Merge remote-tracking branch 'upstream/master'

pom.xml

@@ -8,7 +8,7 @@
     Please follow the naming scheme YEAR.MONTH.RELEASE_NO_OF_MONTH
     (eg. 2016.4.1 for second release in Apr 2016)
     -->
-    <version>2025.2.0</version>
+    <version>2025.2.1-SNAPSHOT</version>
 
     <name>OpenChemLib</name>
     <description>Open Source Chemistry Library</description>
@@ -207,7 +207,7 @@
         <connection>scm:git:[email protected]:Actelion/openchemlib.git</connection>
         <developerConnection>scm:git:[email protected]:Actelion/openchemlib.git</developerConnection>
         <url>https://github.com/Actelion/openchemlib</url>
-      <tag>openchemlib-2025.2.0</tag>
+      <tag>HEAD</tag>
   </scm>
 
     <distributionManagement>

src/main/java/com/actelion/research/chem/AromaticityResolver.java

@@ -450,6 +450,7 @@ private void promoteDelocalizedChains() {
                         int terminalBond = bond;
                         int bridgeAtom = mMol.getBondAtom(1-i, bond);
                         while (terminalBond != -1) {
+							mIsDelocalizedAtom[terminalAtom] = false;
                             mIsDelocalizedBond[terminalBond] = false;
                             mDelocalizedBonds--;
                             mMol.setBondType(terminalBond, Molecule.cBondTypeDelocalized);
@@ -462,13 +463,15 @@ private void promoteDelocalizedChains() {
                                         bridgeAtom = mMol.getConnAtom(terminalAtom, j);
                                         }
                                     else {
-                                        terminalAtom = -1;
+                                        terminalAtom = -1;	// Stop here! We have hit an aromatic branch.
                                         terminalBond = -1;
                                         break;
                                         }
                                     }
                                 }
                             }
+						if (terminalAtom != -1)		// Regular end of aromatic chain (no branch).
+							mIsDelocalizedAtom[bridgeAtom] = false;
                         break;
                         }
                     }

src/main/java/com/actelion/research/chem/ExtendedMolecule.java

@@ -1634,6 +1634,9 @@ public boolean isPseudoRotatableBond(int bond) {
 		return false;
 		}
 
+	/**
+	 * @return number of distinct aromatic rings in the molecule
+	 */
 	public int getAromaticRingCount() {
 		ensureHelperArrays(cHelperRings);
 		int count = 0;
@@ -1775,6 +1778,7 @@ public boolean isHeteroAromaticAtom(int atom) {
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param atom
 	 * @return whether the atom is a member of a delocalized ring (subset of aromatic rings)
 	 */
@@ -1783,11 +1787,21 @@ public boolean isDelocalizedAtom(int atom) {
 	}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of an aromatic ring
+	 */
 	public boolean isAromaticBond(int bond) {
 		return bond<mBonds && mRingSet.isAromaticBond(bond);
 	}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of an aromatic ring that contains at least one hetero atom
+	 */
 	public boolean isHeteroAromaticBond(int bond) {
 		return bond<mBonds && mRingSet.isHeteroAromaticBond(bond);
 	}
@@ -1800,26 +1814,38 @@ public boolean isHeteroAromaticBond(int bond) {
 	 * Indole has 6 delocalized bonds.
 	 * This method also returns true, if the molecule is a fragment and if the bond is explicitly
 	 * defined to be delocalized.
+	 * Requires helper arrays state cHelperRings.
 	 * @param bond
 	 * @return
 	 */
 	@Override
 	public boolean isDelocalizedBond(int bond) {
-		return (bond < mBonds) ? mRingSet.isDelocalizedBond(bond) || mBondType[bond] == cBondTypeDelocalized : false;
+		return bond<mBonds && (mRingSet.isDelocalizedBond(bond) || mBondType[bond] == cBondTypeDelocalized);
 		}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param atom
+	 * @return whether the atom is a member of ring of any size
+	 */
 	public boolean isRingAtom(int atom) {
 		return (mAtomFlags[atom] & cAtomFlagsRingBonds) != 0;
 		}
 
 
-	public boolean isRingBond(int bnd) {
-		return (mBondFlags[bnd] & cBondFlagRing) != 0;
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param bond
+	 * @return whether the bond is a member of ring of any size
+	 */
+	public boolean isRingBond(int bond) {
+		return (mBondFlags[bond] & cBondFlagRing) != 0;
 		}
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param atom
 	 * @return whether atom is a member of a ring not larger than 7 atoms
 	 */
@@ -1829,6 +1855,7 @@ public boolean isSmallRingAtom(int atom) {
 
 
 	/**
+	 * Requires helper arrays state cHelperRings.
 	 * @param bond
 	 * @return whether bond is a member of a ring not larger than 7 atoms
 	 */
@@ -1838,6 +1865,7 @@ public boolean isSmallRingBond(int bond) {
 
