Added vtkMolecule, vtkAtom, and vtkBond to the vtkFiltering kit.

These data objects are in vtkFiltering to prevent circular
dependencies between vtkFiltering, vtkRendering, and vtkChemistry.

Change-Id: I6f6340b531f0364d0b7d7560ac600cefd1e18c2e

Filtering/CMakeLists.txt

@@ -21,11 +21,13 @@ vtkAMRBox.cxx
 vtkAnnotation.cxx
 vtkAnnotationLayers.cxx
 vtkAnnotationLayersAlgorithm.cxx
+vtkAtom.cxx
 vtkAttributesErrorMetric.cxx
 vtkBiQuadraticQuad.cxx
 vtkBiQuadraticQuadraticHexahedron.cxx
 vtkBiQuadraticQuadraticWedge.cxx
 vtkBiQuadraticTriangle.cxx
+vtkBond.cxx
 vtkBSPCuts.cxx
 vtkBSPIntersections.cxx
 vtkCachedStreamingDemandDrivenPipeline.cxx
@@ -151,6 +153,7 @@ vtkMeanValueCoordinatesInterpolator.cxx
 vtkMergePoints.cxx
 vtkMarchingSquaresLineCases.cxx
 vtkMarchingCubesTriangleCases.cxx
+vtkMolecule.cxx
 vtkMultiBlockDataSetAlgorithm.cxx
 vtkMultiBlockDataSet.cxx
 vtkMultiPieceDataSet.cxx
@@ -269,6 +272,8 @@ vtkAbstractImageInterpolator
 vtkAbstractInterpolatedVelocityField
 vtkAbstractMapper
 vtkAbstractPointLocator
+vtkAtom
+vtkBond
 vtkCell
 vtkCell3D
 vtkCompositeDataIterator
@@ -412,4 +417,3 @@ IF(NOT VTK_INSTALL_NO_DEVELOPMENT)
     COMPONENT Development
     )
 ENDIF(NOT VTK_INSTALL_NO_DEVELOPMENT)
-

Filtering/vtkAtom.cxx

+/*=========================================================================
+
+Program:   Visualization Toolkit
+Module:    vtkAtom.cxx
+Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+All rights reserved.
+See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "vtkAtom.h"
+
+#include "vtkMolecule.h"
+#include "vtkVector.h"
+
+#include <assert.h>
+
+//----------------------------------------------------------------------------
+vtkAtom::vtkAtom(vtkMolecule *parent, vtkIdType id)
+  : Molecule(parent), Id(id)
+{
+  assert(parent != 0);
+  assert(id < parent->GetNumberOfAtoms());
+}
+
+//----------------------------------------------------------------------------
+vtkAtom::~vtkAtom()
+{
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::PrintSelf(ostream &os, vtkIndent indent)
+{
+  char buffer[80];
+  double coord[3];
+  this->GetPosition(coord);
+  snprintf(buffer, 80, "Molecule: %p Id: %4d Ele: %3d Pos: %9.5f %9.5f %9.5f\n",
+           this->Molecule, this->Id, this->GetAtomicNumber(),
+           coord[0], coord[1], coord[2]);
+  os << indent << buffer;
+}
+
+//----------------------------------------------------------------------------
+unsigned short vtkAtom::GetAtomicNumber()
+{
+  return this->Molecule->GetAtomAtomicNumber(this->Id);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetAtomicNumber(unsigned short atomicNum)
+{
+  this->Molecule->SetAtomAtomicNumber(this->Id, atomicNum);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::GetPosition(double pos[3])
+{
+  return this->Molecule->GetAtomPosition(this->Id, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetPosition(const double pos[3])
+{
+  this->Molecule->SetAtomPosition(this->Id, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::GetPosition(float pos[3])
+{
+  this->Molecule->GetAtomPosition(this->Id, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetPosition(const float pos[3])
+{
+  this->Molecule->SetAtomPosition(this->Id, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetPosition(float x, float y, float z)
+{
+  this->Molecule->SetAtomPosition(this->Id, x, y, z);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3f vtkAtom::GetPositionAsVector3f()
+{
+  return this->Molecule->GetAtomPositionAsVector3f(this->Id);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetPosition(const vtkVector3f &pos)
+{
+  this->Molecule->SetAtomPosition(this->Id, pos);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3d vtkAtom::GetPositionAsVector3d()
+{
+  return this->Molecule->GetAtomPositionAsVector3d(this->Id);
+}
+
+//----------------------------------------------------------------------------
+void vtkAtom::SetPosition(const vtkVector3d &pos)
+{
+  this->Molecule->SetAtomPosition(this->Id, pos);
+}

