Package biotransformer.fingerprint
Class ChemStructureFingerprinter
- java.lang.Object
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- biotransformer.fingerprint.ChemStructureFingerprinter
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public class ChemStructureFingerprinter extends java.lang.Object
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Constructor Summary
Constructors Constructor Description ChemStructureFingerprinter()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.util.LinkedHashMap<java.lang.String,java.lang.Integer>
generateBTRailsCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer molecule)
java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>
generateClassyfireAtomFingeprint(org.openscience.cdk.interfaces.IAtomContainer mole, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
SFingerprint
generateClassyfireCountFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
java.util.ArrayList[]
generateClassyfireFingerprint(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function generates a unique fingerprint for a molecule.SFingerprint
generateClassyfireFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
This function generates a unique fingerprint for a molecule.SFingerprint
generateClassyfireRinFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule)
void
generateDEREP_NPFingerprint(java.lang.String tsvStructureFileName)
java.util.LinkedHashMap<java.lang.String,java.lang.Integer>
generateDEREP_NPFingerprint(org.openscience.cdk.interfaces.IAtomContainer atc, boolean preprocess)
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getDEREP_NPFingerprintPatterns()
java.util.ArrayList<java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>>
geterateSerialAtomfingerprintToArraylist(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getFingerprintPatterns()
java.util.List<java.util.List<java.lang.Integer>>
getMatchingAtoms(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.smiles.smarts.SMARTSQueryTool smartsPattern)
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getMiniFingerprintPatterns()
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getPhaseIIfingerpint()
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getRINAtomFingerprintPatterns()
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getRINFingerprintPatterns()
static java.util.LinkedHashMap<java.lang.String,java.lang.String>
getTestFingerprintPatterns()
java.lang.String
saveSerialAtomFingerprinterToCSV(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
void
serial_fingerprinter_sdf(java.io.File sdfInput)
void
serialAtomfingerprinterToSdf(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries)
This function creates a tsv file with the atom fingerprints
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Method Detail
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getMatchingAtoms
public java.util.List<java.util.List<java.lang.Integer>> getMatchingAtoms(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.smiles.smarts.SMARTSQueryTool smartsPattern) throws java.lang.Exception
- Throws:
java.lang.Exception
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getMiniFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getMiniFingerprintPatterns()
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getFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getFingerprintPatterns() throws java.lang.Exception
- Returns:
- : A HashMap with the SMARTS expressions for functional groups and structural patterns
- Throws:
java.lang.Exception
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getRINFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getRINFingerprintPatterns() throws java.lang.Exception
- Throws:
java.lang.Exception
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getRINAtomFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getRINAtomFingerprintPatterns() throws java.lang.Exception
- Throws:
java.lang.Exception
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getTestFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getTestFingerprintPatterns() throws java.lang.Exception
- Throws:
java.lang.Exception
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getPhaseIIfingerpint
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getPhaseIIfingerpint()
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generateClassyfireAtomFingeprint
public java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> generateClassyfireAtomFingeprint(org.openscience.cdk.interfaces.IAtomContainer mole, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Parameters:
mole
- : A molecule of interestqueries
- : A HashMap with the functional groups and patterns to detect, with their SMARTS patterns- Returns:
- : A list containing atom-based list of the bits (1 or 0) that describe for every functional group/pattern, whether the atom of interest is part of a match.
- Throws:
java.lang.Exception
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generateClassyfireFingerprint
public java.util.ArrayList[] generateClassyfireFingerprint(org.openscience.cdk.interfaces.IAtomContainer molecule) throws java.lang.Exception
This function generates a unique fingerprint for a molecule.- Parameters:
molecule
- : The molecule of interest- Returns:
- : An array list with the fingerprint of the molecule
- Throws:
java.lang.Exception
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generateClassyfireFingerprintAsDouble
public SFingerprint generateClassyfireFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
This function generates a unique fingerprint for a molecule.- Parameters:
molecule
- : The molecule of interestqueries
- : The dictionary of structural patterns forming the fingerprint- Returns:
- : An SFingerprint representation of the molecule
- Throws:
java.lang.Exception
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generateClassyfireRinFingerprintAsDouble
public SFingerprint generateClassyfireRinFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule) throws java.lang.Exception
- Throws:
java.lang.Exception
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generateClassyfireCountFingerprintAsDouble
public SFingerprint generateClassyfireCountFingerprintAsDouble(org.openscience.cdk.interfaces.IAtomContainer molecule, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Throws:
java.lang.Exception
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generateBTRailsCountFingerprint
public static java.util.LinkedHashMap<java.lang.String,java.lang.Integer> generateBTRailsCountFingerprint(org.openscience.cdk.interfaces.IAtomContainer molecule) throws java.lang.Exception
- Throws:
java.lang.Exception
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serial_fingerprinter_sdf
public void serial_fingerprinter_sdf(java.io.File sdfInput) throws java.lang.Exception
- Parameters:
sdfInput
- : A SDF file- Throws:
java.lang.Exception
- : Throws an Exception
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serialAtomfingerprinterToSdf
public void serialAtomfingerprinterToSdf(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
This function creates a tsv file with the atom fingerprints- Parameters:
sdfInput
- : a SDF filequeries
- : a HashMap with fingerprint patterns and their SMARTS expressions- Throws:
java.lang.Exception
- : Throws an Exception
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geterateSerialAtomfingerprintToArraylist
public java.util.ArrayList<java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>> geterateSerialAtomfingerprintToArraylist(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Parameters:
sdfInput
- : a SDF filequeries
- : a HashMap with fingerprint patterns and their SMARTS expressions- Returns:
- An array list of fingerprints for every atom of each molecule in the SDF file
- Throws:
java.lang.Exception
- : Throws an Exception
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saveSerialAtomFingerprinterToCSV
public java.lang.String saveSerialAtomFingerprinterToCSV(java.io.File sdfInput, java.util.LinkedHashMap<java.lang.String,java.lang.String> queries) throws java.lang.Exception
- Parameters:
sdfInput
- : a SDF filequeries
- : a HashMap with fingerprint patterns and their SMARTS expressions- Returns:
- : A string with the atom-based fingerprints of every molecule. A .csv file is also saved.
- Throws:
java.lang.Exception
- : Throws an Exception
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getDEREP_NPFingerprintPatterns
public static java.util.LinkedHashMap<java.lang.String,java.lang.String> getDEREP_NPFingerprintPatterns() throws java.lang.Exception
- Throws:
java.lang.Exception
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generateDEREP_NPFingerprint
public java.util.LinkedHashMap<java.lang.String,java.lang.Integer> generateDEREP_NPFingerprint(org.openscience.cdk.interfaces.IAtomContainer atc, boolean preprocess) throws java.lang.Exception
- Throws:
java.lang.Exception
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generateDEREP_NPFingerprint
public void generateDEREP_NPFingerprint(java.lang.String tsvStructureFileName) throws java.lang.Exception
- Throws:
java.lang.Exception
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