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.
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 of
AbstractStructureCheckerdetecting atoms with alias labels.A descendant of
AbstractStructureCheckerdetecting aromatization problems.Descendants of the abstract AtomChecker class check every atom for a specific error or property.A descendant of
AtomCheckerdetecting atom maps.A descendant of
AtomCheckerdetecting atoms having an query property set.A descendant of
AtomCheckerchecking different atom types (represented by atom's symbol) in the molecule.A descendant of
AtomCheckerdetecting atoms with atom value.A descendant of
AbstractStructureCheckerdetecting atropisomers in the molecule.A descendant of
AbstractStructureCheckerdetecting 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 for
StructureCheckerimplementationsThis enum defines the constants which represent the severity of the
AbstractStructureCheckerdetecting "absolute stereo flag" on molecule.A descendant of
AbstractStructureCheckerdetecting achiral molecules having a chiral flag set (absolute stereo flag).A descendant of
AbstractStructureCheckerdetecting 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 of
AbstractStructureCheckerdetecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).A descendant of
BondCheckerfor the detection of unspecified double bonds represented by crossed bond type.A descendant of
AbstractStructureCheckerdetecting structures having no atoms.A descendant of
AtomCheckerdetecting explicit hydrogens.A descendant of
AtomCheckerdetecting lone pair type atoms.ExternalStructureChecker class provides a super class for externally implemented structure checkers.A descendant of
AbstractStructureCheckerdetecting 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 of
AbstractStructureCheckerdetecting 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 of
AbstractStructureCheckerdetecting 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 a
StructureCheckershould be persistedA descendant of
AtomCheckerdetecting pseudo atoms.A descendant of
AtomCheckerdetecting generic atoms or ones having query properties.A descendant of
BondCheckerdetecting query bonds.A descendant of
AtomCheckerdetecting asymmetric tetrahedral atoms without specific stereochemistry.A descendant of
AtomCheckerdetecting radical atoms.A descendant of
AtomTypeCheckerdetecting structures containing elements which are usually rare in organic/drug molecules.A descendant of
AbstractStructureCheckerdetecting R-atoms.Checker detects bonds with reacting center bond marks.Descendants of ReactionChecker detect reaction scheme problems.A descendant of
ReactionCheckerdetecting reactions with invalid mapping.
Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.A descendant of
AbstractStructureCheckerdetecting molecules having multiple stereogenic center groupsA descendant of
AbstractStructureCheckerdetecting 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 of
AtomCheckerdetecting 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 of
AbstractStructureCheckerdetecting double bonds in molecule which can be either "E" or "Z".General interface describing functions that are available for a chemical structure checker.Descriptor for
StructureCheckerEnum containing possible error types for structure checkers.Deprecated.use
CheckerFixerFactoryinsteadThis helper class contains utility functions used by
StructureCheckerinstances 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.A descendant of
AtomCheckerdetecting atoms having non-zero Z coordinates.A descendant of
AtomCheckerdetecting reaction schemes having more atoms on one side of the reaction arrow than on the other.A descendant of
AbstractStructureCheckerdetecting unused R-group definitions.A descendant of
AtomCheckerdetecting atoms with invalid valences.A descendant of
AtomCheckerdetecting atoms having an explicitly set valence property.Deprecated.A descendant of
AbstractStructureCheckerdetecting wiggly bonds on tetrahedral stereo centers.A descendant of
BondCheckerdetecting double bonds having wiggly bond ligands representing unspecified double bond stereo configuration.