Package chemaxon.checkers
package chemaxon.checkers
Provides structure checkers, which can be used to identify drawing mistakes or special structural elements
in chemical structures.
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ClassDescriptionA descendant of
AbstractStructureCheckerdetecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.Detects chiral molecules with no chiral flag definedDetects molecules in which all asymmetric centers have absolute stereo configurationAbstract base class of all functions checking and repairing chemical structures.A descendant ofAbstractStructureCheckerdetecting atoms with alias labels.A descendant ofAbstractStructureCheckerdetecting aromatization problems.Descendants of the abstractComponentCheckerclass check every atom for a specific error or property.Stores a list of atom labels to be used for certain structure checkers.A descendant ofAtomCheckerdetecting atoms with atom map numbers.A descendant ofAtomCheckerdetecting atoms having an query property set.A descendant ofAtomCheckerchecking different atom types (represented by atom's symbol) in the molecule.A descendant ofAtomCheckerdetecting atoms with atom values (labels).Deprecated.This checker is no longer supported.A descendant ofAbstractStructureCheckerdetecting attached data in the molecule.A list of Strings to be excluded byAttachedDataChecker.Bond Angle Checker detects non-preferred bond angles in 2D structures.Descentants of the abstract BondChecker class detect bond related problems.Bond Length Checker detects bonds with wrong length in 2D structures.Checker detects bonds with reacting center bond marks.Detects brackets (generic S-groups) in molecules.This annotation is responsible for adding GUI-related metadata forStructureCheckerimplementations.This enum defines the constants which represent the severity of theStructureCheckerimplementationsImplementation ofAbstractStructureCheckerdetecting "absolute stereo flag" on molecule.A descendant ofAbstractStructureCheckerdetecting achiral molecules having a chiral flag set (absolute stereo flag).A descendant ofAbstractStructureCheckerdetecting circular R-group references.Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).Detects errors of multicenter coordination systems.A descendant ofAbstractStructureCheckerdetecting covalently bonded counterions (alkaline alcoholates, carboxylates and thio analogs).A descendant ofBondCheckerfor the detection of unspecified double bonds represented by crossed bond type.Detects invalid either double bonds.A descendant ofAbstractStructureCheckerdetecting structures having no atoms.A descendant ofAtomCheckerdetecting explicit hydrogens.A descendant ofAtomCheckerdetecting lone pair type atoms.ExternalStructureChecker class provides a super class for externally implemented structure checkers.A descendant ofAbstractStructureCheckerdetecting double bonds, that can be cis or trans.Fix mode optionsIncorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.An extremal checker implementation indicating error in the configuration imported from XML or action stringIsotopeChecker detects isotopes (non-elemental atoms).MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.MissingAtomMapChecker detects atoms without atom map numbers.A descendant ofAbstractStructureCheckerdetecting missing R-group definition errors.MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.MultiCenterChecker detects structures containing multicenter atoms.MultiComponentChecker detects structures containing disconnected components/fragments.A descendant ofAbstractStructureCheckerdetecting molecules containing multiple stereocenters.Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.OCRErrorChecker detects structures which do not look like chemical structures.OverlappingAtomsChecker detects atoms that are too close to each other.OverlappingBondsChecker detects bonds that are too close to each other.This annotation signs if a property of aStructureCheckershould be persisted.A descendant ofAtomCheckerdetecting pseudo atoms.A descendant ofAtomCheckerdetecting generic atoms or ones having query properties.A descendant ofBondCheckerdetecting query bonds.A descendant ofAtomCheckerdetecting asymmetric tetrahedral atoms without specific stereochemistry.A descendant ofAtomCheckerdetecting radical atoms.A descendant ofAtomTypeCheckerdetecting structures containing elements which are usually rare in organic/drug molecules.A descendant ofAbstractStructureCheckerdetecting R-atoms.Checker detects bonds with reacting center bond marks.Descendants of ReactionChecker detect reaction scheme problems.A descendant ofReactionCheckerdetecting reactions with invalid mapping.A descendant ofAbstractStructureCheckerdetecting molecules having multiple stereogenic center groupsA descendant ofAbstractStructureCheckerdetecting invalid attachments in R-group definitions.Checker for R-atoms that form R-group bridges.RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.SolventChecker detects common solvents in multi-fragment molecules.A descendant ofAtomCheckerdetecting so called star atoms having "*" as atomic symbol.Checker to find molecules containing Stereo-Care Boxes.Detects reaction inversion/retention marks on atoms.A descendant ofAbstractStructureCheckerdetecting double bonds in molecule which can be either "E" or "Z".General interface describing functions that are available for a chemical structure checker.Descriptor forStructureCheckerEnum containing possible error types for structure checkers.This descendant ofAbstractStructureCheckeris responsible for detecting substructures in aMoleculeinstance.A descendant ofAtomCheckerdetecting atoms with 3D coordinates (non-zero Z coordinates).A descendant ofAtomCheckerdetecting reaction schemes having more atoms on one side of the reaction arrow than on the other.A descendant ofAbstractStructureCheckerdetecting unused R-group definitions.A descendant ofAtomCheckerdetecting atoms with invalid valences.A descendant ofAtomCheckerdetecting atoms having an explicitly set valence property.A descendant ofAbstractStructureCheckerdetecting wiggly bonds on tetrahedral stereo centers.A descendant ofBondCheckerdetecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.