Examples of available checkers and their fixers

Structure Checker GUI

Structure Checker in MarvinSketch

structurechecker Command Line Tool

Checkers

• Abbreviated Group
• Absent Chiral Flag
• Absolute Stereo Configuration
• Alias
• Aromaticity Error
• Atom Map
• Atom Query Property
• Atom Value
• Atropisomer
• Attached Data
• Bond Angle
• Bond Length
• Chiral Flag
• Chiral Flag Error

• Circular R-group Reference
• Coordination System Error
• Covalent Counterion
• Crossed Double-Bond
• Double Bond Stereo Error
• Empty Structure
• Explicit Hydrogen
• Explicit Lone Pairs
• E/Z Double Bond
• Isotope
• Metallocene Error
• Missing Atom Map
• Missing R-group
• Molecule Charge
• Multicenter

• Multicomponent
• Multiple Stereocenter
• OCR Error
• Overlapping Atoms
• Overlapping Bonds
• Pseudo Atom
• Query Atom
• Query Bond
• R-atom
• R-group Attachment Error
• R-group Reference Error
• Racemate
• Radical
• Rare Element
• Reaction Map Error
• Relative Stereo

• Ring Strain Error
• Solvent
• Star Atom
• Stereo Care Box
• Stereo Inversion Retention Mark
• Straight Double Bond
• Substructure
• Three Dimension(3D)
• Unbalanced Reaction
• Unused R-group
• Valence Error
• Valence Property
• Wedge Error
• Wiggly Bond
• Wiggly Double Bond

Deprecation

Abbreviated Group Checker (abbrevgroup)

• Checker searches for abbreviated groups in the structure ^*. Options:
  • expanded (:expanded=true);
  • contracted (:contracted=true);
  • both expanded and contracted groups (default).
  You can specify a list of excluded abbreviated groups, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list. Default and custom abbreviations are also possible to set. The excluded list elements are case sensitive and should be separated by commas (,). (:excluded=Ph,Ala,Gly,MyGroup)
  
• Fixer offers - in order of priority -:
  1. ungroup abbreviated groups (ungroup);
  2. expand abbreviated groups (expandgroup);
  3. contract abbreviated groups (contractgroup).

Example:

Abbreviated Group Checker (abbrevgroup)	Warning:	Fix
		Ungroup (ungroup)	Expand Group (expandgroup)	Contract Group (contractgroup)
Detect Expanded Groups
Detect Contracted Groups
Detect All Groups
Detect Contracted Groups with excluded list

^*Note: User defined abbreviated groups are also available to be applied as recognizable abbreviated group set.
Note: If attachment point is not connected to any atom, ungrouping removes attachment points of the abbreviated group and adds an implicit hydrogen.

List of checkers

Absent Chiral Flag Checker (absentchiralflag)

• Checker searches for Absolute chiral flag attached to the molecule if the molecule is chiral and all stereo centers are precisely marked.
• Fixer adds chiral flag (Absolute) to the molecule (addchiralflag).

Example:

Absent Chiral Flag Checker (absentchiralflag)	Warning:	Fix
		Add Chiral Flag (addchiralflag)
Detect Absent Chiral Flag

List of checkers

Absolute Stereo Configuration Checker (absolutestereoconfiguration)

• Checker searches for molecules in which all asymmetric centers have absolute stereo configuration.
• Fixer: no fixer is available for this checker.

Example:

Absolute Stereo Configuration (absolutestereoconfiguration)	Warning:	Fix
Detect Absolute Stereo Configuration

List of checkers

Alias Checker (alias)

• Checker searches for aliases in the structure.
• Fixer offers:
  1. converting alias to abbreviated group if the alias value corresponds to a group in the abbreviated group list ^* (aliastogroup);
  2. converting alias to atom if the alias value corresponds to an element (e.g., Ar) (aliastoatom);
  3. removing alias (revealing the atom under the alias) ^** (removealias);
  4. deleting the atom having alias information (removeatom).

Example:

Alias Checker (alias)	Warning:	Fix
		Convert Alias to Group (aliastogroup)	Convert to Atom (aliastoatom)	Remove Alias (removealias)	Delete Atom (removeatom)
Detect Alias

Note: "OMe" and "CL" were defined as alias. After converting "OMe" to methoxy group, the abbreviated group is linked correctly to the chain, i.e., bond through the oxygen atom.
^*Note: User defined abbreviated groups are also available to be applied as recognizable abbreviated group set.
^**Note: Alias only covers the atom, and fixer removes this alias from the original atom.

List of checkers

Aromaticity Error Checker (aromaticityerror)

• Checker searches for General, Basic, or Loose aromatic systems that can't be dearomatized or rearomatizing with the given method does not reproduce the initial molecule. Details on aromaticity detection.
• Fixer offers:
  1. rearomatizing (rearomatize);
  2. dearomatizing the aromatic system (dearomatize).

