Class LigandPose
- java.lang.Object
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- com.actelion.research.chem.docking.LigandPose
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Field Summary
Fields Modifier and Type Field Description static long
SEED
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Constructor Summary
Constructors Constructor Description LigandPose(Conformer ligConf, AbstractScoringEngine engine, double e0)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addConstraint(PositionConstraint constraint)
void
addPositionalConstraints(double d)
double[]
getCartState()
java.util.Map<java.lang.String,java.lang.Double>
getContributions()
double
getFGValue(double[] gradient)
Fuhrmann J, Rurainski A, Lenhof HP, Neumann D.double
getGyrationRadius()
Conformer
getLigConf()
double[]
getState()
double[]
getState(double[] v)
void
randomPerturbation(java.util.Random random)
void
removeConstraints()
void
setInitialState()
void
setMCSBondConstraints(java.util.List<java.lang.Integer> constraints)
for MCS docking:create array of bond indices that are allowed to be permutedvoid
setState(double[] state)
void
updateLigandCoordinates()
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Constructor Detail
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LigandPose
public LigandPose(Conformer ligConf, AbstractScoringEngine engine, double e0)
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Method Detail
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setMCSBondConstraints
public void setMCSBondConstraints(java.util.List<java.lang.Integer> constraints)
for MCS docking:create array of bond indices that are allowed to be permuted- Parameters:
constraints
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getFGValue
public double getFGValue(double[] gradient)
Fuhrmann J, Rurainski A, Lenhof HP, Neumann D. A new method for the gradient-based optimization of molecular complexes. J Comput Chem. 2009 Jul 15;30(9):1371-8. doi: 10.1002/jcc.21159. PMID: 19031415.- Specified by:
getFGValue
in interfaceEvaluable
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getContributions
public java.util.Map<java.lang.String,java.lang.Double> getContributions()
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setInitialState
public void setInitialState()
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updateLigandCoordinates
public void updateLigandCoordinates()
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getState
public double[] getState(double[] v)
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getCartState
public double[] getCartState()
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getGyrationRadius
public double getGyrationRadius()
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randomPerturbation
public void randomPerturbation(java.util.Random random)
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addPositionalConstraints
public void addPositionalConstraints(double d)
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addConstraint
public void addConstraint(PositionConstraint constraint)
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removeConstraints
public void removeConstraints()
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getLigConf
public Conformer getLigConf()
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