Package com.actelion.research.chem.docking

Class DockingEngine

java.lang.Object

com.actelion.research.chem.docking.DockingEngine

public class DockingEngine
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DockingEngine.DockingResult
static class	DockingEngine.ScoringFunction	applies molecular docking to find the binding pose of a ligand molecule into the binding site of the protein nativeLigand: defines the location of the binding site this class is not thread safe! every thread requires it's own instance

Field Summary

Fields

Modifier and Type	Field	Description
static double	GRID_DIMENSION
static double	GRID_RESOLUTION
static int	MCS_EXHAUSTIVENESS
static double	MINI_CUTOFF

Constructor Summary

Constructors

Constructor	Description
DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand)
DockingEngine(StereoMolecule rec, StereoMolecule nativeLig, int mcSteps, int startPositions, DockingEngine.ScoringFunction scoringFunction)

Method Summary

Modifier and Type	Method	Description
DockingEngine.DockingResult	dockMolecule(StereoMolecule mol)
static void	getBindingSiteAtoms(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid, boolean includeHydrogens)
static int[]	getReceptorAtomTypes(StereoMolecule receptor)
double	refineNativePose(double d, double[] coords)	the parameter d defines how much the atoms are allowed to move from their original position
void	setMCSReference(StereoMolecule referencePose)
void	setThreadMaster(ThreadMaster tm)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GRID_DIMENSION

public static final double GRID_DIMENSION

See Also:

Constant Field Values

GRID_RESOLUTION

public static final double GRID_RESOLUTION

See Also:

Constant Field Values

MINI_CUTOFF

public static final double MINI_CUTOFF

See Also:

Constant Field Values

MCS_EXHAUSTIVENESS

public static final int MCS_EXHAUSTIVENESS

See Also:

Constant Field Values

Constructor Detail

DockingEngine

public DockingEngine(StereoMolecule rec,
                     StereoMolecule nativeLig,
                     int mcSteps,
                     int startPositions,
                     DockingEngine.ScoringFunction scoringFunction)
              throws DockingFailedException

Throws:

DockingFailedException

DockingEngine

public DockingEngine(StereoMolecule receptor,
                     StereoMolecule nativeLigand)
              throws DockingFailedException

Throws:

DockingFailedException

Method Detail

setThreadMaster

public void setThreadMaster(ThreadMaster tm)

dockMolecule

public DockingEngine.DockingResult dockMolecule(StereoMolecule mol)
                                         throws DockingFailedException

Throws:

DockingFailedException

setMCSReference

public void setMCSReference(StereoMolecule referencePose)

getBindingSiteAtoms

public static void getBindingSiteAtoms(StereoMolecule receptor,
                                       java.util.Set<java.lang.Integer> bindingSiteAtoms,
                                       MoleculeGrid grid,
                                       boolean includeHydrogens)

getReceptorAtomTypes

public static int[] getReceptorAtomTypes(StereoMolecule receptor)

refineNativePose

public double refineNativePose(double d,
                               double[] coords)

the parameter d defines how much the atoms are allowed to move from their original position

Parameters:

d -

Returns: