See: Description
| Interface | Description |
|---|---|
| StructureChecker |
General interface describing functions that are available for a chemical structure checker.
|
| Class | Description |
|---|---|
| AbbreviatedGroupChecker |
A descendant of
AbstractStructureChecker detecting abbreviations
("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in
abbreviated group form. |
| AbbreviatedGroupChecker.Abbreviations |
The abbreviation storage class.
|
| 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.
|
| 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. |
| 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. |
| 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 |
| RgroupAttachmentCountErrorChecker |
A descendant of
AbstractStructureChecker detecting inconsistent
attachment counts in R-group definitions. |
| RgroupAttachmentErrorChecker |
A descendant of
AbstractStructureChecker detecting invalid
attachments in R-group definitions. |
| RgroupOrphanAttachmentErrorChecker |
A descendant of
AbstractStructureChecker detecting orphan
attachments in R-group definitions. |
| RgroupReferenceErrorChecker | Deprecated |
| 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 |
Utility class for stereo chemistry checkers
|
| 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
definition errors. |
| 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.
|
| WigglyBondChecker |
A descendant of
AbstractStructureChecker detecting wiggly bonds on
tetrahedral stereo centers. |
| WigglyDoubleBondChecker |
A descendant of
BondChecker detecting double bonds havong wiggly bond ligands representing
unspecified double bond stereo configuration. |
| 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 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 |