added thin stick construction mode; introduced construction filter co…

…ncept for MoleculeArchitect, now in ribbon/cartoon mode only shows side chains close to ligand
thsa · Dec 27, 2024 · 4023281 · 4023281
1 parent 318f8db
commit 4023281
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Showing 20 changed files with 526 additions and 256 deletions.
diff --git a/src/main/java/org/openmolecules/fx/sunflow/RayTraceDialog.java b/src/main/java/org/openmolecules/fx/sunflow/RayTraceDialog.java
@@ -97,7 +97,7 @@ public RayTraceDialog(Window parent, RayTraceOptions options, V3DMolecule mol) {
 		if (mol != null) {
 			grid.add(new Label("Render mode:"), 0, ++yIndex);
 			mComboboxMode = new ComboBox<>();
-			for (String item : MoleculeArchitect.MODE_TEXT)
+			for (String item : MoleculeArchitect.CONSTRUCTION_MODE_TEXT)
 				mComboboxMode.getItems().add(item);
 			mComboboxMode.getSelectionModel().select(options != null ? options.mode : mol.getConstructionMode());
 			grid.add(mComboboxMode, 1, yIndex);
@@ -119,14 +119,14 @@ public RayTraceDialog(Window parent, RayTraceOptions options, V3DMolecule mol) {
 
 		mComboboxSurfaceMaterial = new ComboBox[MoleculeSurfaceAlgorithm.SURFACE_TYPE.length];
 		for (int type=0; type<mComboboxSurfaceMaterial.length; type++) {
-			if (mol != null && mol.getSurfaceMode(type) != V3DMolecule.SurfaceMode.NONE) {
+			if (mol != null && mol.getSurfaceMode(type) != V3DMolecule.SURFACE_MODE_NONE) {
 				grid.add(new Label(MoleculeSurfaceAlgorithm.SURFACE_TYPE[type]+" surface material:"), 0, ++yIndex);
 				mComboboxSurfaceMaterial[type] = new ComboBox();
 				for (String item : SunflowPrimitiveBuilder.SURFACE_TEXT)
 					mComboboxSurfaceMaterial[type].getItems().add(item);
 				mComboboxSurfaceMaterial[type].getSelectionModel().select(
 						  options != null && options.surfaceMaterial[type] != -1 ? options.surfaceMaterial[type]
-						: mol.getSurfaceMode(type) == V3DMolecule.SurfaceMode.WIRES ? SunflowPrimitiveBuilder.SURFACE_WIRES
+						: mol.getSurfaceMode(type) == V3DMolecule.SURFACE_MODE_WIRES ? SunflowPrimitiveBuilder.SURFACE_WIRES
 						: mol.getSurfaceTransparency(type) > 0.2  ?
 								SunflowPrimitiveBuilder.SURFACE_TRANSPARENT : SunflowPrimitiveBuilder.SURFACE_SHINY);
 				grid.add(mComboboxSurfaceMaterial[type], 1, yIndex);

diff --git a/src/main/java/org/openmolecules/fx/sunflow/RayTraceOptions.java b/src/main/java/org/openmolecules/fx/sunflow/RayTraceOptions.java
@@ -32,7 +32,6 @@
 import org.openmolecules.fx.surface.SurfaceMesh;
 import org.openmolecules.fx.surface.SurfaceTexture;
 import org.openmolecules.fx.viewer3d.V3DMolecule;
-import org.openmolecules.fx.viewer3d.V3DMolecule.SurfaceMode;
 import org.openmolecules.fx.viewer3d.nodes.DashedRod;
 import org.openmolecules.mesh.MoleculeSurfaceAlgorithm;
 import org.openmolecules.render.SunflowMoleculeBuilder;
@@ -125,7 +124,7 @@ public void addMolecule(V3DMolecule fxmol) {
 
 		double surplus = -1;
 		for (int type = 0; type<MoleculeSurfaceAlgorithm.SURFACE_TYPE.length; type++)
-			if (fxmol.getSurfaceMode(type) != V3DMolecule.SurfaceMode.NONE)
+			if (fxmol.getSurfaceMode(type) != V3DMolecule.SURFACE_MODE_NONE)
 				surplus = Math.max(surplus, fxmol.getSurfaceMesh(type).getSurfaceSurplus());
 		Color color = fxmol.getColor();
 		mRenderer.setRenderMode(mode == -1 ? fxmol.getConstructionMode() : mode);
@@ -198,8 +197,8 @@ public org.sunflow.image.Color colorAtPoint(Point3 p) {
 	}
 
