ambit2.smarts

Class SmartsHelper

java.lang.Object

ambit2.smarts.SmartsHelper

public class SmartsHelper
extends Object

Constructor Summary

Constructors

Constructor and Description
SmartsHelper(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
static String	atomPropertiesToString(org.openscience.cdk.interfaces.IAtom atom)
static String	atomToString(org.openscience.cdk.interfaces.IAtom a)
static String	bondAtomNumbersToString(org.openscience.cdk.interfaces.IAtomContainer container, org.openscience.cdk.interfaces.IBond b)
static int	bondOrderToIntValue(org.openscience.cdk.interfaces.IBond b)
static String	bondToString(org.openscience.cdk.interfaces.IBond b)
static String	bondToStringExhaustive(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query, org.openscience.cdk.interfaces.IBond bond)
static void	convertToCarbonSkelleton(org.openscience.cdk.interfaces.IAtomContainer mol)
static String	getAtomExpressionTokens(SmartsAtomExpression expression)
static String	getAtomsAttributes(org.openscience.cdk.interfaces.IAtomContainer container)
static String	getAtomsExpressionTokens(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
static String	getAtomsString(org.openscience.cdk.interfaces.IAtomContainer container)
static String	getAtomsString(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
static String	getBondAttributes(org.openscience.cdk.interfaces.IAtomContainer container)
static String	getBondsString(org.openscience.cdk.interfaces.IAtomContainer query)
static String	getBondsString(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
static String[]	getCarbonSkelletonsFromString(String smiles)
static org.openscience.cdk.interfaces.IAtomContainer	getMoleculeFromSmiles(String smi)
static org.openscience.cdk.interfaces.IAtomContainer	getMoleculeFromSmiles(String smi, boolean FlagExplicitHatoms)
static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	getQueryAtomContainer(org.openscience.cdk.interfaces.IAtomContainer ac, boolean HandleAromaticity)
static List<Integer>	getSmartsPositions(String smartsQuery, org.openscience.cdk.interfaces.IAtomContainer target, boolean FlagSupportDoubleBondAromaticityNotSpecified)
static String	implicitHAtomsVector(org.openscience.cdk.interfaces.IAtomContainer mol)
static boolean	isQueryDoubleBond(org.openscience.cdk.interfaces.IBond bond)
static boolean	isSingleBondOrExpression(org.openscience.cdk.interfaces.IBond b)
static String	moleculeToSMILES(org.openscience.cdk.interfaces.IAtomContainer mol, boolean useAromaticityFlag)
static void	preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
static void	preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol, boolean HandleAromaticity, boolean AddImplicitHAtoms)
static void	preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol, boolean HandleAromaticity, boolean AddImplicitHAtoms, boolean ImplicitHToExplicit)
static void	printIntArray(int[] c)
static void	setAromaticAtomsFromBondFlagInfo(org.openscience.cdk.interfaces.IAtomContainer mol)
static String	smilesBondToString(org.openscience.cdk.interfaces.IBond b, boolean aromaticity)
static String	stereoCenterToString(org.openscience.cdk.interfaces.IAtomContainer container, org.openscience.cdk.interfaces.ITetrahedralChirality chiral)
static String	stereoInfoToString(org.openscience.cdk.interfaces.IAtomContainer container)
String	toSmarts(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
static String	toString(int[] c)

Methods inherited from class java.lang.Object

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

Constructor Detail

SmartsHelper

public SmartsHelper(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

getAtomsString

public static String getAtomsString(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

getAtomExpressionTokens

public static String getAtomExpressionTokens(SmartsAtomExpression expression)

getAtomsExpressionTokens

public static String getAtomsExpressionTokens(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

getAtomsString

public static String getAtomsString(org.openscience.cdk.interfaces.IAtomContainer container)

getAtomsAttributes

public static String getAtomsAttributes(org.openscience.cdk.interfaces.IAtomContainer container)

stereoInfoToString

public static String stereoInfoToString(org.openscience.cdk.interfaces.IAtomContainer container)

