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org::openscience::cdk::tools::ValencyChecker Class Reference

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

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

List of all members.


Detailed Description

This class is an experimental alternative to the SaturationChecker. The main difference is that this checker uses a different atom type list and takes formal charges into account: it first matches against element and charge, and then browses the list for possible matching types.

The atoms are matched against the valency_atomtype.xml list.

Author:
Egon Willighagen .created 2004-01-07
.keyword atom, valency

.module valencycheck

Definition at line 61 of file ValencyChecker.java.


Public Member Functions

boolean allSaturated (IAtomContainer ac) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom, double bondOrderSum, double singleElectronSum, double maxBondOrder, int neighbourCount) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom) throws CDKException
int calculateNumberOfImplicitHydrogens (IAtom atom, IAtomContainer container) throws CDKException
boolean couldMatchAtomType (IAtom atom, double bondOrderSum, double maxBondOrder, IAtomType type)
boolean couldMatchAtomType (IAtomContainer container, IAtom atom, IAtomType type)
boolean isSaturated (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean isSaturated (IAtomContainer container) throws CDKException
boolean isSaturated (IAtom atom, IAtomContainer container) throws CDKException
boolean isUnsaturated (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean saturate (IBond bond, IAtomContainer atomContainer) throws CDKException
boolean saturate (IBond[] bonds, IAtomContainer atomContainer) throws CDKException
void saturate (IAtomContainer atomContainer) throws CDKException
boolean saturateByIncreasingBondOrder (IBond bond, IAtomContainer atomContainer, double increment) throws CDKException
void unsaturate (IAtomContainer atomContainer)
boolean unsaturateByDecreasingBondOrder (IBond bond, double decrement)
 ValencyChecker (String atomTypeList) throws IOException, ClassNotFoundException

Protected Member Functions

AtomTypeFactory getAtomTypeFactory (IChemObjectBuilder builder) throws CDKException

Protected Attributes

LoggingTool logger
AtomTypeFactory structgenATF

Private Attributes

String atomTypeList = null

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

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