ambit2.reactions.rules.scores

Class ChemComplexityUtils

java.lang.Object

ambit2.reactions.rules.scores.ChemComplexityUtils

public class ChemComplexityUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	log_2

Constructor Summary

Constructors

Constructor and Description
ChemComplexityUtils()

Method Summary

Modifier and Type	Method and Description
static List<org.openscience.cdk.interfaces.IAtom[]>	getAtomPaths(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol, int pathLenght, boolean includeImplicitHAtoms)
static List<org.openscience.cdk.interfaces.IAtom[]>	getAtomPaths1(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol, boolean includeImplicitHAtoms)
static List<org.openscience.cdk.interfaces.IAtom[]>	getAtomPaths2(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol, boolean includeImplicitHAtoms)
static int[]	getAtomXDInfo(org.openscience.cdk.interfaces.IAtom atom)
static double	log2(double x)
static void	registerGroup(String group, Map<String,Integer> groupFrequencies)
static double	shannonEntropy(int[] groupFrequencies)
static double	shannonEntropy(int[] groupFrequencies, int totalNum)
static double	shannonEntropy(Map<String,Integer> groupFrequencies)
static double	shannonEntropy(Map<String,Integer> groupFrequencies, int totalNum)
static int	totalGroupNum(Map<String,Integer> groupFrequencies)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log_2

public static double log_2

Constructor Detail

ChemComplexityUtils

public ChemComplexityUtils()

Method Detail

log2

public static double log2(double x)

totalGroupNum

public static int totalGroupNum(Map<String,Integer> groupFrequencies)

shannonEntropy

public static double shannonEntropy(Map<String,Integer> groupFrequencies)

shannonEntropy

public static double shannonEntropy(Map<String,Integer> groupFrequencies,
                                    int totalNum)

shannonEntropy

public static double shannonEntropy(int[] groupFrequencies)

shannonEntropy

public static double shannonEntropy(int[] groupFrequencies,
                                    int totalNum)

getAtomPaths1

public static List<org.openscience.cdk.interfaces.IAtom[]> getAtomPaths1(org.openscience.cdk.interfaces.IAtom atom,
                                                                         org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                         boolean includeImplicitHAtoms)

getAtomPaths2

public static List<org.openscience.cdk.interfaces.IAtom[]> getAtomPaths2(org.openscience.cdk.interfaces.IAtom atom,
                                                                         org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                         boolean includeImplicitHAtoms)

getAtomPaths

public static List<org.openscience.cdk.interfaces.IAtom[]> getAtomPaths(org.openscience.cdk.interfaces.IAtom atom,
                                                                        org.openscience.cdk.interfaces.IAtomContainer mol,
                                                                        int pathLenght,
                                                                        boolean includeImplicitHAtoms)

registerGroup

public static void registerGroup(String group,
                                 Map<String,Integer> groupFrequencies)

getAtomXDInfo

public static int[] getAtomXDInfo(org.openscience.cdk.interfaces.IAtom atom)

Parameters:

atom -

Returns:

array int[2] with smarts X and D primitives values for the atom