Filtering/vtkAtom.h

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    vtkAtom.h
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+// .NAME vtkAtom - convenience proxy for vtkMolecule
+// .SECTION Description
+
+#ifndef __vtkAtom_h
+#define __vtkAtom_h
+
+#include "vtkObject.h" // For macros, defines, etc
+
+class vtkMolecule;
+class vtkVector3d;
+class vtkVector3f;
+
+class VTK_FILTERING_EXPORT vtkAtom
+{
+ public:
+  ~vtkAtom();
+
+  void PrintSelf(ostream &os, vtkIndent indent);
+
+  // Description:
+  // Return the Id used to identify this atom in the parent molecule.
+  vtkIdType GetId()
+  {
+    return this->Id;
+  }
+
+  // Description:
+  // Return the parent molecule of this atom.
+  vtkMolecule * GetMolecule()
+  {
+    return this->Molecule;
+  }
+
+  // Description:
+  // Get/Set the atomic number of this atom
+  unsigned short GetAtomicNumber();
+  void SetAtomicNumber(unsigned short atomicNum);
+
+  // Description:
+  // Get/Set the position of this atom
+  void GetPosition(double pos[3]);
+  void SetPosition(const double pos[3]);
+  void GetPosition(float pos[3]);
+  void SetPosition(const float pos[3]);
+  void SetPosition(float x, float y, float z);
+  vtkVector3f GetPositionAsVector3f();
+  void SetPosition(const vtkVector3f &pos);
+  vtkVector3d GetPositionAsVector3d();
+  void SetPosition(const vtkVector3d &pos);
+
+ protected:
+  friend class vtkMolecule;
+
+  vtkAtom(vtkMolecule *parent, vtkIdType id);
+
+  vtkMolecule *Molecule;
+  vtkIdType Id;
+};
+
+#endif

Filtering/vtkBond.cxx

+/*=========================================================================
+
+Program:   Visualization Toolkit
+Module:    vtkBond.cxx
+Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+All rights reserved.
+See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "vtkBond.h"
+
+#include "vtkAtom.h"
+#include "vtkMolecule.h"
+#include "vtkVector.h"
+#include "vtkVectorOperators.h"
+
+#include <assert.h>
+
+//----------------------------------------------------------------------------
+vtkBond::vtkBond(vtkMolecule *parent, vtkIdType id,
+                 vtkIdType beginAtomId, vtkIdType endAtomId)
+  : Molecule(parent), Id(id), BeginAtomId(beginAtomId), EndAtomId(endAtomId)
+{
+  assert(parent != 0);
+  assert(id < parent->GetNumberOfBonds());
+  assert(beginAtomId < parent->GetNumberOfAtoms());
+  assert(endAtomId < parent->GetNumberOfAtoms());
+}
+
+//----------------------------------------------------------------------------
+vtkBond::~vtkBond()
+{
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::PrintSelf(ostream &os, vtkIndent indent)
+{
+  char buffer[80];
+  double coord[3];
+  snprintf(buffer, 80,
+           "Parent: %p Id: %4d Order: %1d Len: %9.5f BeginAtomId: %d "
+           "EndAtomId: %d\n", this->Molecule, this->Id, this->GetBondOrder(),
+           this->GetBondLength(), this->BeginAtomId, this->EndAtomId);
+  os << indent << buffer;
+
+  os << indent << "Bonded Atoms:\n";
+  this->Molecule->GetAtom(this->BeginAtomId).PrintSelf
+    (os, indent.GetNextIndent());
+  this->Molecule->GetAtom(this->EndAtomId).PrintSelf
+    (os, indent.GetNextIndent());
+}
+
+//----------------------------------------------------------------------------
+double vtkBond::GetBondLength()
+{
+  // Reimplement here to avoid the potential cost of building the EdgeList
+  // (We already know the atomIds, no need to look them up)
+  vtkVector3d pos1 =
+      this->Molecule->GetAtomPositionAsVector3d(this->BeginAtomId);
+  vtkVector3d pos2 =
+      this->Molecule->GetAtomPositionAsVector3d(this->EndAtomId);
+
+  return (pos2 - pos1).Norm();
+}
+
+//----------------------------------------------------------------------------
+vtkAtom vtkBond::GetBeginAtom()
+{
+  return this->Molecule->GetAtom(this->BeginAtomId);
+}
+
+//----------------------------------------------------------------------------
+vtkAtom vtkBond::GetEndAtom()
+{
+  return this->Molecule->GetAtom(this->EndAtomId);
+}
+
+//----------------------------------------------------------------------------
+unsigned short vtkBond::GetBondOrder()
+{
+  return this->Molecule->GetBondOrder(this->Id);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::GetBeginAtomPosition(double pos[3])
+{
+  this->Molecule->GetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetBeginAtomPosition(const double pos[3])
+{
+  this->Molecule->SetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::GetEndAtomPosition(double pos[3])
+{
+  this->Molecule->GetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetEndAtomPosition(const double pos[3])
+{
+  this->Molecule->SetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::GetBeginAtomPosition(float pos[3])
+{
+  this->Molecule->GetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetBeginAtomPosition(const float pos[3])
+{
+  this->Molecule->SetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::GetEndAtomPosition(float pos[3])
+{
+  this->Molecule->GetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetEndAtomPosition(const float pos[3])
+{
+  this->Molecule->SetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetBeginAtomPosition(double x, double y, double z)
+{
+  this->Molecule->SetAtomPosition(this->BeginAtomId, x, y, z);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetEndAtomPosition(double x, double y, double z)
+{
+  this->Molecule->SetAtomPosition(this->EndAtomId, x, y, z);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetBeginAtomPosition(const vtkVector3f &pos)
+{
+  this->Molecule->SetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3f vtkBond::GetBeginAtomPositionAsVector3f()
+{
+  return this->Molecule->GetAtomPositionAsVector3f(this->BeginAtomId);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetEndAtomPosition(const vtkVector3f &pos)
+{
+  this->Molecule->SetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3f vtkBond::GetEndAtomPositionAsVector3f()
+{
+  return this->Molecule->GetAtomPositionAsVector3f(this->EndAtomId);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetBeginAtomPosition(const vtkVector3d &pos)
+{
+  this->Molecule->SetAtomPosition(this->BeginAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3d vtkBond::GetBeginAtomPositionAsVector3d()
+{
+  return this->Molecule->GetAtomPositionAsVector3d(this->BeginAtomId);
+}
+
+//----------------------------------------------------------------------------
+void vtkBond::SetEndAtomPosition(const vtkVector3d &pos)
+{
+  this->Molecule->SetAtomPosition(this->EndAtomId, pos);
+}
+
+//----------------------------------------------------------------------------
+vtkVector3d vtkBond::GetEndAtomPositionAsVector3d()
+{
+  return this->Molecule->GetAtomPositionAsVector3d(this->EndAtomId);
+}

