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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Interface Summary Interface Description StructureChecker General interface describing functions that are available for a chemical structure checker. -
Class Summary Class Description AbbreviatedGroupChecker A descendant ofAbstractStructureChecker
detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.AbsentChiralFlagChecker Detects chiral molecules with no chiral flag definedAbsoluteStereoConfigurationChecker Detects molecules in which all asymmetric centers have absolute stereo configurationAbstractStructureChecker Abstract base class of all functions checking and repairing chemical structures.AliasChecker A descendant ofAbstractStructureChecker
detecting atoms with alias labels.AromaticityErrorChecker A descendant ofAbstractStructureChecker
detecting aromatization problems.AtomChecker Descendants of the abstract AtomChecker class check every atom for a specific error or property.AtomMapChecker A descendant ofAtomChecker
detecting atom maps.AtomQueryPropertyChecker A descendant ofAtomChecker
detecting atoms having an query property set.AtomTypeChecker A descendant ofAtomChecker
checking different atom types (represented by atom's symbol) in the molecule.AtomValueChecker A descendant ofAtomChecker
detecting atoms with atom value.AtropisomerChecker A descendant ofAbstractStructureChecker
detecting atropisomers in the molecule.AttachedDataChecker A descendant ofAbstractStructureChecker
detecting attached data in the molecule.BondAngleChecker Bond Angle Checker detects wrong bond angles in 2D structures.BondChecker Descentants of the abstract BondChecker class detect bond related problems.BondLengthChecker Bond Length Checker detects bonds with wrong length in 2D structures.BracketsChecker Detects brackets (S-groups) in molecules.ChiralFlagChecker Implementation ofAbstractStructureChecker
detecting "absolute stereo flag" on molecule.ChiralFlagErrorChecker A descendant ofAbstractStructureChecker
detecting achiral molecules having a chiral flag set (absolute stereo flag).CircularRGroupReferenceChecker A descendant ofAbstractStructureChecker
detecting circular R-group references.ComponentChecker<E> Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).CoordinationSystemErrorChecker Detects errors of multicenter coordination systems.CovalentCounterionChecker A descendant ofAbstractStructureChecker
detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).CrossedDoubleBondChecker A descendant ofBondChecker
for the detection of unspecified double bonds represented by crossed bond type.EmptyStructureChecker A descendant ofAbstractStructureChecker
detecting structures having no atoms.ExplicitHydrogenChecker A descendant ofAtomChecker
detecting explicit hydrogens.ExplicitLonePairChecker A descendant ofAtomChecker
detecting lone pair type atoms.ExternalStructureChecker ExternalStructureChecker class provides a super class for externally implemented structure checkers.EZDoubleBondChecker A descendant ofAbstractStructureChecker
detecting double bonds, that can be cis or trans.IncorrectTetrahedralStereoChecker Incorrect Tetrahedral Stereo Checker detects stereo wedge configurations around chiral atoms which are not possible.InvalidChecker An extremal checker implementation indicating error in the configuration imported from XML or action stringIsotopeChecker IsotopeChecker detects isotopes (non-elemental atoms).MetalloceneErrorChecker MetalloceneErrorChecker detects metallocenes represented in ionic or covalently bonded formats, that are not coordinate multicenters.MissingAtomMapChecker MissingAtomMapChecker detects unmapped atoms.MissingRGroupChecker A descendant ofAbstractStructureChecker
detecting missing R-group definition errors.MoleculeChargeChecker MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.MultiCenterChecker MultiCenterChecker detects structures containing multicenter atoms.MultiComponentChecker MultiComponentChecker detects structures containing disconnected components/fragments.MultipleStereocenterChecker A descendant ofAbstractStructureChecker
detecting molecules containing multiple stereocenters.NonStandardWedgeSchemeChecker Non-standard Wedge Scheme Checker detects wedge configurations not following the IUPAC recommendations.NonStereoWedgeBondChecker Non-stereo Wedge Bond Checker detects wedge bonds connected to non-stereo atoms.OCRErrorChecker OCRErrorChecker detects structures which do not look like chemical structures.OverlappingAtomsChecker 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 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
).PseudoAtomChecker A descendant ofAtomChecker
detecting pseudo atoms.QueryAtomChecker A descendant ofAtomChecker
detecting generic atoms or ones having query properties.QueryBondChecker A descendant ofBondChecker
detecting query bonds.RacemateChecker A descendant ofAtomChecker
detecting asymmetric tetrahedral atoms without specific stereochemistry.RadicalChecker A descendant ofAtomChecker
detecting radical atoms.RareElementChecker A descendant ofAtomTypeChecker
detecting structures containing elements which are usually rare in organic/drug molecules.RatomChecker A descendant ofAbstractStructureChecker
detecting R-atoms.ReactingCenterBondMarkChecker Checker detects bonds with reacting center bond marks.ReactionChecker Descendants of ReactionChecker detect reaction scheme problems.ReactionMapErrorChecker A descendant ofReactionChecker
detecting reactions with invalid mapping.
Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.RelativeStereoChecker A descendant ofAbstractStructureChecker
detecting molecules having multiple stereogenic center groupsRgroupAttachmentErrorChecker A descendant ofAbstractStructureChecker
detecting invalid attachments in R-group definitions.RgroupBridgeRatomChecker 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 RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.SolventChecker SolventChecker detects common solvents in multicomponent structures.StarAtomChecker A descendant ofAtomChecker
detecting so called star atoms having "*" as atomic symbol.StereoCareBoxChecker Checker to find molecules containing Stereo Care Boxes.StereoCheckUtility Deprecated. Will be removed from the public API.StereoInversionRetentionMarkChecker Detects reaction inversion/retention marks on atoms.StraightDoubleBondChecker A descendant ofAbstractStructureChecker
detecting double bonds in molecule which can be either "E" or "Z".StructureCheck This class contains the command line interface for running innerStructureChecker
andStructureFixer
instances.StructureCheckerDescriptor Descriptor forStructureChecker
StructureCheckerFactory Deprecated. useCheckerFixerFactory
insteadStructureCheckerHelper This helper class contains utility functions used byStructureChecker
instances providing constants and utility functions.StructureCheckerUtility Utility to handle core featuresStructureCheckOptions Options descriptor for structure checker command line interfaceStructureCheckOptions.ModeConverter Converter for Mode enumeration.StructureCheckOptions.TypeConverter Converter for Type enumeration.SubstructureChecker This descendant ofAbstractStructureChecker
is responsible for detecting substructures in aMolecule
instance.ThreeDimensionChecker A descendant ofAtomChecker
detecting atoms having non-zero Z coordinates.UnbalancedReactionChecker A descendant ofAtomChecker
detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.UnusedRGroupChecker A descendant ofAbstractStructureChecker
detecting unused R-group definitions.ValenceErrorChecker A descendant ofAtomChecker
detecting atoms with invalid valences.ValencePropertyChecker A descendant ofAtomChecker
detecting atoms having an explicitly set valence property.WedgeErrorChecker Deprecated. WigglyBondChecker A descendant ofAbstractStructureChecker
detecting wiggly bonds on tetrahedral stereo centers.WigglyDoubleBondChecker A descendant ofBondChecker
detecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration. -
Enum Summary Enum Description CheckerSeverity This enum defines the constants which represent the severity of theStructureChecker
implementationsFixMode fix mode optionsStructureCheckerErrorType Enum containing possible error types for structure checkers.StructureCheckOptions.Mode The mode of the structure checkStructureCheckOptions.Type The output type of the structure check -
Annotation Types Summary Annotation Type Description CheckerInfo This annotation is responsible for adding GUI based meta data forStructureChecker
implementationsPersistent This annotation signs if a property of aStructureChecker
should be persisted