Package com.actelion.research.chem
Class SSSearcherWithIndex
- java.lang.Object
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- com.actelion.research.chem.SSSearcherWithIndex
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public class SSSearcherWithIndex extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
cIndexVersion
static java.lang.String[]
cKeyIDCode
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Constructor Summary
Constructors Constructor Description SSSearcherWithIndex()
SSSearcherWithIndex(int matchMode)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description int[]
createIndex(StereoMolecule mol)
long[]
createLongIndex(StereoMolecule mol)
int
findFragmentInMolecule()
int
findFragmentInMolecule(int countMode, int matchMode)
int
findFragmentInMolecule(int countMode, int matchMode, boolean[] atomExcluded)
int
findFragmentInMoleculeWithoutIndex(int countMode)
int
getFirstHittingLongIndexBlockNo()
static java.lang.String
getHexStringFromIndex(int[] index)
static int[]
getIndexFromHexString(byte[] bytes)
static int[]
getIndexFromHexString(java.lang.String hex)
static StereoMolecule
getKeyFragment(int no)
static long[]
getLongIndexFromHexString(byte[] bytes)
static long[]
getLongIndexFromHexString(java.lang.String hex)
java.util.ArrayList<int[]>
getMatchList()
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e.StereoMolecule
getMolecule()
Returns the most recently defined molecule.static int
getNoOfKeys()
static float
getSimilarityAngleCosine(int[] index1, int[] index2)
static float
getSimilarityTanimoto(int[] index1, int[] index2)
static float
getSimilarityTanimoto(long[] index1, long[] index2)
boolean
isFragmentIndexInMoleculeIndex()
boolean
isFragmentInMolecule()
boolean
isFragmentInMoleculeWithoutIndex()
void
setFragment(byte[] idcode, int[] index)
Deprecated.void
setFragment(byte[] idcode, long[] index)
void
setFragment(StereoMolecule fragment, int[] index)
Deprecated.void
setFragment(StereoMolecule fragment, long[] index)
void
setFragment(java.lang.String idcode, int[] index)
Deprecated.void
setFragment(java.lang.String idcode, long[] index)
void
setMolecule(byte[] idcode, int[] index)
Deprecated.void
setMolecule(byte[] idcode, long[] index)
void
setMolecule(StereoMolecule molecule, int[] index)
Deprecated.void
setMolecule(StereoMolecule molecule, long[] index)
void
setMolecule(java.lang.String idcode, int[] index)
Deprecated.void
setMolecule(java.lang.String idcode, long[] index)
void
stop()
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Field Detail
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cIndexVersion
public static final java.lang.String cIndexVersion
- See Also:
- Constant Field Values
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cKeyIDCode
public static final java.lang.String[] cKeyIDCode
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Method Detail
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getNoOfKeys
public static int getNoOfKeys()
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getKeyFragment
public static StereoMolecule getKeyFragment(int no)
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setFragment
@Deprecated public void setFragment(StereoMolecule fragment, int[] index)
Deprecated.
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setFragment
@Deprecated public void setFragment(java.lang.String idcode, int[] index)
Deprecated.
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setFragment
@Deprecated public void setFragment(byte[] idcode, int[] index)
Deprecated.
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setMolecule
@Deprecated public void setMolecule(StereoMolecule molecule, int[] index)
Deprecated.
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setMolecule
@Deprecated public void setMolecule(java.lang.String idcode, int[] index)
Deprecated.
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setMolecule
@Deprecated public void setMolecule(byte[] idcode, int[] index)
Deprecated.
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setFragment
public void setFragment(StereoMolecule fragment, long[] index)
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setFragment
public void setFragment(java.lang.String idcode, long[] index)
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setFragment
public void setFragment(byte[] idcode, long[] index)
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setMolecule
public void setMolecule(StereoMolecule molecule, long[] index)
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setMolecule
public void setMolecule(java.lang.String idcode, long[] index)
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setMolecule
public void setMolecule(byte[] idcode, long[] index)
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getFirstHittingLongIndexBlockNo
public int getFirstHittingLongIndexBlockNo()
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getMolecule
public StereoMolecule getMolecule()
Returns the most recently defined molecule. If the molecule was passed as idcode and was not created yet, then a molecule is constructed from the idcode and returned.- Returns:
- current Molecule (null, if setMolecule() has never been called)
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isFragmentIndexInMoleculeIndex
public boolean isFragmentIndexInMoleculeIndex()
- Returns:
- whether the fragment fingerprint bits are all present in the molecule bits
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isFragmentInMoleculeWithoutIndex
public boolean isFragmentInMoleculeWithoutIndex()
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findFragmentInMoleculeWithoutIndex
public int findFragmentInMoleculeWithoutIndex(int countMode)
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isFragmentInMolecule
public boolean isFragmentInMolecule()
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findFragmentInMolecule
public int findFragmentInMolecule()
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findFragmentInMolecule
public int findFragmentInMolecule(int countMode, int matchMode)
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findFragmentInMolecule
public int findFragmentInMolecule(int countMode, int matchMode, boolean[] atomExcluded)
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getMatchList
public java.util.ArrayList<int[]> getMatchList()
If the match count mode is one of cCountModeFirstMatch, cCountModeOverlapping, cCountModeRigorous then this method returns an arraylist of all counted matches, i.e. int arrays mapping fragment atoms to molecule atoms. Atoms being part of a matched bridge bond are naturally not covered by the mapping.
Note: If some query fragment atoms are marked as exclude group, then the respective matchlist values are -1.- Returns:
- list of distinct counted matches.
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createIndex
public int[] createIndex(StereoMolecule mol)
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createLongIndex
public long[] createLongIndex(StereoMolecule mol)
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getSimilarityTanimoto
public static float getSimilarityTanimoto(int[] index1, int[] index2)
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getSimilarityTanimoto
public static float getSimilarityTanimoto(long[] index1, long[] index2)
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getSimilarityAngleCosine
public static float getSimilarityAngleCosine(int[] index1, int[] index2)
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getIndexFromHexString
public static int[] getIndexFromHexString(java.lang.String hex)
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getIndexFromHexString
public static int[] getIndexFromHexString(byte[] bytes)
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getLongIndexFromHexString
public static long[] getLongIndexFromHexString(java.lang.String hex)
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getLongIndexFromHexString
public static long[] getLongIndexFromHexString(byte[] bytes)
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getHexStringFromIndex
public static java.lang.String getHexStringFromIndex(int[] index)
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stop
public void stop()
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