Filtering/vtkBond.h

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    vtkBond.h
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+// .NAME vtkBond - convenience proxy for vtkMolecule
+// .SECTION Description
+
+#ifndef __vtkBond_h
+#define __vtkBond_h
+
+#include "vtkObject.h" // For macros, etc
+#include "vtkAtom.h" // For vtkAtom
+
+class vtkMolecule;
+class vtkVector3d;
+class vtkVector3f;
+
+class VTK_FILTERING_EXPORT vtkBond
+{
+ public:
+  ~vtkBond();
+  void PrintSelf(ostream &os, vtkIndent indent);
+
+  // Description:
+  // Return the Id used to identify this bond in the parent molecule.
+  vtkIdType GetId()
+  {
+    return this->Id;
+  }
+
+  // Description:
+  // Return the parent molecule of this bond.
+  vtkMolecule * GetMolecule()
+  {
+    return this->Molecule;
+  }
+
+  // Description:
+  // Get the starting / ending atom ids for this bond.
+  vtkIdType GetBeginAtomId()
+  {
+    return this->BeginAtomId;
+  }
+  vtkIdType GetEndAtomId()
+  {
+    return this->EndAtomId;
+  }
+
+  // Description:
+  // Get a vtkAtom object that refers to the starting / ending atom
+  // for this bond.
+  vtkAtom GetBeginAtom();
+  vtkAtom GetEndAtom();
+
+  // Description:
+  // Get the bond order for this bond.
+  unsigned short GetBondOrder();
+
+  // Description:
+  // Get the distance between the bonded atoms
+  //
+  // @note This function is faster than vtkMolecule::GetBondLength and
+  // should be used when possible.
+  double GetBondLength();
+
+  // Description:
+  // Get/Set the positions of the starting/ending atoms
+  void GetBeginAtomPosition(double pos[3]);
+  void SetBeginAtomPosition(const double pos[3]);
+  void GetEndAtomPosition(double pos[3]);
+  void SetEndAtomPosition(const double pos[3]);
+  void GetBeginAtomPosition(float pos[3]);
+  void SetBeginAtomPosition(const float pos[3]);
+  void GetEndAtomPosition(float pos[3]);
+  void SetEndAtomPosition(const float pos[3]);
+  void SetBeginAtomPosition(double x, double y, double z);
+  void SetEndAtomPosition(double x, double y, double z);
+  void SetBeginAtomPosition(const vtkVector3f &pos);
+  vtkVector3f GetBeginAtomPositionAsVector3f();
+  void SetEndAtomPosition(const vtkVector3f &pos);
+  vtkVector3f GetEndAtomPositionAsVector3f();
+  void SetBeginAtomPosition(const vtkVector3d &pos);
+  vtkVector3d GetBeginAtomPositionAsVector3d();
+  void SetEndAtomPosition(const vtkVector3d &pos);
+  vtkVector3d GetEndAtomPositionAsVector3d();
+
+ protected:
+  friend class vtkMolecule;
+
+  vtkBond(vtkMolecule *parent, vtkIdType id,
+          vtkIdType beginAtomId, vtkIdType endAtomId);
+
+  vtkMolecule *Molecule;
+  vtkIdType Id;
+  vtkIdType BeginAtomId;
+  vtkIdType EndAtomId;
+};
+
+#endif