 
 	/**
+	 * Requires helper arrays state cHelperNeighbours.
 	 * @param atom
 	 * @return whether atom has a neighbor that is connected through a double/triple bond to a hetero atom
 	 */
@@ -1846,6 +1874,11 @@ public boolean isStabilizedAtom(int atom) {
 		}
 
 
+	/**
+	 * Requires helper arrays state cHelperRings.
+	 * @param atom
+	 * @return number of connected bonds, which are member of a ring
+	 */
 	public int getAtomRingBondCount(int atom) {
 		int flags = (mAtomFlags[atom] & cAtomFlagsRingBonds);
 		return (flags == 0) ? 0

src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java

@@ -1096,12 +1096,36 @@ public static boolean containsFiveBindingCarbon(StereoMolecule mol) {
 					int bo = mol.getConnBondOrder(i,j);
 					sumBO+=bo;
 				}
-				five=(sumBO>4)?true:false;
+				if(sumBO>4){
+					five=true;
+					break;
+				}
 			}
 		}
 
 		return five;
 	}
+	public static boolean containsFiveBindingNitrogenWithoutCharge(StereoMolecule mol) {
+
+		boolean fiveBindingNNoPositiveCharge=false;
+		for (int i = 0; i < mol.getAtoms(); i++) {
+			if(mol.getAtomicNo(i)==5){
+				int sumBO=0;
+				for (int j = 0; j < mol.getConnAtoms(i); j++) {
+					int bo = mol.getConnBondOrder(i,j);
+					sumBO+=bo;
+				}
+				if(sumBO==5){
+					if(mol.getAtomCharge(i)!=1) {
+						fiveBindingNNoPositiveCharge = true;
+						break;
+					}
+				}
+			}
+		}
+
+		return fiveBindingNNoPositiveCharge;
+	}
 
 	/**
 	 *

src/main/java/com/actelion/research/jfx/gui/GraphicsContextImpl.java

@@ -53,6 +53,7 @@
  * Date: 11/24/2014
  * Time: 6:24 PM
  */
+@Deprecated
 public class GraphicsContextImpl implements IDrawContext<GraphicsContext>
 {
     GraphicsContext ctx;
@@ -69,10 +70,10 @@ public GraphicsContext getContext()
     }
     public static Color createColor(long color)
     {
-        double r = (double) ((color & 0xFF000000l) >> 24) / 255.0;
-        double g = (double) ((color & 0x00FF0000l) >> 16) / 255.0;
-        double b = (double) ((color & 0x0000FF00l) >> 8) / 255.0;
-        double a = (double) (color & 0x000000FFl ) / 255.0;
+        double r = (double) ((color & 0xFF000000L) >> 24) / 255.0;
+        double g = (double) ((color & 0x00FF0000L) >> 16) / 255.0;
+        double b = (double) ((color & 0x0000FF00L) >> 8) / 255.0;
+        double a = (double) (color & 0x000000FFL ) / 255.0;
         return new Color(r, g, b, a);
     }
 

