Package org.openscience.cdk.tools

Interface Summary

Interface	Description
IDeduceBondOrderTool	A common interface for tools that deduce bond orders from connectivity and optionally additional information, like number of implicit or explicit hydrogens, or hybridization states.
ILoggingTool	Useful for logging messages.
IValencyChecker	A common interface for SaturationChecker and ValencyChecker.

Class Summary

Class	Description
AtomicProperties	Provides atomic property values for descriptor calculations.
AtomTypeAwareSaturationChecker	This class tries to figure out the bond order of the bonds that has the flag SINGLE_OR_DOUBLE raised (i.e.
AtomTypeTools	AtomTypeTools is a helper class for assigning atom types to an atom.
BremserOneSphereHOSECodePredictor
CDKHydrogenAdder	Adds implicit hydrogens based on atom type definitions.
CDKUtilities	Deprecated. better accomplished with SMARTS patterns or simple REGEX
CDKValencyChecker	Assumes CDK atom types to be detected and adds missing hydrogens based on the atom typing.
DataFeatures	Class with constants for possible data features defined in the a Data Feature Ontology.
DataFeaturesTool	Utility that helps determine which data features are present.
DeAromatizationTool	Deprecated. the newer Kekulization provides a faster, more generic and comprehensive algorithm.
ElementComparator	Compares elements based on the order commonly used in molecular formula.
FormatStringBuffer	A class for formatting output similar to the C printf command.
GridGenerator	Generates a grid of points in 3D space within given boundaries.
HOSECodeAnalyser	Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.
HOSECodeGenerator	Generates HOSE codes [Bremser, W.. Analytica Chimica Acta. 1978. 103].
IDCreator	Class that provides methods to give unique IDs to ChemObjects.
IonizationPotentialTool	Deprecated. Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.
LoggingToolFactory	Factory used to instantiate a ILoggingTool.
LonePairElectronChecker	Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.
ProteinBuilderTool	Class that facilitates building protein structures.
SaturationChecker	Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.
SmilesValencyChecker	Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.
StructureResonanceGenerator	This class try to generate resonance structure for a determinate molecule.
SugarRemovalUtility	The Sugar Removal Utility (SRU) implements a generalized algorithm for automated detection of circular and linear sugars in molecular structures and their removal, as described in "Schaub, J., Zielesny, A., Steinbeck, C., Sorokina, M.
SwissArmyKnife	Deprecated.
SystemOutLoggingTool	Deprecated. should not be used directly

Enum Summary

Enum	Description
SugarRemovalUtility.PreservationMode	Enum with options for how to determine whether a substructure that gets disconnected from the molecule during the removal of a sugar moiety should be preserved or can get removed along with the sugar.