Filtering/vtkDataObjectTypes.cxx

@@ -50,6 +50,10 @@ PURPOSE.  See the above copyright notice for more information.
 #include  "vtkArrayData.h"
 #endif
 
+#ifdef VTK_USE_CHEMISTRY
+#include  "vtkMolecule.h"
+#endif
+
 vtkStandardNewMacro(vtkDataObjectTypes);
 
 // This list should contain the data object class names in
@@ -85,6 +89,9 @@ static const char* vtkDataObjectTypesStrings[] = {
   "vtkDirectedAcyclicGraph",
   "vtkArrayData",
   "vtkReebGraph",
+#ifdef VTK_USE_CHEMISTRY
+  "vtkMolecule",
+#endif
   NULL
 };
 
@@ -244,6 +251,12 @@ vtkDataObject* vtkDataObjectTypes::NewDataObject(const char* type)
     {
     return vtkReebGraph::New();
     }
+#ifdef VTK_USE_CHEMISTRY
+  else if(strcmp(type, "vtkMolecule") == 0)
+    {
+    return vtkMolecule::New();
+    }
+#endif
 #ifdef VTK_USE_N_WAY_ARRAYS
   else if(strcmp(type, "vtkArrayData") == 0)
     {

Filtering/vtkMolecule.cxx

+/*=========================================================================
+
+Program:   Visualization Toolkit
+Module:    vtkMolecule.cxx
+Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+All rights reserved.
+See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "vtkMolecule.h"
+
+#include "vtkDataSetAttributes.h"
+#include "vtkEdgeListIterator.h"
+#include "vtkIdTypeArray.h"
+#include "vtkObjectFactory.h"
+#include "vtkPlane.h"
+#include "vtkPoints.h"
+#include "vtkUnsignedShortArray.h"
+#include "vtkVector.h"
+#include "vtkVectorOperators.h"
+
+#include <assert.h>
+
+//----------------------------------------------------------------------------
+vtkStandardNewMacro(vtkMolecule);
+
+//----------------------------------------------------------------------------
+vtkMolecule::vtkMolecule()
+{
+  this->SetPoints(vtkPoints::New());
+  this->Initialize();
+}
+
+//----------------------------------------------------------------------------
+void vtkMolecule::Initialize()
+{
+  // Reset underlying data structure
+  this->Superclass::Initialize();
+
+  // Setup vertex data
+  vtkDataSetAttributes *vertData = this->GetVertexData();
+  vertData->AllocateArrays(1); // atomic nums
+
+  // Atomic numbers
+  vtkUnsignedShortArray *atomicNums = vtkUnsignedShortArray::New();
+  atomicNums->SetNumberOfComponents(1);
+  atomicNums->SetName("Atomic Numbers");
+  vertData->SetScalars(atomicNums);
+
+  // Nuclear coordinates
+  this->Points->Initialize();
+
+  // Setup edge data
+  vtkDataSetAttributes *edgeData = this->GetEdgeData();
+  edgeData->AllocateArrays(1); // Bond orders
+
+  vtkUnsignedShortArray *bondOrders = vtkUnsignedShortArray::New();
+  bondOrders->SetNumberOfComponents(1);
+  bondOrders->SetName("Bond Orders");
+  edgeData->SetScalars(bondOrders);
+
+  this->UpdateBondList();
+
+  this->Modified();
+}
+
+//----------------------------------------------------------------------------