Class GridGenerator

java.lang.Object
org.openscience.cdk.tools.GridGenerator

public class GridGenerator extends Object
Generates a grid of points in 3D space within given boundaries.
Author:
cho
Source code:
main
Created on:
2005-09-30
  • Constructor Details

    • GridGenerator

      public GridGenerator()
    • GridGenerator

      public GridGenerator(double min, double max)
    • GridGenerator

      public GridGenerator(double min, double max, double initialValue)
      Parameters:
      initialValue - used as initial value for the grid points
    • GridGenerator

      public GridGenerator(double[] minMax, double initialValue, boolean cubicGridFlag)
  • Method Details

    • setDimension

      public void setDimension(double min, double max)
      Method sets the maximal 3d dimensions to given min and max values.
    • setDimension

      public void setDimension(double[] minMax, boolean cubicGridFlag)
      Method sets the maximal 3d dimensions to given min and max values.
    • setDimension

      public void setDimension(double minx, double maxx, double miny, double maxy, double minz, double maxz)
      Method sets the maximal 3d dimensions to given min and max values.
    • generateGrid

      public void generateGrid()
      Main method creates a grid between given boundaries (dimensions). The grid my be extended over the given boundaries with the variable extendGrid.
    • initializeGrid

      public void initializeGrid(double value)
      Method initialise the given grid points with a value.
    • initializeGrid

      public double[][][] initializeGrid(double[][][] grid, double value)
      Method initialise the given grid points with a value.
    • gridToGridArray

      public double[] gridToGridArray(double[][][] grid)
      Method transforms the grid to an array.
    • getCoordinatesFromGridPoint

      public javax.vecmath.Point3d getCoordinatesFromGridPoint(javax.vecmath.Point3d gridPoint)
      Method calculates coordinates from a given grid point.
    • getCoordinatesFromGridPoint

      public javax.vecmath.Point3d getCoordinatesFromGridPoint(int gridPoint)
      Method calculates coordinates from a given grid array position.
    • getGridPointFrom3dCoordinates

      public javax.vecmath.Point3d getGridPointFrom3dCoordinates(javax.vecmath.Point3d coord) throws Exception
      Method calculates the nearest grid point from given coordinates.
      Throws:
      Exception
    • writeGridInPmeshFormat

      public void writeGridInPmeshFormat(String outPutFileName) throws IOException
      Method transforms the grid into pmesh format.
      Throws:
      IOException
    • writeGridInPmeshFormat

      public void writeGridInPmeshFormat(String outPutFileName, double cutOff) throws IOException
      Method transforms the grid into pmesh format. Only grid points with specific value defined with cutoff are considered.
      
       cutoff <0, the values considered must be <=cutoff
       cutoff >0, the values considered must be >=cutoff
       
      Throws:
      IOException
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • getDim

      public int[] getDim()
      Returns:
      Returns the dim.
    • setDim

      public void setDim(int[] dim)
      Parameters:
      dim - The dim to set.
    • getExtendGrid

      public double getExtendGrid()
      Returns:
      Returns the extendGrid.
    • setExtendGrid

      public void setExtendGrid(double extendGrid)
      Parameters:
      extendGrid - The extendGrid to set.
    • getGrid

      public double[][][] getGrid()
      Returns:
      Returns the grid.
    • setGrid

      public void setGrid(double[][][] grid)
      Parameters:
      grid - The grid to set.
    • getLatticeConstant

      public double getLatticeConstant()
      Returns:
      Returns the latticeConstant.
    • setLatticeConstant

      public void setLatticeConstant(double latticeConstant)
      Parameters:
      latticeConstant - The latticeConstant to set.
    • getGridArray

      public double[] getGridArray()
      Returns:
      Returns the gridArray.
    • getMaxx

      public double getMaxx()
      Returns:
      Returns the maxx.
    • getMaxy

      public double getMaxy()
      Returns:
      Returns the maxy.
    • getMaxz

      public double getMaxz()
      Returns:
      Returns the maxz.
    • getMinx

      public double getMinx()
      Returns:
      Returns the minx.
    • getMiny

      public double getMiny()
      Returns:
      Returns the miny.
    • getMinz

      public double getMinz()
      Returns:
      Returns the minz.