Example:

Aromaticity Error checker (aromaticity)	Warning:	Fix
		Rearomatize (rearomatize)	Dearomatize (dearomatize)
General
Basic
Loose

Note: The 2-pyridone aromatized in general mode is corrected after a checking of aromatization in basic mode.
In this case, both rearomatization and dearomatization fix yields the same structure.

List of checkers

Atom Map Checker (atommap)

• Checker searches for atom maps.
• Fixer offers removing atom maps (removeatommap).

Example:

Atom Map Checker (atommap)	Warning:	Fix
		Remove Atom Map (removeatommap)
Detect Atom Map

List of checkers

Atom Query Property Checker (atomqueryproperty)

• Checker searches for atoms having query properties. Tick options for searching:
  • Hydrogen Count (:H=true);
  • Connection Count (:X=true);
  • Ring Bond Count (:rb=true);
  • Ring Count (:R=true);
  • Implicit Hydrogen Count (:h=true);
  • Smallest Ring Size (:r=true);
  • Aromaticity (:a=true);
  • Substitution Count (:s=true);
  • Unsaturation (:u=true);
  • Explicit Connection Count (:D=true)
  atom query properties.
• Fixer offers removing the identified query properties (removeatomqueryproperty).

Example:

Atom Query Property Checker (atomqueryproperty)	Warning:	Fix
		Removing query property (removeatomqueryproperty)
Detect Atom Query Property

List of checkers

Atom Value Checker (atomvalue)

• Checker searches for atom values.
• Fixer offers:
  1. removing set atom values (removeatomvalue);
  2. deleting the atom with value (removeatom).

Example:

Atom Value Checker (atomvalue)	Warning:	Fix
		Remove Atom Value (removeatomvalue)	Delete Atom (removeatom)
Detect Atom Value

List of checkers

Atropisomer Checker (atropisomer)

• Checker searches for stereoisomers containing two aromatic rings connected by a single bond with at least three ortho ligands. See details in documentation.
• Fixer: no fixer is available for this checker.

Example:

Atropisomer Checker (atropisomer)	Warning:	Fix
Detect Atropisomer

List of checkers

Attached Data Checker (attacheddata)

• Checker searches for attached data.
• Fixer offers:
  1. removing attached data (removeattacheddata);
  2. deleting the atom having attached data (removeatom).

Example:

Attached Data Checker (attacheddata)	Warning:	Fix
		Remove Attached Data (removeattacheddata)	Delete Atom (removeatom)
Detect Attached Data

List of checkers

Bond Angle Checker (bondangle)

• Checker searches for bonds NOT matching the following rules:

  Triple bond angle 180° (± 0.5 rad):
  Double bond angle 120° or 180° (± 0.5 rad):
  sp2 atom's bond angles 120°:
  sp3 atom's bond angles 90° or 3 bond angles 120°, 4th bond of an angle of n times 15°; or a bond angle of 120° and two adjacent angles equal:

• Fixer offers cleaning the structure by:
  1. 2D clean or (clean);
  2. partial clean (partialclean).

Example:

Bond Angle Checker (bondangle)	Warning:	Fix
		Clean (clean)
Detect Bond Angle errors

Note: The current version of bond angle checker examines chain bonds of 2D molecules. Envelope-shaped cyclic compounds are considered as error. Partial clean is not available.

List of checkers

Bond Length Checker (bondlength)

• Checker searches for bond lengths different than the default setting.
• Fixer offers cleaning the structure by:
  1. 2D clean or (clean);
  2. partial clean (partialclean).

Example:

Bond Length Checker (bondlength)	Warning:	Fix
		Clean (clean)
Detect short bonds
Detect long bonds
Detect both bonds

Note: The current version of bond length checker examines chain bonds of 2D molecules. Partial clean is not available.
Note: Bond length checker does not check the length of coordinate bonds and position variation bonds.

List of checkers

Chiral Flag Checker (chiralflag)

• Checker searches for set chiral flags.
• Fixer offers removing the chiral flag (removechiralflag).

Example:

Chiral Flag Checker (chiralflag)	Warning:	Fix
		Fix Chiral Flag (removechiralflag)
Detect set chiral flag
Detect set chiral flag

Note: Checker will find correctly AND incorrectly set chiral flags. Incorrectly set chiral flags will be find by Chiral Flag Error Checker.

List of checkers

Chiral Flag Error Checker (chiralflagerror)

• Checker searches for incorrectly set chiral flags: "Absolute" flag can only be set when all chirality information is specified for the given molecule.
• Fixer offers removing the chiral flag (removeinvalidchiralflag).

Example:

Chiral Flag Error Checker (chiralflagerror)	Warning:	Fix
		Fix Chiral Flag (removeinvalidchiralflag)
Detect invalid chiral flag

List of checkers

Circular R-group Reference Checker (circularrgroupreference)

• Checker searches for series of R-group references where the R-groups refer to each other resulting in a closed loop.
• Fixer: no fixer is available for this checker.

