Package chemaxon.checkers

Structure checkers can be used to filter drawing mistakes or special structural elements.

See:
Description

Interface Summary

StructureChecker

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

Class Summary

AbbreviatedGroupChecker	A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
AbstractStructureChecker	Abstract base class of all functions checking and repairing chemical structures.
AliasChecker	A descendant of AbstractStructureChecker detecting atoms withalias 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.
AtomValueChecker	A descendant of AtomChecker detecting atoms with atom value.
AttachedDataChecker	A descendant of AbstractStructureChecker detecting attached data in the molecule.
BondAngleChecker	A descendant of BondChecker for the detection of unpreferred bond angles in 2D molecule layouts.
BondChecker	Descentants of the abstract BondChecker class detect bond related problems.
BondLengthChecker	A descendant of BondChecker detecting bonds with unpreferred lengths in 2D molecule layouts.
ComponentChecker<E>	Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
CoordinationSystemErrorChecker	Detects errors of multicenter coordination systems.
CrossedDoubleBondChecker	A descendant of BondChecker for the detection of unspecified double bonds represented by crossed bond type.
DoubleBondStereoErrorChecker	Deprecated. This class is deprecated as of version 5.4 Marvin.
ExternalStructureChecker	ExternalStructureChecker class provides a super class for externally implemented structure checkers.
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.
MoleculeChargeChecker	MoleculeChargeChecker detects molecules where the sum of the formal atom charges is not zero.
MultiCenterChecker	MultiCenterChecker detects structures containing multicenter atoms.
OverlappingAtomsChecker	OverlappingAtomsChecker detects atoms that are too close to each other.
OverlappingBondsChecker	OverlappingBondsChecker detects bonds that are too close to each other.
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.
RadicalChecker	A descendant of AtomChecker detecting radical atoms.
RatomChecker	A descendant of AbstractStructureChecker detecting R-atoms.
ReactionChecker	Descendants of ReactionChecker detect reaction scheme problems.
ReactionMapErrorChecker	A descendant of ReactionChecker detecting reactions with invalid mapping.
RgroupAttachmentErrorChecker	A descendant of AbstractStructureChecker detecting invalid attachments in R-group definitions.
RgroupReferenceErrorChecker	A descendant of AbstractStructureChecker detecting R-group definition errors.
RingStrainErrorChecker	RingStrainErrorChecker detects triple bonds, trans or cumulated double bonds small rings containing less than 8 atoms.
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.
ValenceErrorChecker	A descendant of AtomChecker detecting atoms with invalid valences.
ValencePropertyChecker	A descendant of AtomChecker detecting atoms having an explicitly set valence property.
WedgeErrorChecker	WedgeErrorChecker detecting structures with invalid wedge bonds.
WigglyDoubleBondChecker	A descendant of BondChecker detecting double bonds havong wiggly bond ligands representing unspecified double bond stereo configuration.

Enum Summary

StructureCheckerErrorType

Enum containing possible error types for structure checkers.

Package chemaxon.checkers Description

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.