mutant.descriptors
Class SubstituentExtractor

java.lang.Object
  extended by mutant.descriptors.SubstituentExtractor

public class SubstituentExtractor
extends java.lang.Object


Field Summary
protected static java.lang.String atom_C
           
protected static TTLogger logger
           
protected  org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery
           
protected static java.lang.Boolean yes
           
 
Constructor Summary
SubstituentExtractor()
           
SubstituentExtractor(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)
           
 
Method Summary
protected static boolean breakBond(org.openscience.cdk.interfaces.IAtomContainer ac, org.openscience.cdk.interfaces.IAtom a, java.lang.String mark, int position, java.util.List<org.openscience.cdk.interfaces.IAtom> atoms)
           
static org.openscience.cdk.interfaces.IAtomContainer cloneDiscardRingAtomAndBonds(org.openscience.cdk.interfaces.IAtomContainer ac, java.lang.String mark)
           
 java.util.Hashtable<java.lang.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(java.lang.String property, org.openscience.cdk.interfaces.IAtom atom)
           
static SubstituentPosition getSubstituentNumber(java.lang.String property, org.openscience.cdk.interfaces.IAtomContainer m, int atom)
           
protected  java.util.List getUniqueAtomMaps(java.util.List list)
           
static boolean markAtomsInRing(java.lang.String property, java.util.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(java.lang.String property, org.openscience.cdk.interfaces.IAtomContainer m, int atom, SubstituentPosition position)
           
static void setSubstituentNumber(java.lang.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 java.lang.Boolean yes

atom_C

protected static java.lang.String atom_C

ringQuery

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

logger

protected static TTLogger logger
Constructor Detail

SubstituentExtractor

public SubstituentExtractor()

SubstituentExtractor

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

extractSubstituents

public java.util.Hashtable<java.lang.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:
java.lang.Exception
org.openscience.cdk.exception.CDKException

getUniqueAtomMaps

protected java.util.List getUniqueAtomMaps(java.util.List list)

markAtomsInRing

public static boolean markAtomsInRing(java.lang.String property,
                                      java.util.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,
                                                                                         java.lang.String mark)

breakBond

protected static boolean breakBond(org.openscience.cdk.interfaces.IAtomContainer ac,
                                   org.openscience.cdk.interfaces.IAtom a,
                                   java.lang.String mark,
                                   int position,
                                   java.util.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(java.lang.String property,
                                                       org.openscience.cdk.interfaces.IAtomContainer m,
                                                       int atom)

getSubstituentNumber

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

setSubstituentNumber

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

setSubstituentNumber

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


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