Class SubGraphIndices
- java.lang.Object
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- com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices
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public class SubGraphIndices extends java.lang.Object
SubGraphIndices A class to handle indices in a molecular graph. It is just a hash set for integer with some methods.Copyright: Actelion Pharmaceuticals Ltd., Inc. All Rights Reserved This software is the proprietary information of Actelion Pharmaceuticals, Ltd. Use is subject to license terms.
Created by korffmo1 on 23.02.16.
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Constructor Summary
Constructors Constructor Description SubGraphIndices()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static void
addAtomIndices(HashSetInt hs, java.util.List<SubGraphIndices> liFragment)
Adds the atom indices to the hash set.void
addIndex(int indexAtom)
void
addIndex(int[] arrIndexAtom)
void
clear()
boolean
contains(int indexAtom)
boolean
equals(java.lang.Object obj)
int[]
getAtomIndices()
static java.util.Comparator<SubGraphIndices>
getComparatorNumIndices()
int
getNumIndices()
int
getNumOverlappingIndices(SubGraphIndices frag)
boolean
isOverlap(SubGraphIndices frag)
void
merge(SubGraphIndices frag)
static void
merge(java.util.List<SubGraphIndices> liFragment)
Merges fragments containing a common atom index.static java.util.List<SubGraphIndices>
mergeOverlapping(java.util.List<SubGraphIndices> liFragment, int minNumIndicesOverlapping)
Merges overlapping fragments.java.lang.String
toString()
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Method Detail
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getNumIndices
public int getNumIndices()
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clear
public void clear()
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addIndex
public void addIndex(int indexAtom)
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addIndex
public void addIndex(int[] arrIndexAtom)
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getAtomIndices
public int[] getAtomIndices()
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contains
public boolean contains(int indexAtom)
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equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
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isOverlap
public boolean isOverlap(SubGraphIndices frag)
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getNumOverlappingIndices
public int getNumOverlappingIndices(SubGraphIndices frag)
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merge
public void merge(SubGraphIndices frag)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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merge
public static void merge(java.util.List<SubGraphIndices> liFragment)
Merges fragments containing a common atom index. The fragments in the list are merged and the list is shrinked.- Parameters:
liFragment
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mergeOverlapping
public static java.util.List<SubGraphIndices> mergeOverlapping(java.util.List<SubGraphIndices> liFragment, int minNumIndicesOverlapping)
Merges overlapping fragments. They may share a minimum number of overlapping indices.- Parameters:
liFragment
-minNumIndicesOverlapping
-- Returns:
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addAtomIndices
protected static void addAtomIndices(HashSetInt hs, java.util.List<SubGraphIndices> liFragment)
Adds the atom indices to the hash set.- Parameters:
hs
-liFragment
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getComparatorNumIndices
public static java.util.Comparator<SubGraphIndices> getComparatorNumIndices()
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