toxtree.plugins.ames.descriptors

Class SubstituentExtractor

java.lang.Object

toxtree.plugins.ames.descriptors.SubstituentExtractor

public class SubstituentExtractor
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	atom_C
protected static Logger	logger
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	ringQuery
protected static Boolean	yes

Constructor Summary

Constructors

Constructor and Description
SubstituentExtractor()
SubstituentExtractor(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)

Method Summary

Modifier and Type	Method and Description
protected static boolean	breakBond(org.openscience.cdk.interfaces.IAtomContainer ac, org.openscience.cdk.interfaces.IAtom a, String mark, int position, List<org.openscience.cdk.interfaces.IAtom> atoms)
static org.openscience.cdk.interfaces.IAtomContainer	cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac, String mark)
Hashtable<String,org.openscience.cdk.interfaces.IAtomContainerSet>	extractSubstituents(org.openscience.cdk.interfaces.IAtomContainer a) Note: Aromaticity flags should already be set before running this method.
org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	getRingQuery()
static SubstituentPosition	getSubstituentNumber(String property, org.openscience.cdk.interfaces.IAtom atom)
static SubstituentPosition	getSubstituentNumber(String property, org.openscience.cdk.interfaces.IAtomContainer m, int atom)
protected List	getUniqueAtomMaps(List list)
static boolean	markAtomsInRing(String property, List list, org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
void	setRingQuery(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)
static void	setSubstituentNumber(String property, org.openscience.cdk.interfaces.IAtomContainer m, int atom, SubstituentPosition position)
static void	setSubstituentNumber(String property, org.openscience.cdk.interfaces.IAtom atom, SubstituentPosition position)

Methods inherited from class java.lang.Object

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

Field Detail

yes

protected static Boolean yes

atom_C

protected static String atom_C

ringQuery

protected transient org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery

logger

protected static Logger logger

Constructor Detail

SubstituentExtractor

public SubstituentExtractor()

SubstituentExtractor

public SubstituentExtractor(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)

Method Detail

extractSubstituents

public Hashtable<String,org.openscience.cdk.interfaces.IAtomContainerSet> extractSubstituents(org.openscience.cdk.interfaces.IAtomContainer a)
                                                                                       throws org.openscience.cdk.exception.CDKException

Note: Aromaticity flags should already be set before running this method.

Parameters:

a -

Returns:

Throws:

Exception

org.openscience.cdk.exception.CDKException

getUniqueAtomMaps

protected List getUniqueAtomMaps(List list)

markAtomsInRing

public static boolean markAtomsInRing(String property,
                                      List list,
                                      org.openscience.cdk.interfaces.IAtomContainer mol,
                                      org.openscience.cdk.isomorphism.matchers.QueryAtomContainer q)
                               throws org.openscience.cdk.exception.CDKException

Parameters:

list - List of RMap

mol -

q -

Returns:

Throws:

org.openscience.cdk.exception.CDKException

cloneDiscardRingAtomAndBonds

public static org.openscience.cdk.interfaces.IAtomContainer cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac,
                                                                                         String mark)

breakBond

protected static boolean breakBond(org.openscience.cdk.interfaces.IAtomContainer ac,
                                   org.openscience.cdk.interfaces.IAtom a,
                                   String mark,
                                   int position,
                                   List<org.openscience.cdk.interfaces.IAtom> atoms)

getRingQuery

public org.openscience.cdk.isomorphism.matchers.QueryAtomContainer getRingQuery()

setRingQuery

public void setRingQuery(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)

getSubstituentNumber

public static SubstituentPosition getSubstituentNumber(String property,
                                                       org.openscience.cdk.interfaces.IAtomContainer m,
                                                       int atom)

getSubstituentNumber

public static SubstituentPosition getSubstituentNumber(String property,
                                                       org.openscience.cdk.interfaces.IAtom atom)

setSubstituentNumber

public static void setSubstituentNumber(String property,
                                        org.openscience.cdk.interfaces.IAtomContainer m,
                                        int atom,
                                        SubstituentPosition position)

setSubstituentNumber

public static void setSubstituentNumber(String property,
                                        org.openscience.cdk.interfaces.IAtom atom,
                                        SubstituentPosition position)