Changeset 3844 for branches/1.3/packages/vizservers/vtkvis/Molecule.cpp

Timestamp:

Jul 26, 2013, 6:00:09 PM (11 years ago)

Author:

ldelgass

Message:

Sync with trunk. Branch now differs only from trunk by r3722 (branch is version
1.3, trunk is version 1.4)

Location:

branches/1.3

Files:

• . (modified) (1 prop)
• packages/vizservers/vtkvis/Molecule.cpp (modified) (14 diffs)

branches/1.3/packages/vizservers/vtkvis/Molecule.cpp

@@ -29 +29 @@
 #include <vtkLabelPlacementMapper.h>
 #include <vtkTextProperty.h>
+#include <vtkTransformPolyDataFilter.h>
 
 #include "Molecule.h"
@@ -108 +109 @@
         _atomProp->GetProperty()->SetOpacity(_opacity);
         _atomProp->GetProperty()->SetAmbient(.2);
+        _atomProp->GetProperty()->SetSpecular(.2);
+        _atomProp->GetProperty()->SetSpecularPower(80.0);
         if (!_lighting)
             _atomProp->GetProperty()->LightingOff();
@@ -121 +124 @@
         _bondProp->GetProperty()->SetOpacity(_opacity);
         _bondProp->GetProperty()->SetAmbient(.2);
+        _bondProp->GetProperty()->SetSpecular(.2);
+        _bondProp->GetProperty()->SetSpecularPower(80.0);
         if (!_lighting)
             _bondProp->GetProperty()->LightingOff();
@@ -178 +183 @@
     addLabelArray(ds);
     addRadiusArray(ds, _atomScaling, _radiusScale);
+    computeBonds(ds);
 
     vtkPolyData *pd = vtkPolyData::SafeDownCast(ds);
@@ -231 +237 @@
                 _labelHierarchy = vtkSmartPointer<vtkPointSetToLabelHierarchy>::New();
             }
-#ifdef USE_VTK6
-            _labelHierarchy->SetInputData(pd);
+            if (_labelTransform == NULL) {
+                _labelTransform = vtkSmartPointer<vtkTransform>::New();
+            }
+            vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
+#ifdef USE_VTK6              
+            transformFilter->SetInputData(pd);
 #else
-            _labelHierarchy->SetInput(pd);
+            transformFilter->SetInput(pd);
 #endif
+            transformFilter->SetTransform(_labelTransform);
+            _labelHierarchy->SetInputConnection(transformFilter->GetOutputPort());
             _labelHierarchy->SetLabelArrayName("_atom_labels");
             _labelHierarchy->GetTextProperty()->SetColor(0, 0, 0);
@@ -255 +267 @@
             _atomMapper->SetInputConnection(pd->GetProducerPort());
 #endif
-            if (ds->GetPointData() != NULL &&
-                ds->GetPointData()->GetVectors() != NULL) {
-                _atomMapper->SetScaleArray(vtkDataSetAttributes::VECTORS);
-                _atomMapper->SetScaleModeToScaleByMagnitude();
-                _atomMapper->ScalingOn();
-            } else {
-                _atomMapper->SetScaleModeToNoDataScaling();
-                _atomMapper->ScalingOff();
-            }
+            _atomMapper->SetScaleArray("_radii");
+            _atomMapper->SetScaleModeToScaleByMagnitude();
+            _atomMapper->ScalingOn();
             _atomMapper->OrientOff();
 
@@ -283 +289 @@
     if (pd->GetNumberOfLines() > 0) {
         _bondMapper->Update();
+    }
+}
+
+void Molecule::updateLabelTransform()
+{
+    if (_labelTransform != NULL && getAssembly() != NULL) {
+        _labelTransform->SetMatrix(getAssembly()->GetMatrix());
     }
 }
@@ -797 +810 @@
         if (_atomMapper != NULL) {
              assert(ds->GetPointData() != NULL &&
-                    ds->GetPointData()->GetVectors() != NULL);
+                    ds->GetPointData()->GetArray("_radii") != NULL);
             _atomMapper->SetScaleModeToScaleByMagnitude();
-            _atomMapper->SetScaleArray(vtkDataSetAttributes::VECTORS);
+            _atomMapper->SetScaleArray("_radii");
             _atomMapper->ScalingOn();
         }
@@ -887 +900 @@
         bondPoints->InsertNextPoint(newPt1);
 
