Class DockingEngine
- java.lang.Object
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- com.actelion.research.chem.docking.DockingEngine
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public class DockingEngine extends java.lang.Object
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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
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Field Summary
Fields Modifier and Type Field Description static double
GRID_DIMENSION
static double
GRID_RESOLUTION
static int
MCS_EXHAUSTIVENESS
static double
MINI_CUTOFF
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Constructor Summary
Constructors Constructor Description DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand)
DockingEngine(StereoMolecule rec, StereoMolecule nativeLig, int mcSteps, int startPositions, DockingEngine.ScoringFunction scoringFunction)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 positionvoid
setMCSReference(StereoMolecule referencePose)
void
setThreadMaster(ThreadMaster tm)
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Field Detail
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GRID_DIMENSION
public static final double GRID_DIMENSION
- See Also:
- Constant Field Values
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GRID_RESOLUTION
public static final double GRID_RESOLUTION
- See Also:
- Constant Field Values
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MINI_CUTOFF
public static final double MINI_CUTOFF
- See Also:
- Constant Field Values
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MCS_EXHAUSTIVENESS
public static final int MCS_EXHAUSTIVENESS
- See Also:
- Constant Field Values
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Constructor Detail
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DockingEngine
public DockingEngine(StereoMolecule rec, StereoMolecule nativeLig, int mcSteps, int startPositions, DockingEngine.ScoringFunction scoringFunction) throws DockingFailedException
- Throws:
DockingFailedException
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DockingEngine
public DockingEngine(StereoMolecule receptor, StereoMolecule nativeLigand) throws DockingFailedException
- Throws:
DockingFailedException
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Method Detail
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setThreadMaster
public void setThreadMaster(ThreadMaster tm)
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dockMolecule
public DockingEngine.DockingResult dockMolecule(StereoMolecule mol) throws DockingFailedException
- Throws:
DockingFailedException
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setMCSReference
public void setMCSReference(StereoMolecule referencePose)
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getBindingSiteAtoms
public static void getBindingSiteAtoms(StereoMolecule receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid, boolean includeHydrogens)
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getReceptorAtomTypes
public static int[] getReceptorAtomTypes(StereoMolecule receptor)
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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:
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