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.

Interface Summary

Interface	Description
StructureChecker	General interface describing functions that are available for a chemical structure checker.

Class Summary

Class	Description
AbbreviatedGroupChecker	A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
AbsentChiralFlagChecker	Detects chiral molecules with no chiral flag defined
AbsoluteStereoConfigurationChecker	Detects molecules in which all asymmetric centers have absolute stereo configuration
AbstractStructureChecker	Abstract base class of all functions checking and repairing chemical structures.
AliasChecker	A descendant of AbstractStructureChecker detecting atoms with alias labels.
AromaticityErrorChecker	A descendant of AbstractStructureChecker detecting aromatization problems.
AtomChecker	Descendants of the abstract AtomChecker class check every atom for a specific error or property.
AtomMapChecker	A descendant of AtomChecker detecting atom maps.
AtomQueryPropertyChecker	A descendant of AtomChecker detecting atoms having an query property set.
AtomTypeChecker	A descendant of AtomChecker checking different atom types (represented by atom's symbol) in the molecule.
AtomValueChecker	A descendant of AtomChecker detecting atoms with atom value.
AtropisomerChecker	A descendant of AbstractStructureChecker detecting atropisomers in the molecule.
AttachedDataChecker	A descendant of AbstractStructureChecker 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 of AbstractStructureChecker detecting "absolute stereo flag" on molecule.
ChiralFlagErrorChecker	A descendant of AbstractStructureChecker detecting achiral molecules having a chiral flag set (absolute stereo flag).
CircularRGroupReferenceChecker	A descendant of AbstractStructureChecker 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 of AbstractStructureChecker detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs).
CrossedDoubleBondChecker	A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.
EmptyStructureChecker	A descendant of AbstractStructureChecker detecting structures having no atoms.
ExplicitHydrogenChecker	A descendant of AtomChecker detecting explicit hydrogens.
ExplicitLonePairChecker	A descendant of AtomChecker detecting lone pair type atoms.
ExternalStructureChecker	ExternalStructureChecker class provides a super class for externally implemented structure checkers.
EZDoubleBondChecker	A descendant of AbstractStructureChecker 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 string
IsotopeChecker	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 of AbstractStructureChecker 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 of AbstractStructureChecker 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 of AtomChecker detecting pseudo atoms.
QueryAtomChecker	A descendant of AtomChecker detecting generic atoms or ones having query properties.
QueryBondChecker	A descendant of BondChecker detecting query bonds.
RacemateChecker	A descendant of AtomChecker detecting asymmetric tetrahedral atoms without specific stereochemistry.
RadicalChecker	A descendant of AtomChecker detecting radical atoms.
RareElementChecker	A descendant of AtomTypeChecker detecting structures containing elements which are usually rare in organic/drug molecules.
RatomChecker	A descendant of AbstractStructureChecker detecting R-atoms.
ReactingCenterBondMarkChecker	Checker detects bonds with reacting center bond marks.
ReactionChecker	Descendants of ReactionChecker detect reaction scheme problems.
ReactionMapErrorChecker	A descendant of ReactionChecker detecting reactions with invalid mapping. Reaction components should contain at least two mapped atoms, otherwise they are considered incorrectly mapped.
RelativeStereoChecker	A descendant of AbstractStructureChecker detecting molecules having multiple stereogenic center groups
RgroupAttachmentErrorChecker	A descendant of AbstractStructureChecker 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 of AtomChecker 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 of AbstractStructureChecker detecting double bonds in molecule which can be either "E" or "Z".
StructureCheck	This class contains the command line interface for running inner StructureChecker and StructureFixer instances.
StructureCheckerDescriptor	Descriptor for StructureChecker
StructureCheckerFactory	Deprecated. use CheckerFixerFactory instead
StructureCheckerHelper	This helper class contains utility functions used by StructureChecker instances providing constants and utility functions.
StructureCheckerUtility	Utility to handle core features
StructureCheckOptions	Options descriptor for structure checker command line interface
StructureCheckOptions.ModeConverter	Converter for Mode enumeration.
StructureCheckOptions.TypeConverter	Converter for Type enumeration.
SubstructureChecker	This descendant of AbstractStructureChecker is responsible for detecting substructures in a Molecule instance.
ThreeDimensionChecker	A descendant of AtomChecker detecting atoms having non-zero Z coordinates.
UnbalancedReactionChecker	A descendant of AtomChecker detecting reaction schemes having more atoms on one side of the reaction arrow than on the other.
UnusedRGroupChecker	A descendant of AbstractStructureChecker detecting unused R-group definitions.
ValenceErrorChecker	A descendant of AtomChecker detecting atoms with invalid valences.
ValencePropertyChecker	A descendant of AtomChecker detecting atoms having an explicitly set valence property.
WedgeErrorChecker	Deprecated.
WigglyBondChecker	A descendant of AbstractStructureChecker detecting wiggly bonds on tetrahedral stereo centers.
WigglyDoubleBondChecker	A descendant of BondChecker 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 the StructureChecker implementations
FixMode	fix mode options
StructureCheckerErrorType	Enum containing possible error types for structure checkers.
StructureCheckOptions.Mode	The mode of the structure check
StructureCheckOptions.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 for StructureChecker implementations
Persistent	This annotation signs if a property of a StructureChecker should be persisted