Package org.openmolecules.chem.conf.so

Class SelfOrganizedConformer

java.lang.Object

com.actelion.research.chem.conf.Conformer

org.openmolecules.chem.conf.so.SelfOrganizedConformer

All Implemented Interfaces:

java.lang.Comparable<Conformer>

public class SelfOrganizedConformer
extends Conformer

Constructor Summary

Constructors

Constructor	Description
SelfOrganizedConformer(StereoMolecule mol)

Method Summary

Modifier and Type	Method	Description
void	calculateDescriptor(int[] rotatableBond)	Calculates the torsion descriptor for the current coordinates.
void	calculateStrain(java.util.ArrayList<ConformationRule> ruleList)
boolean	equals(SelfOrganizedConformer conformer)	Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.
double	getAtomStrain(int atom)
double	getHighestAtomStrain()
double	getLikelyhood()	Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.
double	getRuleStrain(int rule)
double	getTotalStrain()
void	invalidateStrain()
protected boolean	isAcceptable(java.util.ArrayList<ConformationRule> ruleList)
boolean	isUsed()
boolean	isWorseThan(SelfOrganizedConformer conformer)	Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.
void	setUsed(boolean isUsed)

Methods inherited from class com.actelion.research.chem.conf.Conformer

calculateTorsion, center, compareTo, copyFrom, copyFrom, copyTo, deleteAtoms, equals, getBondTorsion, getCoordinates, getCoordinates, getEnergy, getMolecule, getName, getSize, getX, getY, getZ, setBondTorsion, setCoordinates, setCoordinatesReplace, setEnergy, setName, setX, setY, setZ, toMolecule, toMolecule, translate

Methods inherited from class java.lang.Object

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

Constructor Detail

SelfOrganizedConformer

public SelfOrganizedConformer(StereoMolecule mol)

Method Detail

isWorseThan

public boolean isWorseThan(SelfOrganizedConformer conformer)

Checks whether the total strain of this Conformer is larger than that of conformer, assuming that the calculated strain values are up-to-date.

Parameters:

conformer -

Returns:

calculateStrain

public void calculateStrain(java.util.ArrayList<ConformationRule> ruleList)

getAtomStrain

public double getAtomStrain(int atom)

getRuleStrain

public double getRuleStrain(int rule)

getHighestAtomStrain

public double getHighestAtomStrain()

getTotalStrain

public double getTotalStrain()

getLikelyhood

public double getLikelyhood()

Tries to estimate the relative likelyhood of this conformer from atom strains considering an unstrained conformer to have a likelyhood of 1.0.

Returns:

conformer likelyhood

isAcceptable

protected boolean isAcceptable(java.util.ArrayList<ConformationRule> ruleList)

Parameters:

ruleList - may be null, if isAcceptable() was called earlier and neither ruleList not conformer were changes since

Returns:

invalidateStrain

public void invalidateStrain()

calculateDescriptor

public void calculateDescriptor(int[] rotatableBond)

Calculates the torsion descriptor for the current coordinates. Use calculateRotatableBondsForDescriptor() once and pass it for every new conformer to this method.

Parameters:

rotatableBond - set of rotatable bonds to be considered

equals

public boolean equals(SelfOrganizedConformer conformer)

Returns true, if none of the torsion angles between both conformers are more different than TorsionDescriptor.TORSION_EQUIVALENCE_TOLERANCE; Calling this method requires that calculateDescriptor() has been called earlier.

Parameters:

conformer -

Returns:

true if all torsions are similar

isUsed

public boolean isUsed()

setUsed

public void setUsed(boolean isUsed)