Package org.openscience.cdk.tools
package org.openscience.cdk.tools
-
ClassDescriptionProvides atomic property values for descriptor calculations.This class tries to figure out the bond order of the bonds that has the flag
SINGLE_OR_DOUBLEraised (i.e.AtomTypeTools is a helper class for assigning atom types to an atom.Adds implicit hydrogens based on atom type definitions.Deprecated.better accomplished with SMARTS patterns or simple REGEXAssumes CDK atom types to be detected and adds missing hydrogens based on the atom typing.Class with constants for possible data features defined in the a Data Feature Ontology.Utility that helps determine which data features are present.Deprecated.the newerKekulizationprovides a faster, more generic and comprehensive algorithm.Compares elements based on the order commonly used in molecular formula.A class for formatting output similar to the Cprintfcommand.Generates a grid of points in 3D space within given boundaries.Analyses a molecular formula given in String format and builds an AtomContainer with the Atoms in the molecular formula.Generates HOSE codes [Bremser, W.. Analytica Chimica Acta. 1978. 103].Class that provides methods to give unique IDs to ChemObjects.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.Useful for logging messages.Deprecated.Results depend on the order of atoms in bonds, resolving this would require retraining the models which are not available.A common interface for SaturationChecker and ValencyChecker.Factory used to instantiate aILoggingTool.Provides methods for checking whether an atoms lone pair electrons are saturated with respect to a particular atom type.Class that facilitates building protein structures.Provides methods for checking whether an atoms valences are saturated with respect to a particular atom type.Small customization of ValencyHybridChecker suggested by Todd Martin specially tuned for SMILES parsing.This class try to generate resonance structure for a determinate molecule.Deprecated.Deprecated.should not be used directly