Class ProteinPocketFinder

java.lang.Object
org.openscience.cdk.protein.ProteinPocketFinder

public class ProteinPocketFinder extends Object
The detection of pocket and cavities in a bioPolymer is done similar to the program LIGSITE [Hendlich, M. et. al.. Journal of Molecular Graphics and Modelling. 1997. 15].

TODO: Optimisation of the cubic grid placement

Author:
cho
Source code:
main
Belongs to CDK module:
extra
Keywords:
protein, pocket
Created on:
2005-09-30
  • Constructor Details

    • ProteinPocketFinder

      public ProteinPocketFinder(String biopolymerFile, boolean cubicGrid)
      Parameters:
      biopolymerFile - The file name containing the protein
      cubicGrid - if true generate the grid
    • ProteinPocketFinder

      public ProteinPocketFinder(String biopolymerFile, double latticeConstant, boolean cubicGrid)
    • ProteinPocketFinder

      public ProteinPocketFinder(String biopolymerFile, double[][][] grid)
    • ProteinPocketFinder

      public ProteinPocketFinder(IBioPolymer protein, double[][][] grid)
  • Method Details

    • findGridBoundaries

      public double[] findGridBoundaries()
      Method determines the minimum and maximum values of a coordinate space up to 3D space.
      Returns:
      double[] stores min,max,min,max,min,max
    • createCubicGrid

      public void createCubicGrid()
      Method creates a cubic grid with the grid generator class.
    • assignProteinToGrid

      public void assignProteinToGrid() throws Exception
      Method assigns the atoms of a biopolymer to the grid. For every atom the corresponding grid point is identified and set to the value of the proteinInterior variable. The atom radius and solvent radius is accounted for with the variables: double rAtom, and double rSolvent.
      Throws:
      Exception
    • debuggCheckPSPEvent

      public void debuggCheckPSPEvent()
    • sitefinder

      public void sitefinder()
      Main method which calls the methods: assignProteinToGrid, GridScan, and FindPockets.
    • clusterPSPPocket

      public List<javax.vecmath.Point3d> clusterPSPPocket(javax.vecmath.Point3d root, List<javax.vecmath.Point3d> subPocket, int[] dim)
      Method performs the clustering, is called by findPockets().
    • diagonalAxisScanXZY

      public void diagonalAxisScanXZY(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • diagonalAxisScanYZX

      public void diagonalAxisScanYZX(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • diagonalAxisScanYXZ

      public void diagonalAxisScanYXZ(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • diagonalAxisScanXYZ

      public void diagonalAxisScanXYZ(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • axisScanX

      public void axisScanX(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • axisScanY

      public void axisScanY(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • axisScanZ

      public void axisScanZ(int dimK, int dimL, int dimM)
      Method performs a scan; works only for cubic grids!
      Parameters:
      dimK - first dimension
      dimL - second dimension
      dimM - third dimension
    • assignVdWRadiiToProtein

      public void assignVdWRadiiToProtein()
      Method which assigns van der Waals radii to the biopolymer default org/openscience/cdk/config/data/pdb_atomtypes.xml stored in the variable String vanDerWaalsFile.
    • gridToPmesh

      public void gridToPmesh(String outPutFileName)
      Method writes the grid to pmesh format.
    • pspGridToPmesh

      public void pspGridToPmesh(String outPutFileName)
      Method writes the PSP points (≥minPSPocket) to pmesh format.
    • proteinGridToPmesh

      public void proteinGridToPmesh(String outPutFileName)
      Method writes the protein grid points to pmesh format.
    • writePocketsToPMesh

      public void writePocketsToPMesh(String outPutFileName)
      Method writes the pockets to pmesh format.
    • 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.
    • getLinkageRadius

      public double getLinkageRadius()
      Returns:
      Returns the linkageRadius.
    • setLinkageRadius

      public void setLinkageRadius(double linkageRadius)
      Parameters:
      linkageRadius - The linkageRadius to set.
    • getMinPSCluster

      public int getMinPSCluster()
      Returns:
      Returns the minPSCluster.
    • setMinPSCluster

      public void setMinPSCluster(int minPSCluster)
      Parameters:
      minPSCluster - The minPSCluster to set.
    • getMinPSPocket

      public int getMinPSPocket()
      Returns:
      Returns the minPSPocket.
    • setMinPSPocket

      public void setMinPSPocket(int minPSPocket)
      Parameters:
      minPSPocket - The minPSPocket to set.
    • getPocketSize

      public int getPocketSize()
      Returns:
      Returns the pocketSize.
    • setPocketSize

      public void setPocketSize(int pocketSize)
      Parameters:
      pocketSize - The pocketSize to set.
    • getProtein

      public IBioPolymer getProtein()
      Returns:
      Returns the protein.
    • setProtein

      public void setProtein(IBioPolymer protein)
      Parameters:
      protein - The protein to set.
    • getProteinInterior

      public int getProteinInterior()
      Returns:
      Returns the proteinInterior.
    • setProteinInterior

      public void setProteinInterior(int proteinInterior)
      Parameters:
      proteinInterior - The proteinInterior to set.
    • getRAtom

      public double getRAtom()
      Returns:
      Returns the rAtom.
    • setRAtom

      public void setRAtom(double atom)
      Parameters:
      atom - The rAtom to set.
    • getRSolvent

      public double getRSolvent()
      Returns:
      Returns the rSolvent.
    • setRSolvent

      public void setRSolvent(double solvent)
      Parameters:
      solvent - The rSolvent to set.
    • getSolvantValue

      public int getSolvantValue()
      Returns:
      Returns the solvantValue.
    • setSolvantValue

      public void setSolvantValue(int solvantValue)
      Parameters:
      solvantValue - The solvantValue to set.
    • getVanDerWaalsFile

      public String getVanDerWaalsFile()
      Returns:
      Returns the vanDerWaalsFile.
    • setVanDerWaalsFile

      public void setVanDerWaalsFile(String vanDerWaalsFile)
      Parameters:
      vanDerWaalsFile - The vanDerWaalsFile to set.
    • getPockets

      public List<List<javax.vecmath.Point3d>> getPockets()
      Returns:
      Returns the pockets.
    • setAtomCheckRadius

      public void setAtomCheckRadius(double atomCheckRadius)
      Parameters:
      atomCheckRadius - The atomCheckRadius to set.