Package org.openscience.cdk.protein

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

Keywords:

protein, pocket

Created on:

2005-09-30

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	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 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.