Class QueryProcessor
- java.lang.Object
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- org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor
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@Deprecated public class QueryProcessor extends Object
Deprecated.SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.Class to handle mappings of query molecule.- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
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Constructor Summary
Constructors Modifier Constructor Description protected
QueryProcessor(List<String> cTab1Copy, List<String> cTab2Copy, String[] signArray, int neighborBondnumA, int setBondnumA, List<Integer> iBondNeighborsA, List<String> cBondNeighborsA, int mappingSize, List<Integer> iBondSetA, List<String> cBondSetA)
Deprecated.Query molecule
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description protected int
getBondNumA()
Deprecated.protected List<String>
getCTab1()
Deprecated.protected List<String>
getCTab2()
Deprecated.protected int
getNeighborBondNumA()
Deprecated.protected void
process(int setNumA, int setNumB, List<Integer> iBondSetA, List<Integer> iBondSetB, List<Integer> unmappedAtomsMolA, List<Integer> newMapping, int counter)
Deprecated.protected void
process(IAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter)
Deprecated.protected void
process(IQueryAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter)
Deprecated.
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Constructor Detail
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QueryProcessor
protected QueryProcessor(List<String> cTab1Copy, List<String> cTab2Copy, String[] signArray, int neighborBondnumA, int setBondnumA, List<Integer> iBondNeighborsA, List<String> cBondNeighborsA, int mappingSize, List<Integer> iBondSetA, List<String> cBondSetA)
Deprecated.Query molecule- Parameters:
cTab1Copy
-cTab2Copy
-signArray
-neighborBondnumA
-setBondnumA
-iBondNeighborsA
-cBondNeighborsA
-mappingSize
-iBondSetA
-cBondSetA
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Method Detail
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process
protected void process(IAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter)
Deprecated.- Parameters:
query
-target
-unmappedAtomsMolA
-mappedAtoms
-counter
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process
protected void process(IQueryAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter)
Deprecated.- Parameters:
query
-target
-unmappedAtomsMolA
-mappedAtoms
-counter
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process
protected void process(int setNumA, int setNumB, List<Integer> iBondSetA, List<Integer> iBondSetB, List<Integer> unmappedAtomsMolA, List<Integer> newMapping, int counter)
Deprecated.- Parameters:
setNumA
-setNumB
-iBondSetA
-iBondSetB
-unmappedAtomsMolA
-newMapping
-counter
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getNeighborBondNumA
protected int getNeighborBondNumA()
Deprecated.- Returns:
- number of remaining molecule A bonds after the clique search, which are neighbors of the MCS
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getBondNumA
protected int getBondNumA()
Deprecated.- Returns:
- number of remaining molecule A bonds after the clique search, which aren't neighbors
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