public class AtomTypeAwareSaturationChecker extends Object implements IValencyChecker, IDeduceBondOrderTool
SINGLE_OR_DOUBLE
raised (i.e. set to true
).AtomContainerManipulator
.
This class uses the SaturationChecker
internally.Constructor and Description |
---|
AtomTypeAwareSaturationChecker()
Constructs an
AtomTypeAwareSaturationChecker checker. |
Modifier and Type | Method and Description |
---|---|
boolean |
bondOrderCanBeIncreased(IBond bond,
IAtomContainer atomContainer)
Check if the bond order can be increased.
|
void |
decideBondOrder(IAtomContainer atomContainer)
This method decides the bond order on bonds that has the
SINGLE_OR_DOUBLE -flag raised. |
void |
decideBondOrder(IAtomContainer atomContainer,
boolean atomsSaturated)
This method decides the bond order on bonds that has the
SINGLE_OR_DOUBLE -flag raised. |
double |
getMaxNoOfBonds(IAtom atom)
This method calculates the number of bonds that an
IAtom
can have. |
boolean |
isSaturated(IAtomContainer container) |
boolean |
isSaturated(IAtom atom,
IAtomContainer container) |
void |
saturate(IAtomContainer container) |
public AtomTypeAwareSaturationChecker()
AtomTypeAwareSaturationChecker
checker.public void decideBondOrder(IAtomContainer atomContainer, boolean atomsSaturated) throws CDKException
SINGLE_OR_DOUBLE
-flag raised.atomContainer
- The molecule to investigateatomsSaturated
- Set to true if you want to make sure that all
atoms are saturated.CDKException
public void decideBondOrder(IAtomContainer atomContainer) throws CDKException
SINGLE_OR_DOUBLE
-flag raised.atomContainer
- The molecule to investigate.CDKException
public boolean bondOrderCanBeIncreased(IBond bond, IAtomContainer atomContainer) throws CDKException
bond
- The bond to checkatomContainer
- The IAtomContainer
that the bond belongs toCDKException
public double getMaxNoOfBonds(IAtom atom) throws CDKException
IAtom
can have.atom
- The IAtom
to be investigatedIAtom
can haveCDKException
- when the atom's valency is not setpublic void saturate(IAtomContainer container) throws CDKException
saturate
in interface IDeduceBondOrderTool
CDKException
public boolean isSaturated(IAtomContainer container) throws CDKException
isSaturated
in interface IValencyChecker
CDKException
public boolean isSaturated(IAtom atom, IAtomContainer container) throws CDKException
isSaturated
in interface IValencyChecker
CDKException
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