stereoCenterToString

public static String stereoCenterToString(org.openscience.cdk.interfaces.IAtomContainer container,
                                          org.openscience.cdk.interfaces.ITetrahedralChirality chiral)

getBondAttributes

public static String getBondAttributes(org.openscience.cdk.interfaces.IAtomContainer container)

getBondsString

public static String getBondsString(org.openscience.cdk.interfaces.IAtomContainer query)

bondToStringExhaustive

public static String bondToStringExhaustive(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query,
                                            org.openscience.cdk.interfaces.IBond bond)

getBondsString

public static String getBondsString(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

getQueryAtomContainer

public static org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer getQueryAtomContainer(org.openscience.cdk.interfaces.IAtomContainer ac,
                                                                                                 boolean HandleAromaticity)

bondOrderToIntValue

public static int bondOrderToIntValue(org.openscience.cdk.interfaces.IBond b)

atomToString

public static String atomToString(org.openscience.cdk.interfaces.IAtom a)

bondToString

public static String bondToString(org.openscience.cdk.interfaces.IBond b)

isQueryDoubleBond

public static boolean isQueryDoubleBond(org.openscience.cdk.interfaces.IBond bond)

isSingleBondOrExpression

public static boolean isSingleBondOrExpression(org.openscience.cdk.interfaces.IBond b)

smilesBondToString

public static String smilesBondToString(org.openscience.cdk.interfaces.IBond b,
                                        boolean aromaticity)

bondAtomNumbersToString

public static String bondAtomNumbersToString(org.openscience.cdk.interfaces.IAtomContainer container,
                                             org.openscience.cdk.interfaces.IBond b)

toSmarts

public String toSmarts(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

Parameters:

query -

Returns:

SMARTS string

moleculeToSMILES

public static String moleculeToSMILES(org.openscience.cdk.interfaces.IAtomContainer mol,
                                      boolean useAromaticityFlag)
                               throws Exception

Throws:

Exception

convertToCarbonSkelleton

public static void convertToCarbonSkelleton(org.openscience.cdk.interfaces.IAtomContainer mol)

getMoleculeFromSmiles

public static org.openscience.cdk.interfaces.IAtomContainer getMoleculeFromSmiles(String smi)
                                                                           throws Exception

Throws:

Exception

getMoleculeFromSmiles

public static org.openscience.cdk.interfaces.IAtomContainer getMoleculeFromSmiles(String smi,
                                                                                  boolean FlagExplicitHatoms)
                                                                           throws Exception

Throws:

Exception

getCarbonSkelletonsFromString

public static String[] getCarbonSkelletonsFromString(String smiles)
                                              throws Exception

Throws:

Exception

printIntArray

public static void printIntArray(int[] c)

toString

public static String toString(int[] c)

atomPropertiesToString

public static String atomPropertiesToString(org.openscience.cdk.interfaces.IAtom atom)

getSmartsPositions

public static List<Integer> getSmartsPositions(String smartsQuery,
                                               org.openscience.cdk.interfaces.IAtomContainer target,
                                               boolean FlagSupportDoubleBondAromaticityNotSpecified)
                                        throws Exception

Throws:

Exception

setAromaticAtomsFromBondFlagInfo

public static void setAromaticAtomsFromBondFlagInfo(org.openscience.cdk.interfaces.IAtomContainer mol)

preProcessStructure

public static void preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
                                throws Exception

Throws:

Exception

preProcessStructure

public static void preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                       boolean HandleAromaticity,
                                       boolean AddImplicitHAtoms)
                                throws Exception

Throws:

Exception

preProcessStructure

public static void preProcessStructure(org.openscience.cdk.interfaces.IAtomContainer mol,
                                       boolean HandleAromaticity,
                                       boolean AddImplicitHAtoms,
                                       boolean ImplicitHToExplicit)
                                throws Exception

Throws:

Exception

implicitHAtomsVector

public static String implicitHAtomsVector(org.openscience.cdk.interfaces.IAtomContainer mol)