src/main/java/com/actelion/research/jfx/gui/chem/JFXCanvasDepictor.java

@@ -1 +1 @@
-/** Copyright (c) 1997 - 2016* Actelion Pharmaceuticals Ltd.* Gewerbestrasse 16* CH-4123 Allschwil, Switzerland** All rights reserved.** Redistribution and use in source and binary forms, with or without* modification, are permitted provided that the following conditions are met:** 1. Redistributions of source code must retain the above copyright notice, this*    list of conditions and the following disclaimer.* 2. Redistributions in binary form must reproduce the above copyright notice,*    this list of conditions and the following disclaimer in the documentation*    and/or other materials provided with the distribution.* 3. Neither the name of the the copyright holder nor the*    names of its contributors may be used to endorse or promote products*    derived from this software without specific prior written permission.** THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.**/package com.actelion.research.jfx.gui.chem;import com.actelion.research.chem.AbstractDepictor;import com.actelion.research.chem.StereoMolecule;import com.actelion.research.gui.generic.GenericPolygon;import com.actelion.research.jfx.gui.GraphicsContextImpl;import javafx.geometry.Bounds;import javafx.geometry.VPos;import javafx.scene.canvas.GraphicsContext;import javafx.scene.paint.Color;import javafx.scene.shape.ArcType;import javafx.scene.shape.StrokeLineCap;import javafx.scene.shape.StrokeLineJoin;import javafx.scene.text.Font;import javafx.scene.text.Text;import javafx.scene.text.TextAlignment;/** * Project: * User: rufenec * Date: 10/12/11 * Time: 6:00 PM */public class JFXCanvasDepictor extends AbstractDepictor{    private GraphicsContext ctx = null;    private Font currentFont = Font.font("Helvetica", 8);    ;    private double lineWidth = 1.0f;    public JFXCanvasDepictor(StereoMolecule mol, int mode)    {        super(mol != null ? mol : new StereoMolecule());        super.setDisplayMode(mode);    }    public JFXCanvasDepictor(StereoMolecule mol)    {        this(mol, 0);    }    protected void init() {        super.init();    }    @Override    public void paint(Object g)    {        if (g instanceof GraphicsContext) {            ctx = (GraphicsContext) g;        } else if (g instanceof GraphicsContextImpl) {            ctx = ((GraphicsContextImpl) g).getContext();        } else {            throw new IllegalArgumentException("Need to pass a Canvas object " + g);        }        super.paint(g);    }    @Override    protected void drawBlackLine(DepictorLine theLine)    {        ctx.save();        ctx.setLineWidth(lineWidth);        ctx.setLineCap(StrokeLineCap.ROUND);        ctx.setLineJoin(StrokeLineJoin.MITER);//        ctx.setStroke(colormap.color);        ctx.beginPath();        ctx.moveTo(theLine.x1, theLine.y1);        ctx.lineTo(theLine.x2,theLine.y2);        ctx.stroke();//        ctx.strokeLine(theLine.x1, theLine.y1, theLine.x2, theLine.y2);        ctx.restore();    }    @Override    protected void drawDottedLine(DepictorLine theLine)    {        ctx.save();//        ctx.setStroke(colormap.color);        ctx.setLineCap(StrokeLineCap.ROUND);        ctx.beginPath();        ctx.moveTo(theLine.x1,theLine.y1);        ctx.lineTo(theLine.x2,theLine.y2);        ctx.stroke();//        ctx.strokeLine(theLine.x1, theLine.y1, theLine.x2, theLine.y2);        ctx.restore();    }    @Override    protected void drawPolygon(GenericPolygon p)    {        ctx.save();//        ctx.setStroke(colormap.color);//        ctx.setFill(colormap.color);        double[] x = new double[p.getSize()];        double[] y = new double[p.getSize()];        for (int i = 0; i < p.getSize(); i++) {            x[i] = p.getX(i);            y[i] = p.getY(i);        }        ctx.fillPolygon(x, y, p.getSize());//        ctx.strokePolygon(x, y, count);        ctx.restore();    }    @Override    protected void drawString(String theString, double x, double y)    {        ctx.save();        ctx.setFont(currentFont);        ctx.setTextAlign(TextAlignment.CENTER);        ctx.setTextBaseline(VPos.CENTER);//        ctx.setFill(colormap.color);        ctx.fillText(theString, x, y);        ctx.restore();    }    private Bounds getBounds(String s)    {        Text t = new Text(s);        t.setFont(currentFont);        return t.getLayoutBounds();    }    @Override    protected void fillCircle(double x, double y, double r)    {        ctx.save();//        if (colormap != null) {//            ctx.setFill(colormap.color);//        }        ctx.fillArc(            (double) x, (double) y,            (double) r, (double) r, (double) 0,            (double) 360, ArcType.ROUND);        ctx.restore();    }    @Override    protected double getStringWidth(String theString)    {//        Trace.trace(theString);        return (double) getBounds(theString).getWidth();    }    @Override    protected int getTextSize()    {        return (int) currentFont.getSize();    }    @Override    protected void setTextSize(int theSize)    {        currentFont = Font.font("Helvetica", theSize);    }    @Override    protected void setLineWidth(double lineWidth)    {        this.lineWidth = lineWidth;    }    @Override    protected double getLineWidth()    {        return lineWidth;    }    @Override    protected void setRGB(int rgb)    {        if (ctx != null) {            Color color = new Color(((rgb & 0x00FF0000) >> 16) / 255.0, ((rgb & 0x0000FF00) >> 8) / 255.0, (rgb & 0x000000FF) / 255.0, 1.0);            ctx.setStroke(color);            ctx.setFill(color);        }         //colormap = getColor(theColor);    }}
