Package org.openmolecules.chem.conf.so
Class DistanceRule
- java.lang.Object
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- org.openmolecules.chem.conf.so.ConformationRule
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- org.openmolecules.chem.conf.so.DistanceRule
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public class DistanceRule extends ConformationRule
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Field Summary
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Fields inherited from class org.openmolecules.chem.conf.so.ConformationRule
mAtom, mIsEnabled, RULE_NAME, RULE_TYPE_BINAP, RULE_TYPE_DISTANCE, RULE_TYPE_LINE, RULE_TYPE_PLANE, RULE_TYPE_STEREO, RULE_TYPE_TORSION
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Constructor Summary
Constructors Constructor Description DistanceRule()
Creates a dummy rule to be neglectedDistanceRule(int[] atom, double minDistance, double maxDistance, int priority)
DistanceRule(int[] atom, int[] notList, double minDistance, double maxDistance, int priority)
DistanceRule(int[] atom, int[] notList, double distance, int priority)
Constructor for 2 bonds in between.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description double
addStrain(Conformer conformer, double[] atomStrain)
boolean
apply(Conformer conformer, double cycleFactor)
static void
calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)
int
getRuleType()
boolean
isFixedDistance()
java.lang.String
toString()
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Methods inherited from class org.openmolecules.chem.conf.so.ConformationRule
addAtomList, getAtomList, isEnabled, moveAtomWithUnboundedNeighbors, moveGroup, moveSubstituent, rotateAtom, setEnabled
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Constructor Detail
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DistanceRule
public DistanceRule()
Creates a dummy rule to be neglected
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DistanceRule
public DistanceRule(int[] atom, int[] notList, double distance, int priority)
Constructor for 2 bonds in between.- Parameters:
atom
-notList
- atoms (direct neighbors of atom[0] and atom[1]) to be excluded from movementdistance
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DistanceRule
public DistanceRule(int[] atom, double minDistance, double maxDistance, int priority)
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DistanceRule
public DistanceRule(int[] atom, int[] notList, double minDistance, double maxDistance, int priority)
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Method Detail
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getRuleType
public int getRuleType()
- Specified by:
getRuleType
in classConformationRule
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isFixedDistance
public boolean isFixedDistance()
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calculateRules
public static void calculateRules(java.util.ArrayList<ConformationRule> ruleList, StereoMolecule mol)
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apply
public boolean apply(Conformer conformer, double cycleFactor)
- Specified by:
apply
in classConformationRule
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addStrain
public double addStrain(Conformer conformer, double[] atomStrain)
- Specified by:
addStrain
in classConformationRule
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toString
public java.lang.String toString()
- Specified by:
toString
in classConformationRule
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