Package chemaxon.checkers
package chemaxon.checkers
Structure checkers can be used to filter drawing mistakes or special structural elements.
This package provides basic structure checkers that can give warnings for specific features or errors in molecules.
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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 abstract AtomChecker class check every atom for a specific error or property.A descendant ofAtomCheckerdetecting atom maps.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 value.A descendant ofAbstractStructureCheckerdetecting atropisomers in the molecule.A descendant ofAbstractStructureCheckerdetecting attached data in the molecule.Bond Angle Checker detects wrong 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 (S-groups) in molecules.This annotation is responsible for adding GUI based meta data forStructureCheckerimplementationsThis 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 an thio analogs).A descendant ofBondCheckerfor the detection of unspecified double bonds represented by crossed bond type.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 unmapped atoms.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.
This checker checks 2D structures only.
Two atoms considered as overlapping when their euclidean distance is less than the half of the Chemaxon standard bond length (MolBond.CCLENGTH).OverlappingBondsChecker detects bonds that are too close to each other.
This checker checks two dimensional structures only.
Two bonds considered as overlapping when they crossing each other, or their distance is smaller then the 80% of the standard Chemaxon bond length (MolBond.CCLENGTH).This annotation signs if a property of aStructureCheckershould be persistedA 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.
Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.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: One R-group can be involved in at most one bridge. Two R-atoms that represent a bridge must be in the scaffold or in the same R-group definition member. The R-group number that represents an R-group bridge cannot represent an ordinary R-group.RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.SolventChecker detects common solvents in multicomponent structures.A descendant ofAtomCheckerdetecting so called star atoms having "*" as atomic symbol.Checker to find molecules containing Stereo Care Boxes.Deprecated.Will be removed from the public API.Detects reaction inversion/retention marks on atoms.A descendant ofAbstractStructureCheckerdetecting double bonds in molecule which can be either "E" or "Z".This class contains the command line interface for running innerStructureCheckerandStructureFixerinstances.General interface describing functions that are available for a chemical structure checker.Descriptor forStructureCheckerEnum containing possible error types for structure checkers.Deprecated.useCheckerFixerFactoryinsteadThis helper class contains utility functions used byStructureCheckerinstances providing constants and utility functions.Utility to handle core featuresOptions descriptor for structure checker command line interfaceThe mode of the structure checkConverter for Mode enumeration.The output type of the structure checkConverter for Type enumeration.This descendant ofAbstractStructureCheckeris responsible for detecting substructures in aMoleculeinstance.A descendant ofAtomCheckerdetecting atoms having 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.Deprecated.A descendant ofAbstractStructureCheckerdetecting wiggly bonds on tetrahedral stereo centers.A descendant ofBondCheckerdetecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.