Package org.openmolecules.chem.conf.so
Class SelfOrganizedConformer
- java.lang.Object
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- com.actelion.research.chem.conf.Conformer
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- org.openmolecules.chem.conf.so.SelfOrganizedConformer
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Constructor Summary
Constructors Constructor Description SelfOrganizedConformer(StereoMolecule mol)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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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
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Constructor Detail
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SelfOrganizedConformer
public SelfOrganizedConformer(StereoMolecule mol)
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Method Detail
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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:
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calculateStrain
public void calculateStrain(java.util.ArrayList<ConformationRule> ruleList)
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getAtomStrain
public double getAtomStrain(int atom)
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getRuleStrain
public double getRuleStrain(int rule)
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getHighestAtomStrain
public double getHighestAtomStrain()
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getTotalStrain
public double getTotalStrain()
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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
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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:
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invalidateStrain
public void invalidateStrain()
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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
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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
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isUsed
public boolean isUsed()
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setUsed
public void setUsed(boolean isUsed)
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