Package chemaxon.fixers

Structure fixers can be used to fix problems identified by structure checker instances.

Interface Summary

Interface	Description
StructureFixer	A StructureFixer can fix a Molecule problem identified by a StructureCheckerResult

Class Summary

Class	Description
AbsentChiralFlagFixer	Deprecated. use AddChiralFlagFixer
AbsoluteStereoFixer	Deprecated. use RemoveInvalidChiralFlagFixer
AbstractStructureFixer	This class is the default abstract implementation of StructureFixer interface
AddChiralFlagFixer	Absent chiral flag fixer.
BondAngleFixer	Bond Angle Fixer fixes wrong bond angles in 2D structures.
BondLengthFixer	Bond Length Fixer fixes bonds with wrong length in 2D structures.
CleanFixer	A descendant of AbstractStructureFixer which cleans the molecule in 2d
ClearWedgeFixer	Clears wedges.
ContractGroupFixer	A descendant of AbstractStructureFixer which contracts the abbreviated groups in the molecule
ConvertAliasToGroupFixer	A descendant of AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule
ConvertPseudoToGroupFixer	A descendant of AbstractStructureFixer which converts the pseudo informations to contracted abbreviated groups in the molecule
ConvertToAtomFixer	A descendant of AbstractStructureFixer which converts the aliases to atom with atom number contained in the alias information
ConvertToCarbonFixer	A descendant of AbstractStructureFixer which converts pseudo atoms to carbon atoms
ConvertToCrossedDoubleBondFixer	A descendant of AbstractStructureFixer which sets wiggly bond to crossed double bond
ConvertToElementalFormFixer	A descendant of AbstractStructureFixer which converts the isotopes to non isotope atoms
ConvertToIonicFormFixer	A descendant of AbstractStructureFixer which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.
ConvertToPlainDoubleBondFixer	Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
ConvertToSingleBondFixer	A descendant of AbstractStructureFixer which converts the bond to single bond.
ConvertToWigglyDoubleBondFixer	A descendant of AbstractStructureFixer which converts crossed double bond to wiggly
CrossedDoubleBondFixer	Deprecated. use ConvertToWigglyDoubleBondFixer
DearomatizeFixer	A descendant of AbstractStructureFixer which converts the aromatic rings in the molecule into Kekule representation.
DistanceBasedMetalloceneFixer	A descendant of AbstractStructureFixer which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.
ExpandGroupFixer	A descendant of AbstractStructureFixer which expands all abbreviated groups in the molecule
ExplicitHydrogenFixer	Deprecated. use RemoveExplicitHydrogenFixer
FixerPriorityComparator	Comparator of structure fixer for priority Default fixer and order of fixers is defined this way.
FlipWedgeBondFixer	Flips wedge bonds.
IsotopeFixer	Deprecated. use ConvertToElementalFormFixer
MapMoleculeFixer	A descendant of AbstractStructureFixer which maps the atoms of the molecule incrementally
MapReactionFixer	A descendant of AbstractStructureFixer which maps the reaction with AutoMapper.
MetalloceneFixer	A descendant of AbstractStructureFixer which converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.
NeutralizeChargeFixer	A descendant of AbstractStructureFixer which neutralize the charge of the atoms of the molecule
PartialCleanFixer	Partial clean
RearomatizeFixer	A descendant of AbstractStructureFixer which rearomatize the molecule
RearrangeWedgesFixer	Rearranges stereo wedge bonds according to IUPAC recommendations.
RemoveAliasFixer	A descendant of AbstractStructureFixer which removes the alias information from the atoms of the molecule
RemoveAtomFixer	A descendant of AbstractStructureFixer which removes the atoms of the molecule signed in the result
RemoveAtomMapFixer	A descendant of AbstractStructureFixer which removes the atom maps from the molecule
RemoveAtomQueryPropertyFixer	A descendant of AbstractStructureFixer which removes query properties from the given atoms.
RemoveAtomValueFixer	A descendant of AbstractStructureFixer which removes the atom value from the molecule
RemoveAttachedDataFixer	A descendant of AbstractStructureFixer which removes the attached data from the molecule.
RemoveBondFixer	A descendant of AbstractStructureFixer which removes the bonds of the molecule signed by the result
RemoveBracketsFixer	Removes brackets from molecule by ungrouping S-groups surrounded by brackets.
RemoveChiralFlagFixer	A StructureFixer implementation which removes absolute stereo property from the molecule.
RemoveExplicitHydrogenFixer	A descendant of AbstractStructureFixer which implicitize the hydrogens in the molecule
RemoveInvalidChiralFlagFixer	A StructureFixer implementation which removes absolute stereo property from the molecule.
RemoveRadicalFixer	A descendant of AbstractStructureFixer which removes the radicals from the atoms of the molecule
RemoveReactingCenterBondMarkFixer	Fixer removes reactiong center bond marks from bonds.
RemoveStereoCareBoxFixer	Fixer for molecules containing Stereo Care Boxes.
RemoveStereoInversionRetentionMarkFixer	Removes stereo inversion retention marks.
RemoveUnreferencedRgroupDefinitionsFixer	A descendant of AbstractStructureFixer that removes unused R-group definitions.
RemoveValencePropertyFixer	A descendant of AbstractStructureFixer which removes valence properties from the given atoms.
RemoveZCoordinateFixer	A descendant of AbstractStructureFixer which sets the z-coordinates of atoms to zero.
RgroupAttachmentFixer	A descendant of AbstractStructureFixer that can fix attachment errors in R-group definition members.
StructureFixerDescriptor	Descriptor class for StructureFixer classes.
StructureFixerFactory	Deprecated. use CheckerFixerFactory instead
SubstructureFixer	Fixer to fix substructure issues.
UngroupFixer	A descendant of AbstractStructureFixer which ungroups all abbreviated groups in the molecule
ValenceFixer	A descendant of AbstractStructureFixer which fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding charge
WedgeCleanFixer	Deprecated.
WigglyDoubleBondFixer	Deprecated. use ConvertToCrossedDoubleBondFixer

Annotation Types Summary

Annotation Type	Description
FixerInfo	This annotation is responsible for adding UI based meta data for StructureFixer implementations
Fixes	This annotation is used to annotate the StructureFixer implementations which StructureCheckerErrorType can be fixed by the current fixer
FixesExternal	This annotation is used to annotate the StructureFixer implementations which error codes (identified by a unqie String) can be fixed by the current fixer