 	private int getOriginalSurfaceMaterial(V3DMolecule fxmol, int surfaceType) {
-		SurfaceMode surfaceMode = fxmol.getSurfaceMode(surfaceType);
-		if (surfaceMode == V3DMolecule.SurfaceMode.WIRES)
+		int surfaceMode = fxmol.getSurfaceMode(surfaceType);
+		if (surfaceMode == V3DMolecule.SURFACE_MODE_WIRES)
 			return SunflowPrimitiveBuilder.SURFACE_WIRES;
 		if (fxmol.getSurfaceTransparency(surfaceType) >= 0.1)
 			return SunflowPrimitiveBuilder.SURFACE_TRANSPARENT;

diff --git a/src/main/java/org/openmolecules/fx/surface/SurfaceMesh.java b/src/main/java/org/openmolecules/fx/surface/SurfaceMesh.java
@@ -52,6 +52,7 @@ public class SurfaceMesh extends TriangleMesh implements MeshBuilder {
 //	public static final int SURFACE_COLOR_ELECTRONEGATIVITY = ?;  // dummy for now
 	public static final int SURFACE_COLOR_DONORS_ACCEPTORS = 3;	// this and above have 1D color gradient
 	public static final int SURFACE_COLOR_ATOMIC_NOS = 4;	// this has 2D color gradients
+	public static final String[] SURFACE_COLOR_MODE_CODE = { "inherit", "plain", "polarity", "donorsAcceptors", "atomicNo" };
 
 	public static final boolean VERBOSE_POINTS_AND_TRIANGLES = false;    // print addPoint and addTriangle
 

diff --git a/src/main/java/org/openmolecules/fx/tasks/V3DMinimizer.java b/src/main/java/org/openmolecules/fx/tasks/V3DMinimizer.java
@@ -116,7 +116,7 @@ private void minimize() {
 		for(V3DMolecule fxmol : mFXMol) {
 			// remove any surfaces
 			for (int type = 0; type<MoleculeSurfaceAlgorithm.SURFACE_TYPE.length; type++)
-				fxmol.setSurfaceMode(type ,V3DMolecule.SurfaceMode.NONE);
+				fxmol.setSurfaceMode(type ,V3DMolecule.SURFACE_MODE_NONE);
 
 			StereoMolecule mol = fxmol.getMolecule();
 			molScenery.addMolecule(mol);

diff --git a/src/main/java/org/openmolecules/fx/tasks/V3DShapeAlignerInPlace.java b/src/main/java/org/openmolecules/fx/tasks/V3DShapeAlignerInPlace.java
@@ -1,35 +1,23 @@
 package org.openmolecules.fx.tasks;
 
-import com.actelion.research.calc.Matrix;
 import com.actelion.research.chem.Canonizer;
 import com.actelion.research.chem.Coordinates;
 import com.actelion.research.chem.StereoMolecule;
 import com.actelion.research.chem.alignment3d.transformation.Rotation;
 import com.actelion.research.chem.conf.Conformer;
-import com.actelion.research.chem.forcefield.ForceField;
-import com.actelion.research.chem.forcefield.ForceFieldChangeListener;
-import com.actelion.research.chem.forcefield.mmff.ForceFieldMMFF94;
 import com.actelion.research.chem.phesa.DescriptorHandlerShape;
 import com.actelion.research.chem.phesa.DescriptorHandlerShapeOneConf;
 import com.actelion.research.chem.phesa.MolecularVolume;
-import com.actelion.research.chem.phesa.PheSAAlignment;
 import com.actelion.research.chem.phesa.PheSAMolecule;
-import com.actelion.research.chem.phesa.VolumeGaussian;
-import com.actelion.research.util.ArrayUtils;
-import com.actelion.research.util.DoubleFormat;
 import javafx.application.Platform;
 import javafx.collections.ObservableList;
-import javafx.geometry.Point3D;
 import javafx.scene.Node;
 import javafx.scene.control.Alert;
 import javafx.scene.control.Alert.AlertType;
-import javafx.scene.transform.Rotate;
 import javafx.scene.transform.Transform;
-
-import org.openmolecules.fx.viewer3d.CarbonAtomColorPalette;
+import org.openmolecules.fx.viewer3d.V3DCustomizablePheSA;
 import org.openmolecules.fx.viewer3d.V3DMolecule;
 import org.openmolecules.fx.viewer3d.V3DMoleculeUpdater;
-import org.openmolecules.fx.viewer3d.V3DCustomizablePheSA;
 import org.openmolecules.fx.viewer3d.V3DScene;
 import org.openmolecules.mesh.MoleculeSurfaceAlgorithm;
 
