mutant.descriptors
Class SubstituentExtractor
java.lang.Object
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
|
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 |
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
SubstituentExtractor
public SubstituentExtractor()
SubstituentExtractor
public SubstituentExtractor(org.openscience.cdk.isomorphism.matchers.QueryAtomContainer ringQuery)
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 RMapmol
- 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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