Package org.openscience.cdk.protein
Class ProteinPocketFinder
- java.lang.Object
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- org.openscience.cdk.protein.ProteinPocketFinder
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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
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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)
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Constructor Detail
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ProteinPocketFinder
public ProteinPocketFinder(String biopolymerFile, boolean cubicGrid)
- Parameters:
biopolymerFile
- The file name containing the proteincubicGrid
- if true generate the grid
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ProteinPocketFinder
public ProteinPocketFinder(String biopolymerFile, double latticeConstant, boolean cubicGrid)
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ProteinPocketFinder
public ProteinPocketFinder(String biopolymerFile, double[][][] grid)
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ProteinPocketFinder
public ProteinPocketFinder(IBioPolymer protein, double[][][] grid)
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Method Detail
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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
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createCubicGrid
public void createCubicGrid()
Method creates a cubic grid with the grid generator class.
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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
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debuggCheckPSPEvent
public void debuggCheckPSPEvent()
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sitefinder
public void sitefinder()
Main method which calls the methods: assignProteinToGrid, GridScan, and FindPockets.
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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().
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diagonalAxisScanXZY
public void diagonalAxisScanXZY(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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diagonalAxisScanYZX
public void diagonalAxisScanYZX(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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diagonalAxisScanYXZ
public void diagonalAxisScanYXZ(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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diagonalAxisScanXYZ
public void diagonalAxisScanXYZ(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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axisScanX
public void axisScanX(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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axisScanY
public void axisScanY(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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axisScanZ
public void axisScanZ(int dimK, int dimL, int dimM)
Method performs a scan; works only for cubic grids!- Parameters:
dimK
- first dimensiondimL
- second dimensiondimM
- third dimension
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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.
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gridToPmesh
public void gridToPmesh(String outPutFileName)
Method writes the grid to pmesh format.
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pspGridToPmesh
public void pspGridToPmesh(String outPutFileName)
Method writes the PSP points (≥minPSPocket) to pmesh format.
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proteinGridToPmesh
public void proteinGridToPmesh(String outPutFileName)
Method writes the protein grid points to pmesh format.
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writePocketsToPMesh
public void writePocketsToPMesh(String outPutFileName)
Method writes the pockets to pmesh format.
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getGrid
public double[][][] getGrid()
- Returns:
- Returns the grid.
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setGrid
public void setGrid(double[][][] grid)
- Parameters:
grid
- The grid to set.
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getLatticeConstant
public double getLatticeConstant()
- Returns:
- Returns the latticeConstant.
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setLatticeConstant
public void setLatticeConstant(double latticeConstant)
- Parameters:
latticeConstant
- The latticeConstant to set.
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getLinkageRadius
public double getLinkageRadius()
- Returns:
- Returns the linkageRadius.
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setLinkageRadius
public void setLinkageRadius(double linkageRadius)
- Parameters:
linkageRadius
- The linkageRadius to set.
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getMinPSCluster
public int getMinPSCluster()
- Returns:
- Returns the minPSCluster.
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setMinPSCluster
public void setMinPSCluster(int minPSCluster)
- Parameters:
minPSCluster
- The minPSCluster to set.
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getMinPSPocket
public int getMinPSPocket()
- Returns:
- Returns the minPSPocket.
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setMinPSPocket
public void setMinPSPocket(int minPSPocket)
- Parameters:
minPSPocket
- The minPSPocket to set.
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getPocketSize
public int getPocketSize()
- Returns:
- Returns the pocketSize.
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setPocketSize
public void setPocketSize(int pocketSize)
- Parameters:
pocketSize
- The pocketSize to set.
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getProtein
public IBioPolymer getProtein()
- Returns:
- Returns the protein.
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setProtein
public void setProtein(IBioPolymer protein)
- Parameters:
protein
- The protein to set.
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getProteinInterior
public int getProteinInterior()
- Returns:
- Returns the proteinInterior.
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setProteinInterior
public void setProteinInterior(int proteinInterior)
- Parameters:
proteinInterior
- The proteinInterior to set.
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getRAtom
public double getRAtom()
- Returns:
- Returns the rAtom.
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setRAtom
public void setRAtom(double atom)
- Parameters:
atom
- The rAtom to set.
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getRSolvent
public double getRSolvent()
- Returns:
- Returns the rSolvent.
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setRSolvent
public void setRSolvent(double solvent)
- Parameters:
solvent
- The rSolvent to set.
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getSolvantValue
public int getSolvantValue()
- Returns:
- Returns the solvantValue.
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setSolvantValue
public void setSolvantValue(int solvantValue)
- Parameters:
solvantValue
- The solvantValue to set.
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getVanDerWaalsFile
public String getVanDerWaalsFile()
- Returns:
- Returns the vanDerWaalsFile.
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setVanDerWaalsFile
public void setVanDerWaalsFile(String vanDerWaalsFile)
- Parameters:
vanDerWaalsFile
- The vanDerWaalsFile to set.
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setAtomCheckRadius
public void setAtomCheckRadius(double atomCheckRadius)
- Parameters:
atomCheckRadius
- The atomCheckRadius to set.
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