test_class.file: descriptor/qsarmolecular/src/test/java/org/openscience/cdk/geometry/surface/NumericalSurfaceTest.java
test_class.identifier: NumericalSurfaceTest
test_case.body: @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));
      }
test_case.class_method_signature: NumericalSurfaceTest.testCranbinSurface()
test_case.full_signature: @Test public void testCranbinSurface()
test_case.identifier: testCranbinSurface
test_case.invocations: getInstance getResourceAsStream getClass read newInstance get getAllAtomContainers getAtomSurfaceMap assertThat size is assertThat getAtomCount is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCranbinSurface()
focal_class.declarator: logger         = LoggingToolFactory.createLoggingTool(NumericalSurface.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger         = LoggingToolFactory.createLoggingTool(NumericalSurface.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: solventRadius  = 1.4
focal_class.original_string: double          solventRadius  = 1.4;
focal_class.type: double
focal_class.var_name: solventRadius
focal_class.declarator: tesslevel      = 4
focal_class.original_string: int             tesslevel      = 4;
focal_class.type: int
focal_class.var_name: tesslevel
focal_class.declarator: atoms
focal_class.original_string: IAtom[]         atoms;
focal_class.type: IAtom[]
focal_class.var_name: atoms
focal_class.declarator: surfPoints
focal_class.original_string: List<Point3d>[] surfPoints;
focal_class.type: List<Point3d>[]
focal_class.var_name: surfPoints
focal_class.declarator: areas
focal_class.original_string: double[]        areas;
focal_class.type: double[]
focal_class.var_name: areas
focal_class.declarator: volumes
focal_class.original_string: double[]        volumes;
focal_class.type: double[]
focal_class.var_name: volumes
focal_class.file: descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java
focal_class.identifier: NumericalSurface
focal_class.class_method_signature: NumericalSurface.NumericalSurface(IAtomContainer atomContainer)
focal_class.full_signature: public  NumericalSurface(IAtomContainer atomContainer)
focal_class.identifier: NumericalSurface
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.signature:  NumericalSurface(IAtomContainer atomContainer)
focal_class.class_method_signature: NumericalSurface.NumericalSurface(IAtomContainer atomContainer, double solventRadius, int tesslevel)
focal_class.full_signature: public  NumericalSurface(IAtomContainer atomContainer, double solventRadius, int tesslevel)
focal_class.identifier: NumericalSurface
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, double solventRadius, int tesslevel)
focal_class.signature:  NumericalSurface(IAtomContainer atomContainer, double solventRadius, int tesslevel)
focal_class.class_method_signature: NumericalSurface.calculateSurface()
focal_class.full_signature: @Deprecated public void calculateSurface()
focal_class.identifier: calculateSurface
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void calculateSurface()
focal_class.class_method_signature: NumericalSurface.init()
focal_class.full_signature: private void init()
focal_class.identifier: init
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void init()
focal_class.class_method_signature: NumericalSurface.getAllSurfacePoints()
focal_class.full_signature: public Point3d[] getAllSurfacePoints()
focal_class.identifier: getAllSurfacePoints
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Point3d[]
focal_class.signature: Point3d[] getAllSurfacePoints()
focal_class.class_method_signature: NumericalSurface.getAtomSurfaceMap()
focal_class.full_signature: public Map<IAtom, List<Point3d>> getAtomSurfaceMap()
focal_class.identifier: getAtomSurfaceMap
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Map<IAtom, List<Point3d>>
focal_class.signature: Map<IAtom, List<Point3d>> getAtomSurfaceMap()
focal_class.class_method_signature: NumericalSurface.getSurfacePoints(int atomIdx)
focal_class.full_signature: public Point3d[] getSurfacePoints(int atomIdx)
focal_class.identifier: getSurfacePoints
focal_class.modifiers: public
focal_class.parameters: (int atomIdx)
focal_class.return: Point3d[]
focal_class.signature: Point3d[] getSurfacePoints(int atomIdx)
focal_class.class_method_signature: NumericalSurface.getSurfaceArea(int atomIdx)
focal_class.full_signature: public double getSurfaceArea(int atomIdx)
focal_class.identifier: getSurfaceArea
focal_class.modifiers: public
focal_class.parameters: (int atomIdx)
focal_class.return: double
focal_class.signature: double getSurfaceArea(int atomIdx)
focal_class.class_method_signature: NumericalSurface.getAllSurfaceAreas()
focal_class.full_signature: public double[] getAllSurfaceAreas()
focal_class.identifier: getAllSurfaceAreas
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double[]
focal_class.signature: double[] getAllSurfaceAreas()
focal_class.class_method_signature: NumericalSurface.getTotalSurfaceArea()
focal_class.full_signature: public double getTotalSurfaceArea()
focal_class.identifier: getTotalSurfaceArea
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getTotalSurfaceArea()
focal_class.class_method_signature: NumericalSurface.translatePoints(int atmIdx, Point3d[][] points, int pointDensity, IAtom atom, Point3d cp)
focal_class.full_signature: private void translatePoints(int atmIdx, Point3d[][] points, int pointDensity, IAtom atom, Point3d cp)
focal_class.identifier: translatePoints
focal_class.modifiers: private
focal_class.parameters: (int atmIdx, Point3d[][] points, int pointDensity, IAtom atom, Point3d cp)
focal_class.return: void
focal_class.signature: void translatePoints(int atmIdx, Point3d[][] points, int pointDensity, IAtom atom, Point3d cp)
focal_class.class_method_signature: NumericalSurface.atomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, IAtom atom, Tessellate tess)
focal_class.full_signature: private Point3d[][] atomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, IAtom atom, Tessellate tess)
focal_class.identifier: atomicSurfacePoints
focal_class.modifiers: private
focal_class.parameters: (NeighborList nbrlist, int currAtomIdx, IAtom atom, Tessellate tess)
focal_class.return: Point3d[][]
focal_class.signature: Point3d[][] atomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, IAtom atom, Tessellate tess)
focal_method.body: public Map<IAtom, List<Point3d>> getAtomSurfaceMap() {
          Map<IAtom,List<Point3d>> map = new HashMap<>();
          for (int i = 0; i < this.surfPoints.length; i++) {
              if (!this.surfPoints[i].isEmpty())
                  map.put(this.atoms[i], Collections.unmodifiableList(this.surfPoints[i]));
          }
          return map;
      }
focal_method.class_method_signature: NumericalSurface.getAtomSurfaceMap()
focal_method.full_signature: public Map<IAtom, List<Point3d>> getAtomSurfaceMap()
focal_method.identifier: getAtomSurfaceMap
focal_method.invocations: isEmpty put unmodifiableList
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: Map<IAtom, List<Point3d>>
focal_method.signature: Map<IAtom, List<Point3d>> getAtomSurfaceMap()