Package biotransformer.utils
Class FeatureGenerator
- java.lang.Object
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- biotransformer.utils.FeatureGenerator
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public class FeatureGenerator extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
str
definition for all the adopted SYBYL atom types
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Constructor Summary
Constructors Constructor Description FeatureGenerator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
generateAllFeatures(java.util.ArrayList<java.lang.String> molf, java.util.ArrayList<java.util.ArrayList<java.lang.String>> atomf, java.lang.String pathToInputFile)
This function is used to generate all the features for the molecules contained in the input filejava.lang.String[]
generateAtomicFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function is used to generate the atomic features for a single moleculejava.util.ArrayList<java.util.ArrayList<java.lang.String>>
generateAtomicFeatures(org.openscience.cdk.interfaces.IAtomContainerSet containers)
This function is used to generate the atomic features for the molecules contained in the input file.java.lang.String[]
generateAtomType(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function is used to generate the atomic type for a single molecule.java.lang.String
generateExtendedMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function generates molecular features for a single moleculejava.lang.String
generateMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule)
This function generates molecular features for a single moleculejava.util.ArrayList<java.lang.String>
generateMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainerSet set, java.lang.String pathToInputFile)
This function is used to generate the molecular features for the molecules contained in the input file.java.lang.String[]
generatePath(org.openscience.cdk.interfaces.IAtomContainer molecule, int depth)
This function is used to generate the environmental features for a single molecule.org.openscience.cdk.interfaces.IAtomContainerSet
readFile(java.lang.String pathToInputFile)
This functions reads molecules from a chemical file and preprocess the molecules.
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Method Detail
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readFile
public org.openscience.cdk.interfaces.IAtomContainerSet readFile(java.lang.String pathToInputFile) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
This functions reads molecules from a chemical file and preprocess the molecules.- Parameters:
pathToInputFile
- : path of the file which contains the input molecules- Returns:
- an IAtomContainerSet contains all the input molecules
- Throws:
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
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generateMolecularFeatures
public java.util.ArrayList<java.lang.String> generateMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainerSet set, java.lang.String pathToInputFile) throws java.io.IOException, org.openscience.cdk.exception.CDKException
This function is used to generate the molecular features for the molecules contained in the input file.- Parameters:
pathToInputFile
- : path of the file which contains the input molecules- Returns:
- an arraylist which contains the molecular features.
- Throws:
java.io.IOException
org.openscience.cdk.exception.CDKException
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generateMolecularFeatures
public java.lang.String generateMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
This function generates molecular features for a single molecule- Parameters:
molecule
-- Returns:
- String representation of molecular features where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
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generateExtendedMolecularFeatures
public java.lang.String generateExtendedMolecularFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
This function generates molecular features for a single molecule- Parameters:
molecule
-- Returns:
- String representation of molecular features where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
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generateAtomicFeatures
public java.util.ArrayList<java.util.ArrayList<java.lang.String>> generateAtomicFeatures(org.openscience.cdk.interfaces.IAtomContainerSet containers) throws org.openscience.cdk.exception.CDKException, java.io.IOException
This function is used to generate the atomic features for the molecules contained in the input file.- Parameters:
containers
- : IAtomContainerSet, which contains the input molecules- Returns:
- String representation of atomic features where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
java.io.IOException
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generateAtomType
public java.lang.String[] generateAtomType(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException
This function is used to generate the atomic type for a single molecule.- Parameters:
molecule
-- Returns:
- String representation of atomic type of one molecule where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
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generatePath
public java.lang.String[] generatePath(org.openscience.cdk.interfaces.IAtomContainer molecule, int depth) throws org.openscience.cdk.exception.CDKException
This function is used to generate the environmental features for a single molecule.- Parameters:
molecule
-depth
- : the bond length of an atom to the centered atom.- Returns:
- String representation of the environmental features for a single molecule where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
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generateAtomicFeatures
public java.lang.String[] generateAtomicFeatures(org.openscience.cdk.interfaces.IAtomContainer molecule) throws org.openscience.cdk.exception.CDKException, org.openscience.cdk.exception.NoSuchAtomTypeException
This function is used to generate the atomic features for a single molecule- Parameters:
molecule
-- Returns:
- String representation of the atomic features for a single molecule where each feature is separated by a comma
- Throws:
org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.NoSuchAtomTypeException
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generateAllFeatures
public java.lang.String generateAllFeatures(java.util.ArrayList<java.lang.String> molf, java.util.ArrayList<java.util.ArrayList<java.lang.String>> atomf, java.lang.String pathToInputFile) throws java.lang.Exception
This function is used to generate all the features for the molecules contained in the input file- Parameters:
molf
- : the molecular features of all the moleculesatomf
- : the atomic features of all the moleculespathToInputFile
- : path of the file which contains the input molecules- Returns:
- the path of the output csv file which contains all the features for the molecules
- Throws:
java.lang.Exception
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