@@ -101,7 +89,7 @@ else if(fxmol.isSelected()) {
 
 		for(V3DMolecule v3dMol : mFitMols) {
 			for (int type = 0; type<MoleculeSurfaceAlgorithm.SURFACE_TYPE.length; type++)
-				v3dMol.setSurfaceMode(type ,V3DMolecule.SurfaceMode.NONE);
+				v3dMol.setSurfaceMode(type ,V3DMolecule.SURFACE_MODE_NONE);
 				mScene.removeMeasurements(v3dMol);
 		}
 

diff --git a/src/main/java/org/openmolecules/fx/viewer3d/V3DBindingSite.java b/src/main/java/org/openmolecules/fx/viewer3d/V3DBindingSite.java
@@ -11,10 +11,8 @@
 import javafx.scene.Node;
 import org.openmolecules.fx.surface.SurfaceMesh;
 import org.openmolecules.fx.tasks.V3DMinimizer;
-import org.openmolecules.fx.viewer3d.V3DMolecule.SurfaceMode;
 import org.openmolecules.fx.viewer3d.nodes.NodeDetail;
 import org.openmolecules.render.MoleculeArchitect;
-import org.openmolecules.render.MoleculeArchitect.HydrogenMode;
 
 import java.util.HashSet;
 import java.util.List;
@@ -35,8 +33,7 @@ public enum DisplayMode {MODE1, MODE2, MODE3, MODE4};
 
 	private V3DMolecule nativeLigand;
 	private V3DMolecule receptor;
-	private MoleculeGrid grid;
-	private Set<Integer> bindingSiteAtoms;
+	private final Set<Integer> bindingSiteAtoms;
 	private List<V3DMolecule> solventMols;
 	private SimpleObjectProperty<DisplayMode> displayModeProperty;
 
@@ -48,8 +45,8 @@ public void initialize() {
 		nativeLigand.assignLikelyProtonationStates();
 		nativeLigand.setConstructionMode(MoleculeArchitect.CONSTRUCTION_MODE_BALL_AND_STICKS);
 		receptor.assignLikelyProtonationStates();
-		receptor.setHydrogenMode(HydrogenMode.POLAR);
-		grid = new MoleculeGrid(nativeLigand.getMolecule(),GRID_RESOLUTION,
+		receptor.setHydrogenMode(MoleculeArchitect.HYDROGEN_MODE_POLAR);
+		MoleculeGrid grid = new MoleculeGrid(nativeLigand.getMolecule(),GRID_RESOLUTION,
 				new Coordinates(GRID_DIMENSION,GRID_DIMENSION,
 						GRID_DIMENSION));
 		DockingEngine.getBindingSiteAtoms(receptor.getMolecule(), bindingSiteAtoms, grid, true);
@@ -88,7 +85,7 @@ private void customizeView() {
 			receptor.removeAllSurfaces();
 			nativeLigand.setConstructionMode(MoleculeArchitect.CONSTRUCTION_MODE_BALL_AND_STICKS);
 			receptor.setConstructionMode(MoleculeArchitect.CONSTRUCTION_MODE_STICKS);
-			receptor.setSurface(0, SurfaceMode.FILLED, SurfaceMesh.SURFACE_COLOR_ATOMIC_NOS, 0.5);
+			receptor.setSurface(0, V3DMolecule.SURFACE_MODE_FILLED, SurfaceMesh.SURFACE_COLOR_ATOMIC_NOS, 0.5);
 			break;
 		default:
 			receptor.removeAllSurfaces();