ProteinPocketFinder (cdk 2.7.1 API)

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:
master

Belongs to CDK module:
extra

Keywords:

protein, pocket

Created on:

2005-09-30

Constructor Summary

Constructors
Constructor and Description
`ProteinPocketFinder(IBioPolymer protein, double[][][] grid)`
`ProteinPocketFinder(String biopolymerFile, boolean cubicGrid)`
`ProteinPocketFinder(String biopolymerFile, double[][][] grid)`
`ProteinPocketFinder(String biopolymerFile, double latticeConstant, boolean cubicGrid)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`assignProteinToGrid()` Method assigns the atoms of a biopolymer to the grid.
`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.
`void`	`axisScanX(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`void`	`axisScanY(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`void`	`axisScanZ(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`List<javax.vecmath.Point3d>`	`clusterPSPPocket(javax.vecmath.Point3d root, List<javax.vecmath.Point3d> subPocket, int[] dim)` Method performs the clustering, is called by findPockets().
`void`	`createCubicGrid()` Method creates a cubic grid with the grid generator class.
`void`	`debuggCheckPSPEvent()`
`void`	`diagonalAxisScanXYZ(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`void`	`diagonalAxisScanXZY(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`void`	`diagonalAxisScanYXZ(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`void`	`diagonalAxisScanYZX(int dimK, int dimL, int dimM)` Method performs a scan; works only for cubic grids!
`double[]`	`findGridBoundaries()` Method determines the minimum and maximum values of a coordinate space up to 3D space.
`double[][][]`	`getGrid()`
`double`	`getLatticeConstant()`
`double`	`getLinkageRadius()`
`int`	`getMinPSCluster()`
`int`	`getMinPSPocket()`
`List<List<javax.vecmath.Point3d>>`	`getPockets()`
`int`	`getPocketSize()`
`IBioPolymer`	`getProtein()`
`int`	`getProteinInterior()`
`double`	`getRAtom()`
`double`	`getRSolvent()`
`int`	`getSolvantValue()`
`String`	`getVanDerWaalsFile()`
`void`	`gridToPmesh(String outPutFileName)` Method writes the grid to pmesh format.
`void`	`proteinGridToPmesh(String outPutFileName)` Method writes the protein grid points to pmesh format.
`void`	`pspGridToPmesh(String outPutFileName)` Method writes the PSP points (≥minPSPocket) to pmesh format.
`void`	`setAtomCheckRadius(double atomCheckRadius)`
`void`	`setGrid(double[][][] grid)`
`void`	`setLatticeConstant(double latticeConstant)`
`void`	`setLinkageRadius(double linkageRadius)`
`void`	`setMinPSCluster(int minPSCluster)`
`void`	`setMinPSPocket(int minPSPocket)`
`void`	`setPocketSize(int pocketSize)`
`void`	`setProtein(IBioPolymer protein)`
`void`	`setProteinInterior(int proteinInterior)`
`void`	`setRAtom(double atom)`
`void`	`setRSolvent(double solvent)`
`void`	`setSolvantValue(int solvantValue)`
`void`	`setVanDerWaalsFile(String vanDerWaalsFile)`
`void`	`sitefinder()` Main method which calls the methods: assignProteinToGrid, GridScan, and FindPockets.
`void`	`writePocketsToPMesh(String outPutFileName)` Method writes the pockets to pmesh format.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - 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 Detail
  - 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.

Class ProteinPocketFinder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ProteinPocketFinder

ProteinPocketFinder

ProteinPocketFinder

ProteinPocketFinder

Method Detail

findGridBoundaries

createCubicGrid

assignProteinToGrid

debuggCheckPSPEvent

sitefinder

clusterPSPPocket

diagonalAxisScanXZY

diagonalAxisScanYZX

diagonalAxisScanYXZ

diagonalAxisScanXYZ

axisScanX

axisScanY

axisScanZ

assignVdWRadiiToProtein

gridToPmesh

pspGridToPmesh

proteinGridToPmesh

writePocketsToPMesh

getGrid

setGrid

getLatticeConstant

setLatticeConstant

getLinkageRadius

setLinkageRadius

getMinPSCluster

setMinPSCluster

getMinPSPocket

setMinPSPocket

getPocketSize

setPocketSize

getProtein

setProtein

getProteinInterior

setProteinInterior

getRAtom

setRAtom

getRSolvent

setRSolvent

getSolvantValue

setSolvantValue

getVanDerWaalsFile

setVanDerWaalsFile

getPockets

setAtomCheckRadius