Package org.openmolecules.chem.conf.gen
Class RigidFragment
- java.lang.Object
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- org.openmolecules.chem.conf.gen.RigidFragment
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public class RigidFragment extends java.lang.Object
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Constructor Summary
Constructors Constructor Description RigidFragment(int coreAtomCount, int[] coreToFragmentAtom, int[] fragmentToOriginalAtom, int[] extendedToFragmentAtom, int[] originalToExtendedAtom, Conformer[] conformerList, double[] conformerLikelyhood)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
coreToOriginalAtom(int atom)
int
extendedToOriginalAtom(int atom)
int
getConformerCount()
double
getConformerLikelihood(int i)
int
getConnectionPointCount()
Coordinates
getCoreCoordinates(int conformer, int atom)
int
getCoreSize()
Coordinates
getExtendedCoordinates(int conformer, int atom)
int
getExtendedSize()
int
getLikelyRandomConformerIndex(double random, double progress)
Calculates a random conformer index giving conformers with lower strains a higher chance to be selected.int
originalToExtendedAtom(int originalAtom)
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Constructor Detail
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RigidFragment
public RigidFragment(int coreAtomCount, int[] coreToFragmentAtom, int[] fragmentToOriginalAtom, int[] extendedToFragmentAtom, int[] originalToExtendedAtom, Conformer[] conformerList, double[] conformerLikelyhood)
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Method Detail
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getCoreCoordinates
public Coordinates getCoreCoordinates(int conformer, int atom)
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getExtendedCoordinates
public Coordinates getExtendedCoordinates(int conformer, int atom)
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getConformerCount
public int getConformerCount()
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getConformerLikelihood
public double getConformerLikelihood(int i)
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getLikelyRandomConformerIndex
public int getLikelyRandomConformerIndex(double random, double progress)
Calculates a random conformer index giving conformers with lower strains a higher chance to be selected. With a progress value of 0.0 selection likelyhoods are proportional to conformer likelyhoods due to lower strains. With increasing progress value the higher frequent conformers get less and less preferred until 1.0 without any preference.- Parameters:
random
-progress
- 0...1
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originalToExtendedAtom
public int originalToExtendedAtom(int originalAtom)
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coreToOriginalAtom
public int coreToOriginalAtom(int atom)
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extendedToOriginalAtom
public int extendedToOriginalAtom(int atom)
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getConnectionPointCount
public int getConnectionPointCount()
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getCoreSize
public int getCoreSize()
- Returns:
- count of core atoms, i.e. atoms inside of rotatable bonds
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getExtendedSize
public int getExtendedSize()
- Returns:
- count of core and 1st shell atoms, i.e. core and rotatable bond atoms
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