Exemplo n.º 1
0
 AtomSetCollection readAtomSetCollection(BufferedReader reader) throws Exception {
   this.reader = reader;
   atomSetCollection = new AtomSetCollection("mol2");
   setFractionalCoordinates(false);
   readLine();
   modelNumber = 0;
   while (line != null) {
     if (line.equals("@<TRIPOS>MOLECULE")) {
       if (++modelNumber == desiredModelNumber || desiredModelNumber <= 0) {
         try {
           processMolecule();
         } catch (Exception e) {
           Logger.error("Could not read file at line: " + line, e);
         }
         if (desiredModelNumber > 0) break;
         continue;
       }
     }
     readLine();
   }
   return atomSetCollection;
 }
Exemplo n.º 2
0
  void setProperty(String propertyName, Object value, BitSet bs) {

    Logger.debug("MeshCollection.setProperty(" + propertyName + "," + value + ")");
    /*
    Logger.debug("meshCount=" + meshCount +
                       " currentMesh=" + currentMesh);
    for (int i = 0; i < meshCount; ++i) {
      Mesh mesh = meshes[i];
      Logger.debug("i=" + i +
                         " mesh.thisID=" + mesh.thisID +
                         " mesh.visible=" + mesh.visible +
                         " mesh.translucent=" + mesh.translucent +
                         " mesh.colix=" + mesh.meshColix);
    }
    */

    if ("thisID" == propertyName) {
      setMesh((String) value);
      return;
    }

    if ("reset" == propertyName) {
      String thisID = (String) value;
      if (setMesh(thisID) == null) return;
      deleteMesh();
      setMesh(thisID);
      return;
    }

    if ("on" == propertyName) {
      if (currentMesh != null) currentMesh.visible = true;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].visible = true;
      }
      return;
    }
    if ("off" == propertyName) {
      if (currentMesh != null) currentMesh.visible = false;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].visible = false;
      }
      return;
    }

    if ("background" == propertyName) {
      boolean doHide = !((Boolean) value).booleanValue();
      if (currentMesh != null) currentMesh.hideBackground = doHide;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].hideBackground = doHide;
      }
      return;
    }
    if ("title" == propertyName) {
      if (currentMesh != null) {
        currentMesh.title = (String[]) value;
      }
      return;
    }

    if ("color" == propertyName) {
      if (value == "sets") {
        currentMesh.allocVertexColixes();
        for (int i = 0; i < currentMesh.surfaceSet.length; i++)
          for (int j = 0; j < currentMesh.vertexCount; j++)
            if (currentMesh.surfaceSet[i].get(j))
              currentMesh.vertexColixes[j] = Graphics3D.getColix(Graphics3D.colorNames[i]);
        return;
      }
      if (value != null) {
        colix = Graphics3D.getColix(value);
        if (currentMesh != null) {
          currentMesh.colix = colix;
          currentMesh.vertexColixes = null;
        } else {
          for (int i = meshCount; --i >= 0; ) {
            Mesh mesh = meshes[i];
            mesh.colix = colix;
            mesh.vertexColixes = null;
          }
        }
      }
      return;
    }
    if ("translucency" == propertyName) {
      boolean isTranslucent = ("translucent" == value);
      if (currentMesh != null) currentMesh.setTranslucent(isTranslucent);
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].setTranslucent(isTranslucent);
      }
      return;
    }
    if ("dots" == propertyName) {
      boolean showDots = value == Boolean.TRUE;
      if (currentMesh != null) currentMesh.showPoints = showDots;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].showPoints = showDots;
      }
      return;
    }
    if ("mesh" == propertyName) {
      boolean showMesh = value == Boolean.TRUE;
      if (currentMesh != null) currentMesh.drawTriangles = showMesh;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].drawTriangles = showMesh;
      }
      return;
    }
    if ("fill" == propertyName) {
      boolean showFill = value == Boolean.TRUE;
      if (currentMesh != null) currentMesh.fillTriangles = showFill;
      else {
        for (int i = meshCount; --i >= 0; ) meshes[i].fillTriangles = showFill;
      }
      return;
    }
    if ("delete" == propertyName) {
      deleteMesh();
      return;
    }
  }