Package com.actelion.research.chem.docking

Class LigandPose

java.lang.Object

com.actelion.research.chem.docking.LigandPose

All Implemented Interfaces:

Evaluable

public class LigandPose
extends java.lang.Object
implements Evaluable

Field Summary

Fields

Modifier and Type	Field	Description
static long	SEED

Constructor Summary

Constructors

Constructor	Description
LigandPose(Conformer ligConf, AbstractScoringEngine engine, double e0)

Method Summary

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 permuted
void	setState(double[] state)
void	updateLigandCoordinates()

Methods inherited from class java.lang.Object

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

Field Detail

SEED

public static long SEED

Constructor Detail

LigandPose

public LigandPose(Conformer ligConf,
                  AbstractScoringEngine engine,
                  double e0)

Method Detail

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 -

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 interface Evaluable

getContributions

public java.util.Map<java.lang.String,java.lang.Double> getContributions()

setInitialState

public void setInitialState()

updateLigandCoordinates

public void updateLigandCoordinates()

setState

public void setState(double[] state)

Specified by:

setState in interface Evaluable

getState

public double[] getState(double[] v)

getCartState

public double[] getCartState()

getGyrationRadius

public double getGyrationRadius()

getState

public double[] getState()

Specified by:

getState in interface Evaluable

randomPerturbation

public void randomPerturbation(java.util.Random random)

addPositionalConstraints

public void addPositionalConstraints(double d)

addConstraint

public void addConstraint(PositionConstraint constraint)

removeConstraints

public void removeConstraints()

getLigConf

public Conformer getLigConf()