Package chemaxon.fixers
package chemaxon.fixers
Structure fixers can be used to fix problems identified by structure checker instances.
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ClassDescriptionDeprecated, for removal: This API element is subject to removal in a future version.Deprecated, for removal: This API element is subject to removal in a future version.This class is the default abstract implementation of
StructureFixerinterfaceAbsent chiral flag fixer.Bond Angle Fixer fixes wrong bond angles in 2D structures.Bond Length Fixer fixes bonds with wrong length in 2D structures.A descendant ofAbstractStructureFixerwhich cleans the molecule in 2dClears wedges.A descendant ofAbstractStructureFixerwhich contracts the abbreviated groups in the moleculeA descendant ofAbstractStructureFixerwhich converts the aliases to contracted abbreviated groups in the moleculeA descendant ofAbstractStructureFixerwhich converts the pseudo informations to contracted abbreviated groups in the moleculeA descendant ofAbstractStructureFixerwhich converts the aliases to atom with atom number contained in the alias informationA descendant ofAbstractStructureFixerwhich converts pseudo atoms to carbon atomsA descendant ofAbstractStructureFixerwhich sets wiggly bond to crossed double bondA descendant ofAbstractStructureFixerwhich converts the isotopes to non isotope atomsA descendant ofAbstractStructureFixerwhich converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form.Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.A descendant ofAbstractStructureFixerwhich converts the bond to single bond.A descendant ofAbstractStructureFixerwhich converts crossed double bond to wigglyDeprecated, for removal: This API element is subject to removal in a future version.A descendant ofAbstractStructureFixerwhich converts the aromatic rings in the molecule into Kekule representation.A descendant ofAbstractStructureFixerwhich converts incorrectly drawn metallocenes into multicenter based coordinate bond representation.A descendant ofAbstractStructureFixerwhich expands all abbreviated groups in the moleculeDeprecated, for removal: This API element is subject to removal in a future version.This annotation is responsible for adding UI based meta data forStructureFixerimplementationsComparator of structure fixer for priority Default fixer and order of fixers is defined this way.This annotation is used to annotate theStructureFixerimplementations whichStructureCheckerErrorTypecan be fixed by the current fixerThis annotation is used to annotate theStructureFixerimplementations which error codes (identified by a unqieString) can be fixed by the current fixerFlips wedge bonds.Deprecated, for removal: This API element is subject to removal in a future version.A descendant ofAbstractStructureFixerwhich maps the atoms of the molecule incrementallyA descendant ofAbstractStructureFixerwhich maps the reaction withAutoMapper.A descendant ofAbstractStructureFixerwhich converts a single incorrectly drawn metallocene into multicenter based coordinate bond representation.A descendant ofAbstractStructureFixerwhich neutralize the charge of the atoms of the moleculePartial cleanA descendant ofAbstractStructureFixerwhich rearomatize the moleculeRearranges stereo wedge bonds according to IUPAC recommendations.A descendant ofAbstractStructureFixerwhich removes the alias information from the atoms of the moleculeA descendant ofAbstractStructureFixerwhich removes the atoms of the molecule signed in the resultA descendant ofAbstractStructureFixerwhich removes the atom maps from the moleculeA descendant ofAbstractStructureFixerwhich removes query properties from the given atoms.A descendant ofAbstractStructureFixerwhich removes the atom value from the moleculeA descendant ofAbstractStructureFixerwhich removes the attached data from the molecule.A descendant ofAbstractStructureFixerwhich removes the bonds of the molecule signed by the resultFixer removes reactiong center bond marks from bonds.Removes brackets from molecule by ungrouping S-groups surrounded by brackets.AStructureFixerimplementation which removes absolute stereo property from the molecule.A descendant ofAbstractStructureFixerwhich implicitize the hydrogens in the moleculeAStructureFixerimplementation which removes absolute stereo property from the molecule.A descendant ofAbstractStructureFixerwhich removes the radicals from the atoms of the moleculeFixer removes reactiong center bond marks from bonds.Fixer for molecules containing Stereo Care Boxes.Removes stereo inversion retention marks.A descendant ofAbstractStructureFixerthat removes unused R-group definitions.A descendant ofAbstractStructureFixerwhich removes valence properties from the given atoms.A descendant ofAbstractStructureFixerwhich sets the z-coordinates of atoms to zero.A descendant ofAbstractStructureFixerthat can fix attachment errors in R-group definition members.Descriptor class forStructureFixerclasses.Deprecated.useCheckerFixerFactoryinsteadFixer to fix substructure issues.A descendant ofAbstractStructureFixerwhich ungroups all abbreviated groups in the moleculeA descendant ofAbstractStructureFixerwhich fixes valence problem in the molecule if it is possible with removing explicit hydrogens or by adding chargeDeprecated.Deprecated, for removal: This API element is subject to removal in a future version.
AddChiralFlagFixer