+#ifdef DEBUG
         TRACE("Bond %d: (%g,%g,%g)-(%g,%g,%g)-(%g,%g,%g)", i,
               pt0[0], pt0[1], pt0[2], 
               center[0], center[1], center[2],
               pt1[0], pt1[1], pt1[2]);
+#endif
 
         double vec[3];
@@ -898 +913 @@
         bondVectors->InsertNextTupleValue(vec);
         bondVectors->InsertNextTupleValue(vec);
+#ifdef DEBUG
         TRACE("Bond %d, vec: %g,%g,%g", i, vec[0], vec[1], vec[2]);
+#endif
 
         double scale[3];
@@ -910 +927 @@
         if (elements != NULL) {
             int element = (int)elements->GetComponent(pts[0], 0);
+#ifdef DEBUG
             TRACE("Bond %d, elt 0: %d", i, element);
+#endif
             bondElements->InsertNextValue(element);
             element = (int)elements->GetComponent(pts[1], 0);
+#ifdef DEBUG
             TRACE("Bond %d, elt 1: %d", i, element);
+#endif
             bondElements->InsertNextValue(element);
         }
@@ -984 +1005 @@
         ;
     }
-    vtkSmartPointer<vtkFloatArray> radii = vtkSmartPointer<vtkFloatArray>::New();
-    radii->SetName("_radii");
-    radii->SetNumberOfComponents(3);
     vtkPolyData *pd = vtkPolyData::SafeDownCast(dataSet);
     if (pd == NULL) {
@@ -992 +1010 @@
         return;
     }
+    vtkDataArray *array = dataSet->GetPointData()->GetArray("_radii");
+    vtkSmartPointer<vtkFloatArray> radii;
+    if (array == NULL) {
+        radii = vtkSmartPointer<vtkFloatArray>::New();
+        radii->SetName("_radii");
+        radii->SetNumberOfComponents(1);
+        radii->SetNumberOfValues(pd->GetNumberOfPoints());
+    } else {
+        radii = vtkFloatArray::SafeDownCast(array);
+        assert(radii != NULL);
+    }
     for (int i = 0; i < pd->GetNumberOfPoints(); i++) {
-        float tuple[3];
-        tuple[1] = tuple[2] = 0;
+        float value;
         if (elements != NULL && radiusSource != NULL) {
             int elt = (int)elements->GetComponent(i, 0);
-            tuple[0] = radiusSource[elt] * scaleFactor;
+            value = radiusSource[elt] * scaleFactor;
         } else {
-            tuple[0] = scaleFactor;
-        }
-        radii->InsertNextTupleValue(tuple);
-    }
-    dataSet->GetPointData()->SetVectors(radii);
+            value = scaleFactor;
+        }
+        radii->SetValue(i, value);
+    }
+    radii->Modified();
+    if (array == NULL) {
+        dataSet->GetPointData()->AddArray(radii);
+    }
 }
 
@@ -1037 +1068 @@
     return elementCmap;
 }
+
+int Molecule::computeBonds(vtkDataSet *dataSet, float tolerance)
+{
+    vtkPolyData *pd = vtkPolyData::SafeDownCast(dataSet);
+    if (pd == NULL) {
+        ERROR("DataSet not a PolyData");
+        return -1;
+    }
+
+    if (pd->GetNumberOfPoints() < 2 ||
+        pd->GetNumberOfLines() > 0) {
+        return 0;
+    }
+
+    vtkDataArray *elements = NULL;
+    if (pd->GetPointData() != NULL &&
+        pd->GetPointData()->GetScalars() != NULL &&
+        strcmp(pd->GetPointData()->GetScalars()->GetName(), "element") == 0) {
+        elements = pd->GetPointData()->GetScalars();
+    } else {
+        TRACE("Can't compute bonds without an element array");
+        return -1;
+    }
+    int numAtoms = pd->GetNumberOfPoints();
+    vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
+    for (int i = 0; i < numAtoms; i++) {
+        double pt1[3];
+        int elem1 = (int)elements->GetComponent(i, 0);
+        float r1 = g_covalentRadii[elem1];
+        pd->GetPoint(i, pt1);
+        for (int j = i+1; j < numAtoms; j++) {
+            float r2, dist;
+            double pt2[3];
+            int elem2 = (int)elements->GetComponent(j, 0);
+
+            if (elem1 == 1 && elem2 == 1)
+                continue;
+
+            r2 = g_covalentRadii[elem2];
+            pd->GetPoint(j, pt2);
+
+            double x = pt1[0] - pt2[0];
+            double y = pt1[1] - pt2[1];
+            double z = pt1[2] - pt2[2];
+            dist = (float)sqrt(x*x + y*y + z*z);
+            //TRACE("i=%d,j=%d elem1=%d,elem2=%d r1=%g,r2=%g, dist=%g", i, j, elem1, elem2, r1, r2, dist); 
+            if (dist < (r1 + r2 + tolerance)) {
+                vtkIdType pts[2];
+                pts[0] = i;
+                pts[1] = j;
+                cells->InsertNextCell(2, pts);
+            }
+        }
+    }
+
+    if (cells->GetNumberOfCells() > 0) {
+        pd->SetLines(cells);
+    }
+
+    TRACE("Generated %d bonds", cells->GetNumberOfCells());
+    return cells->GetNumberOfCells();
+}