Remove introduced Point_Type and replace with a map, add test on 1CRN.

descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java

@@ -30,7 +30,10 @@
 
 import javax.vecmath.Point3d;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
  * A class representing the solvent accessible surface area surface of a molecule.
@@ -119,8 +122,8 @@ private void init() {
         for (IAtom atom : atoms) {
             if (atom.getPoint3d() == null)
                 throw new IllegalArgumentException("One or more atoms had no 3D coordinate set");
-        }                
-        
+        }
+
         // get r_f and geometric center
         Point3d cp = new Point3d(0, 0, 0);
         double maxRadius = 0;
@@ -165,7 +168,7 @@ private void init() {
         logger.info("Obtained points, areas and volumes");
 
     }
-	
+
     /**
      * Get an array of all the points on the molecular surface.
      *
@@ -187,24 +190,20 @@ public Point3d[] getAllSurfacePoints() {
         }
         return (ret);
     }
-
-    public ArrayList<Point_Type> getAllPointswithAtomType() {
-    	int npt = 0;
-        for (List<Point3d> surfPoint : this.surfPoints)
-            npt += surfPoint.size();
-        ArrayList<Point_Type> point_types = new ArrayList<Point_Type>(npt);
-        int j = 0;
+
+    /**
+     * Get the map from atom to surface points. If an atom does not appear in
+     * the map it is buried. Atoms may share surface points with other atoms.
+     *
+     * @return surface atoms and associated points on the surface
+     */
+    public Map<IAtom, List<Point3d>> getAtomSurfaceMap() {
+        Map<IAtom,List<Point3d>> map = new HashMap<>();
         for (int i = 0; i < this.surfPoints.length; i++) {
-            List<Point3d> arl = this.surfPoints[i];
-            for (Point3d p : arl) {
-                Point_Type point_type = new Point_Type();
-                point_type.setAtom(this.atoms[i].getAtomicNumber());
-                point_type.setCoord(p);
-                point_types.add(point_type);
-                j++;
-            }
+            if (!this.surfPoints[i].isEmpty())
+                map.put(this.atoms[i], Collections.unmodifiableList(this.surfPoints[i]));
         }
-        return (point_types);
+        return map;
     }
 
     /**

descriptor/qsarmolecular/src/test/java/org/openscience/cdk/geometry/surface/NumericalSurfaceTest.java

@@ -0,0 +1,63 @@
+/*
+ * Copyright (C) 2019  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. All we ask is that proper credit is given
+ * for our work, which includes - but is not limited to - adding the above
+ * copyright notice to the beginning of your source code files, and to any
+ * copyright notice that you may distribute with programs based on this work.
+ *
+ * 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 org.hamcrest.CoreMatchers;
+import org.junit.Test;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.io.PDBReader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+
+import javax.vecmath.Point3d;
+import java.io.InputStream;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import static org.junit.Assert.assertThat;
+
+public class NumericalSurfaceTest {
+
+    @Test
+    public void testCranbinSurface() throws Exception {
+        IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
+        IChemFile chemFile;
+        String path = "/data/pdb/1crn.pdb";
+        try (InputStream in = getClass().getResourceAsStream(path);
+             PDBReader pdbr = new PDBReader(in)) {
+            chemFile = pdbr.read(bldr.newInstance(IChemFile.class));
+        }
+        IAtomContainer   mol     = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
+        NumericalSurface surface = new NumericalSurface(mol);
+        Map<IAtom, List<Point3d>> map = surface.getAtomSurfaceMap();
+        assertThat(map.size(), CoreMatchers.is(222));
+        assertThat(mol.getAtomCount(), CoreMatchers.is(327));
+    }
+
+}