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org::openscience::cdk::tools::SaturationChecker Class Reference

Inheritance diagram for org::openscience::cdk::tools::SaturationChecker:

org::openscience::cdk::tools::IValencyChecker org::openscience::cdk::tools::IDeduceBondOrderTool

List of all members.


Detailed Description

Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.

Important: this class does not deal with hybridization states, which makes it fail, for example, for situations where bonds are marked as aromatic (either 1.5 or single an AROMATIC).

Author:
steinbeck

Egon Willighagen .created 2001-09-04

.keyword saturation .keyword atom, valency

.module valencycheck

Definition at line 67 of file SaturationChecker.java.


Public Member Functions

boolean allSaturated (IAtomContainer ac) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom, double bondOrderSum, double singleElectronSum, java.util.List connectedBonds, boolean throwExceptionForUnknowAtom) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom, IAtomContainer container) throws CDKException
boolean couldMatchAtomType (IAtomContainer atomContainer, IAtom atom, IAtomType atomType)
double getCurrentMaxBondOrder (IAtom atom, IAtomContainer ac) throws CDKException
boolean hasPerfectConfiguration (IAtom atom, IAtomContainer ac) throws CDKException
boolean isOverSaturated (IAtom atom, IAtomContainer ac) throws CDKException
boolean isSaturated (IAtom atom, IAtomContainer ac) throws CDKException
boolean isSaturated (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean isSaturated (IAtomContainer container) throws CDKException
boolean isUnsaturated (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean newSaturate (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean newSaturate (IBond[] bonds, IAtomContainer atomContainer) throws CDKException
void newSaturate (IAtomContainer atomContainer) throws CDKException
void saturate (IAtomContainer atomContainer) throws CDKException
void saturateRingSystems (IAtomContainer atomContainer) throws CDKException
void unsaturate (IAtomContainer atomContainer)
void unsaturateBonds (IAtomContainer container)

Protected Member Functions

AtomTypeFactory getAtomTypeFactory (IChemObjectBuilder builder) throws CDKException

Package Attributes

AtomTypeFactory structgenATF

Private Attributes

LoggingTool logger

The documentation for this class was generated from the following file:

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