelBoolean("add_atom_indices", |
| 223 | + RDKIT_DEFAULT_PARAMETERS.getAddAtomIndices()); |
| 224 | + } |
| 225 | + |
| 226 | + static final SettingsModelBoolean createAddBondIndicesOptionModel() { |
| 227 | + return new SettingsModelBoolean("add_bond_indices", |
| 228 | + RDKIT_DEFAULT_PARAMETERS.getAddBondIndices()); |
| 229 | + } |
| 230 | + |
| 231 | + static final SettingsModelBoolean createIsotopeLabelsOptionModel() { |
| 232 | + return new SettingsModelBoolean("isotope_labels", |
| 233 | + RDKIT_DEFAULT_PARAMETERS.getIsotopeLabels()); |
| 234 | + } |
| 235 | + |
| 236 | + static final SettingsModelBoolean createDummyIsotopeLabelsOptionModel() { |
| 237 | + return new SettingsModelBoolean("dummy_isotope_labels", |
| 238 | + RDKIT_DEFAULT_PARAMETERS.getDummyIsotopeLabels()); |
| 239 | + } |
| 240 | + |
| 241 | + static final SettingsModelBoolean createAddStereoAnnotationOptionModel() { |
| 242 | + return new SettingsModelBoolean("add_stereo_annotation", |
| 243 | + true); // here the RDKit default is a bad one |
| 244 | + } |
| 245 | + |
| 246 | + static final SettingsModelBoolean createCenterBeforeDrawingOptionModel() { |
| 247 | + return new SettingsModelBoolean("center_before_drawing", |
| 248 | + RDKIT_DEFAULT_PARAMETERS.getCentreMoleculesBeforeDrawing()); |
| 249 | + } |
| 250 | + |
| 251 | + static final SettingsModelBoolean createPrepareBeforeDrawingOptionModel() { |
| 252 | + return new SettingsModelBoolean("prepare_before_drawing", |
| 253 | + RDKIT_DEFAULT_PARAMETERS.getPrepareMolsBeforeDrawing()); |
| 254 | + } |
| 255 | + |
| 256 | + static final SettingsModelBoolean createExplicitMethylOptionModel() { |
| 257 | + return new SettingsModelBoolean("explicit_methyl", |
| 258 | + RDKIT_DEFAULT_PARAMETERS.getExplicitMethyl()); |
| 259 | + } |
| 260 | + |
| 261 | + static final SettingsModelBoolean createIncludeRadicalsOptionModel() { |
| 262 | + return new SettingsModelBoolean("include_radicals", |
| 263 | + RDKIT_DEFAULT_PARAMETERS.getIncludeRadicals()); |
| 264 | + } |
| 265 | + |
| 266 | + static final SettingsModelBoolean createComicModeOptionModel() { |
| 267 | + return new SettingsModelBoolean("comic_mode", |
| 268 | + RDKIT_DEFAULT_PARAMETERS.getComicMode()); |
| 269 | + } |
| 270 | + |
| 271 | + static final SettingsModelBoolean createBWModeOptionModel() { |
| 272 | + return new SettingsModelBoolean("bw_mode",false); // not actually an option in the RDKit API |
| 273 | + } |
| 274 | + |
| 275 | + static final SettingsModelBoolean createNoAtomLabelsOptionModel() { |
| 276 | + return new SettingsModelBoolean("no_atom_labels", |
| 277 | + RDKIT_DEFAULT_PARAMETERS.getNoAtomLabels()); |
| 278 | + } |
| 279 | + |
| 280 | + static final SettingsModelBoolean createIncludeChiralFlagOptionModel() { |
| 281 | + return new SettingsModelBoolean("include_chiral_flag", |
| 282 | + RDKIT_DEFAULT_PARAMETERS.getIncludeChiralFlagLabel()); |
| 283 | + } |
| 284 | + |
| 285 | + static final SettingsModelBoolean createSimplifiedStereoGroupsOptionModel() { |
| 286 | + return new SettingsModelBoolean("simplified_stereo_groups", |
| 287 | + RDKIT_DEFAULT_PARAMETERS.getSimplifiedStereoGroupLabel()); |
| 288 | + } |
| 289 | + |
| 290 | + static final SettingsModelBoolean createSingleColorWedgeBondsOptionModel() { |
| 291 | + return new SettingsModelBoolean("single_color_wedge_bonds", |
| 292 | + RDKIT_DEFAULT_PARAMETERS.getSingleColourWedgeBonds()); |
| 293 | + } |
| 294 | + |
| 295 | + static final SettingsModelIntegerBounded createBondLineWidthOptionModel() { |
| 296 | + return new SettingsModelIntegerBounded("bond_line_width", |
| 297 | + RDKIT_DEFAULT_PARAMETERS.getBondLineWidth(), 0, 100); |
| 298 | + } |
| 299 | + |
| 300 | + static final SettingsModelIntegerBounded createMinFontSizeOptionModel() { |
| 301 | + return new SettingsModelIntegerBounded("min_font_size", |
| 302 | + RDKIT_DEFAULT_PARAMETERS.getMinFontSize(), 0, 100); |
| 303 | + } |
| 304 | + |
| 305 | + static final SettingsModelIntegerBounded createMaxFontSizeOptionModel() { |
| 306 | + return new SettingsModelIntegerBounded("max_font_size", |
| 307 | + RDKIT_DEFAULT_PARAMETERS.getMaxFontSize(), 0, 100); |
| 308 | + } |
| 309 | + |
| 310 | + static final SettingsModelDoubleBounded createAnnotationFontScaleOptionModel() { |
| 311 | + return new SettingsModelDoubleBounded("annotation_font_scale", |
| 312 | + RDKIT_DEFAULT_PARAMETERS.getAnnotationFontScale(), 0, 2); |
| 313 | + } |
| 314 | + |
| 315 | +} |
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