Class ChemPLP
- java.lang.Object
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- com.actelion.research.chem.docking.scoring.AbstractScoringEngine
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- com.actelion.research.chem.docking.scoring.ChemPLP
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public class ChemPLP extends AbstractScoringEngine
Implementation of ChemPLP scoring function as described in: doi: 10.1021/ci800298z THIS SCORING FUNCTION REQUIRES EXPLICIT HYDROGENS TO BE PRESENT!- Author:
- joel
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Field Summary
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Fields inherited from class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
bindingSiteAtoms, candidatePose, constraints, grid, receptorConf
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Constructor Summary
Constructors Constructor Description ChemPLP(Molecule3D receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.Map<java.lang.String,java.lang.Double>
getContributions()
double
getFGValue(double[] grad)
double
getScore()
static void
identifyHBondFunctionality(StereoMolecule mol, java.util.Set<java.lang.Integer> acceptors, java.util.Set<java.lang.Integer> donorHs, java.util.Set<java.lang.Integer> donors, java.util.Set<java.lang.Integer> metals, java.util.Set<java.lang.Integer> chargedAcceptors, java.util.Set<java.lang.Integer> chargedDonorHs)
void
init(LigandPose candidatePose, double e0)
void
updateState()
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Methods inherited from class com.actelion.research.chem.docking.scoring.AbstractScoringEngine
addConstraint, getBumpTerm, getCandidatePose, getReceptorConf, removeConstraints
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Constructor Detail
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ChemPLP
public ChemPLP(Molecule3D receptor, java.util.Set<java.lang.Integer> bindingSiteAtoms, MoleculeGrid grid)
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Method Detail
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getFGValue
public double getFGValue(double[] grad)
- Specified by:
getFGValue
in classAbstractScoringEngine
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updateState
public void updateState()
- Specified by:
updateState
in classAbstractScoringEngine
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getScore
public double getScore()
- Specified by:
getScore
in classAbstractScoringEngine
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init
public void init(LigandPose candidatePose, double e0)
- Specified by:
init
in classAbstractScoringEngine
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identifyHBondFunctionality
public static void identifyHBondFunctionality(StereoMolecule mol, java.util.Set<java.lang.Integer> acceptors, java.util.Set<java.lang.Integer> donorHs, java.util.Set<java.lang.Integer> donors, java.util.Set<java.lang.Integer> metals, java.util.Set<java.lang.Integer> chargedAcceptors, java.util.Set<java.lang.Integer> chargedDonorHs)
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getContributions
public java.util.Map<java.lang.String,java.lang.Double> getContributions()
- Specified by:
getContributions
in classAbstractScoringEngine
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