Package biotransformer.utils
Class ChemStructureSimilarity
- java.lang.Object
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- biotransformer.utils.ChemStructureSimilarity
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public class ChemStructureSimilarity extends java.lang.Object
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Constructor Summary
Constructors Constructor Description ChemStructureSimilarity()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static double
calculateTanimoto(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
static double
calculateTanimotoWithCustomSmarts(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts)
static double
calculateTanimotoWithCustomSmartsAndCounts(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts)
static double
calculateTanimotoWithMACCS(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2)
static void
generateCsv(java.util.HashMap<java.lang.String,java.lang.Double> tanimotoList, java.lang.String outputname)
static java.lang.String[]
getSmarts()
static java.util.HashMap<java.lang.String,java.lang.Double>
tanimotoListCreator(java.util.HashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainer> compounds, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
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Method Detail
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calculateTanimotoWithCustomSmarts
public static double calculateTanimotoWithCustomSmarts(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts) throws java.lang.Exception
- Throws:
java.lang.Exception
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calculateTanimotoWithCustomSmartsAndCounts
public static double calculateTanimotoWithCustomSmartsAndCounts(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.lang.String[] smarts) throws java.lang.Exception
- Throws:
java.lang.Exception
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calculateTanimoto
public static double calculateTanimoto(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Throws:
java.lang.Exception
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calculateTanimotoWithMACCS
public static double calculateTanimotoWithMACCS(org.openscience.cdk.interfaces.IAtomContainer molecule1, org.openscience.cdk.interfaces.IAtomContainer molecule2) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSmarts
public static java.lang.String[] getSmarts() throws java.lang.Exception
- Throws:
java.lang.Exception
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tanimotoListCreator
public static java.util.HashMap<java.lang.String,java.lang.Double> tanimotoListCreator(java.util.HashMap<java.lang.String,org.openscience.cdk.interfaces.IAtomContainer> compounds, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Throws:
java.lang.Exception
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generateCsv
public static void generateCsv(java.util.HashMap<java.lang.String,java.lang.Double> tanimotoList, java.lang.String outputname)
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