+/** Copyright (c) 1997 - 2016* Actelion Pharmaceuticals Ltd.* Gewerbestrasse 16* CH-4123 Allschwil, Switzerland** All rights reserved.** Redistribution and use in source and binary forms, with or without* modification, are permitted provided that the following conditions are met:** 1. Redistributions of source code must retain the above copyright notice, this*    list of conditions and the following disclaimer.* 2. Redistributions in binary form must reproduce the above copyright notice,*    this list of conditions and the following disclaimer in the documentation*    and/or other materials provided with the distribution.* 3. Neither the name of the the copyright holder nor the*    names of its contributors may be used to endorse or promote products*    derived from this software without specific prior written permission.** THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.**/package com.actelion.research.jfx.gui.chem;import com.actelion.research.chem.AbstractDepictor;import com.actelion.research.chem.StereoMolecule;import com.actelion.research.gui.generic.GenericPolygon;import com.actelion.research.gui.fx.FXDrawContext;import com.actelion.research.jfx.gui.GraphicsContextImpl;import javafx.geometry.Bounds;import javafx.geometry.VPos;import javafx.scene.canvas.GraphicsContext;import javafx.scene.paint.Color;import javafx.scene.shape.ArcType;import javafx.scene.shape.StrokeLineCap;import javafx.scene.shape.StrokeLineJoin;import javafx.scene.text.Font;import javafx.scene.text.Text;import javafx.scene.text.TextAlignment;/** * Project: * User: rufenec * Date: 10/12/11 * Time: 6:00 PM */@Deprecated // use a GenericDepictor instaedpublic class JFXCanvasDepictor extends AbstractDepictor{    private GraphicsContext ctx = null;    private Font currentFont = Font.font("Helvetica", 8);    ;    private double lineWidth = 1.0f;    public JFXCanvasDepictor(StereoMolecule mol, int mode)    {        super(mol != null ? mol : new StereoMolecule());        super.setDisplayMode(mode);    }    public JFXCanvasDepictor(StereoMolecule mol)    {        this(mol, 0);    }    protected void init() {        super.init();    }    @Override    public void paint(Object g)    {        if (g instanceof GraphicsContext) {            ctx = (GraphicsContext) g;        } else if (g instanceof GraphicsContextImpl) {            ctx = ((GraphicsContextImpl) g).getContext();        } else {            throw new IllegalArgumentException("Need to pass a Canvas object " + g);        }        super.paint(g);    }    @Override    protected void drawBlackLine(DepictorLine theLine)    {        ctx.save();        ctx.setLineWidth(lineWidth);        ctx.setLineCap(StrokeLineCap.ROUND);        ctx.setLineJoin(StrokeLineJoin.MITER);//        ctx.setStroke(colormap.color);        ctx.beginPath();        ctx.moveTo(theLine.x1, theLine.y1);        ctx.lineTo(theLine.x2,theLine.y2);        ctx.stroke();//        ctx.strokeLine(theLine.x1, theLine.y1, theLine.x2, theLine.y2);        ctx.restore();    }    @Override    protected void drawDottedLine(DepictorLine theLine)    {        ctx.save();//        ctx.setStroke(colormap.color);        ctx.setLineCap(StrokeLineCap.ROUND);        ctx.beginPath();        ctx.moveTo(theLine.x1,theLine.y1);        ctx.lineTo(theLine.x2,theLine.y2);        ctx.stroke();//        ctx.strokeLine(theLine.x1, theLine.y1, theLine.x2, theLine.y2);        ctx.restore();    }    @Override    protected void drawPolygon(GenericPolygon p)    {        ctx.save();//        ctx.setStroke(colormap.color);//        ctx.setFill(colormap.color);        double[] x = new double[p.getSize()];        double[] y = new double[p.getSize()];        for (int i = 0; i < p.getSize(); i++) {            x[i] = p.getX(i);            y[i] = p.getY(i);        }        ctx.fillPolygon(x, y, p.getSize());//        ctx.strokePolygon(x, y, count);        ctx.restore();    }    @Override    protected void drawString(String theString, double x, double y)    {        ctx.save();        ctx.setFont(currentFont);        ctx.setTextAlign(TextAlignment.CENTER);        ctx.setTextBaseline(VPos.CENTER);//        ctx.setFill(colormap.color);        ctx.fillText(theString, x, y);        ctx.restore();    }    private Bounds getBounds(String s)    {        Text t = new Text(s);        t.setFont(currentFont);        return t.getLayoutBounds();    }    @Override    protected void fillCircle(double x, double y, double r)    {        ctx.save();//        if (colormap != null) {//            ctx.setFill(colormap.color);//        }        ctx.fillArc(            (double) x, (double) y,            (double) r, (double) r, (double) 0,            (double) 360, ArcType.ROUND);        ctx.restore();    }    @Override    protected double getStringWidth(String theString)    {//        Trace.trace(theString);        return (double) getBounds(theString).getWidth();    }    @Override    protected int getTextSize()    {        return (int) currentFont.getSize();    }    @Override    protected void setTextSize(int theSize)    {        currentFont = Font.font("Helvetica", theSize);    }    @Override    protected void setLineWidth(double lineWidth)    {        this.lineWidth = lineWidth;    }    @Override    protected double getLineWidth()    {        return lineWidth;    }    @Override    protected void setRGB(int rgb)    {        if (ctx != null) {            Color color = new Color(((rgb & 0x00FF0000) >> 16) / 255.0, ((rgb & 0x0000FF00) >> 8) / 255.0, (rgb & 0x000000FF) / 255.0, 1.0);            ctx.setStroke(color);            ctx.setFill(color);        }         //colormap = getColor(theColor);    }}