See: Description
| Interface | Description |
|---|---|
| StructureFixer |
| Class | Description |
|---|---|
| AbsentChiralFlagFixer | Deprecated |
| AbsoluteStereoFixer | Deprecated |
| 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 |
| 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 |
| CovalentCounterionFixer | Deprecated |
| CrossedDoubleBondFixer | Deprecated |
| 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 |
| FixerPriorityComparator |
Comparator of structure fixer for priority
Default fixer and order of fixers is defined this way.
|
| IsotopeFixer | Deprecated |
| 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 |
| 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 |
| 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 which 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 R-group
attachment errors by adding missing attachment to R-group members having a
single attachment position available. |
| RgroupReferenceFixer | Deprecated |
| 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 |
A descendant of
AbstractStructureFixer which fixes invalid wedge problem |
| WigglyDoubleBondFixer | Deprecated |
| 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 |