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
static class	DockingEngine.StartPosition

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
DockingEngine(Molecule3D receptor, Molecule3D nativeLigand)
DockingEngine(Molecule3D rec, Molecule3D nativeLig, int mcSteps, int startPositions, DockingEngine.ScoringFunction scoringFunction, DockingEngine.StartPosition startPosition)

Method Summary

Modifier and Type	Method	Description
DockingEngine.DockingResult	dockMolecule(StereoMolecule mol)
double	evaluateNativePose()
static void	getBindingSiteAtoms(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid, boolean includeHydrogens)
static int[]	getReceptorAtomTypes(StereoMolecule receptor)

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

Constructor Detail

DockingEngine

public DockingEngine(Molecule3D rec,
                     Molecule3D nativeLig,
                     int mcSteps,
                     int startPositions,
                     DockingEngine.ScoringFunction scoringFunction,
                     DockingEngine.StartPosition startPosition)

DockingEngine

public DockingEngine(Molecule3D receptor,
                     Molecule3D nativeLigand)

Method Detail

dockMolecule

public DockingEngine.DockingResult dockMolecule(StereoMolecule mol)
                                         throws DockingFailedException

Throws:

DockingFailedException

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)

evaluateNativePose

public double evaluateNativePose()