Add a method for Numerical Surface: Can get both coordinates and atom type

Luckick · johnmay · commit 1bf61af285ae · 2019-04-11T10:39:09.000+01:00
getAllPointswithAtomType(): Will return an ArrayList, where each
element will include both Coordinates and Atom Type by
Atom.getAtomicNumber().
diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java
@@ -31,6 +31,7 @@
 import javax.vecmath.Point3d;
 import java.util.ArrayList;
 import java.util.Iterator;
+import org.openscience.cdk.geometry.surface.Point_Type;
 
 /**
  * A class representing the solvent accessible surface area surface of a molecule.
@@ -165,7 +166,7 @@ private void init() {
         logger.info("Obtained points, areas and volumes");
 
     }
-
+	
     /**
      * Get an array of all the points on the molecular surface.
      *
@@ -189,6 +190,29 @@ public Point3d[] getAllSurfacePoints() {
         }
         return (ret);
     }
+    
+    public ArrayList<Point_Type> getAllPointswithAtomType() {
+    	int npt = 0;
+        for (int i = 0; i < this.surfPoints.length; i++)
+            npt += this.surfPoints[i].size();
+        //Point3d[] ret = new Point3d[npt];
+        ArrayList<Point_Type> point_types = new ArrayList<Point_Type>(npt);
+        //ArrayList<Integer> atomtype = new ArrayList<Integer>(npt);
+        int j = 0;
+        for (int i = 0; i < this.surfPoints.length; i++) {
+            ArrayList arl = this.surfPoints[i];
+            //atomtype.add(this.atoms[i].getAtomicNumber());
+            for (Iterator it = arl.iterator(); it.hasNext();) {
+                //ret[j] = (Point3d) it.next();
+                Point_Type point_type = new Point_Type();
+                point_type.setAtom(this.atoms[i].getAtomicNumber());
+                point_type.setCoord((Point3d) it.next());
+                point_types.add(point_type);
+                j++;
+            }
+        }
+        return (point_types);
+    }
 
     /**
      * Get an array of the points on the accessible surface of a specific atom.
diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/Point_Type.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/Point_Type.java
@@ -0,0 +1,49 @@
+/*
+ * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
+ *
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+
+package org.openscience.cdk.geometry.surface;
+
+import javax.vecmath.Point3d;
+
+
+public class Point_Type
+{
+    public int number;
+    public Point3d coord;
+    // Add constructor, get, set, as needed.
+    
+    public int getAtom() {
+    return number;
+	}
+
+	public void setAtom(int number) {
+    	this.number = number;
+	}
+
+	public Point3d getCoord() {
+    	return coord;
+	}
+
+	public void setCoord(Point3d coord) {
+    	this.coord = coord;
+	}
+}
+
+