Example:

Circular R-group Reference Checker (circularrgroupreference)	Warning:	Fix
Detect circular R-group references

List of checkers

Coordination System Error Checker (coordsystem)

• Checker searches for errors in the use of coordinative bonds:
  • 2 multicenters connected with a bond;
  • coordinated atom is connected to an atom of the same multicenter with a coordinative bond;
  • multicenter merged with one of its atoms.
• Fixer offers deleting the wrong bond (removebond).

Example:

Coordination System Error Checker (coordsystem)	Warning:	Fix
		Delete bond (removebond)
Detect coordinative bond
Detect coordinative bond

List of checkers

Covalent Counterion Checker (covalentcounterion)

• Checker searches for covalently bound counter ions.
• Fixer offers changing the structure to the ionic form (converttoionicform).

Example:

Covalent Counterion Checker (covalentcounterion)	Warning:	Fix
		Convert to Ionic Form (converttoionicform)
Detect Covalent Counterion

List of checkers

Crossed Double-Bond Checker (crosseddoublebond)

• Checker searches for crossed double bond types (molecules with unknown or unspecified configuration).
• Fixer offers changing crossed double bond to wiggly double bond type (converttowigglydoublebond).

Example:

Crossed Double Bond Checker (crosseddoublebond)	Warning:	Fix
		Convert to Wiggly Double Bond (converttowigglydoublebond)
Detect crossed double bond

Note: Reverse action is: Wiggly Double Bond Checker.

List of checkers

Double Bond Stereo Error Checker (doublebondstereoerror)

• Checker searches for either double bonds that do not correspond to asymmetric double bonds that can exist as two different isomers (e.g. terminal double bonds, double bonds in rigid structural moieties).
• Fixer offers converting the invalid either double bonds to plain double bonds. (converttoplaindoublebond).

Example:

Double Bond Stereo Error Checker (doublebondstereoerror)	Warning:	Fix
		Convert to Plain Double Bond (converttoplaindoublebond)
Detect invalid either double bond
Detect invalid either double bond

Note: Either double bonds can be represented in two different ways. A crossed double bond representation is just the same as drawing a wavy bond next to the given double bond.

List of checkers

Empty Structure Checker (empty)

• Checker searches for empty structure fields (available in multiple structures files).

List of checkers

Explicit Hydrogen Checker (explicith)

• Checker searches for explicit hydrogens. Tick options for searching:
  • Lonely: hydrogen atom without connection (:lonely=true)
  • Isotopic: hydrogen isotopes (:isotopic=true)
  • Charged: charged hydrogen atoms (:charged=true)
  • Radical: hydrogen radicals (:radical=true)
  • Mapped: mapped hydrogens (:mapped=true)
  • Wedged: hydrogen connecting with wedged bond (:wedged=true)
  • H Connected: hydrogen connected to a hydrogen atom (:hconnected=true)
  • Polymer End Group: hydrogen connected to a SRU S-group (:polymerendgroup=true)
  • S-group End: hydrogen connected to a Superatom S-group (:sgroupend=true)
  • S-group: hydrogen which is the only atom in a S-group (:sgroup=true)
  • Valence Error: hydrogen connected to an atom which has valence error (:valenceerror=true)
  • Bridgehead: hydrogen connected to a bridgehead atom (:bridgehead=true)
  explicit hydrogens.
• Fixer offers removing explicit hydrogens and the selected special atoms (removeexplicith).

Example:

Explicit Hydrogen Checker (explicith)	Warning:	Fix
		Remove Explicit Hydrogen (removeexplicith)
Detect Explicit Hydrogen

List of checkers

Explicit Lone Pairs Checker (explicitlp)

• Checker searches for explicitly drawn lone pairs (inserted as Special node from the Advanced tab of the Periodic Table).
• Fixer offers removing the explicit lone pair (removeatom).

Example:

Explicit Lone Pairs checker (explicitlp)	Warning:	Fix
		Delete Atom (removeatom)
Detect Explicit Lone Pair

List of checkers

E/Z Double Bond Checker (ezdoublebond)

• Checker searches for marked E or Z double bond configuraion.
• Fixer: no fixer is available for this checker.

Example:

E/Z Double Bond checker (ezdoublebond)	Warning:	Fix
Detect E/Z Double Bond
Detect E/Z Double Bond

List of checkers

Isotope Checker (isotope)

• Checker searches for isotopic atoms.
• Fixer offers changing the isotopic atom to the most abundant natural isotope of that element (converttoelementalform).

Example:

Isotope Checker (isotope)	Warning:	Fix
		Convert to Element (converttoelementalform)
Detect Isotopic Atom

Note: Deuterium and tritium are recognized as symbols D and T, respectively as well.

List of checkers

Metallocene Error Checker (metallocene)

• Checker searches for incorrect metallocene representations.
• Fixer offers converting to a valid structure: aromatizing the rings, inserting coordination bonds, and fixing charge values (fixmetallocene).

Example:

Metallocene Error Checker (metallocene)	Warning:	Fix
		Fix Multiple Metallocenes (fixmetallocene)
Detect Metallcoene

List of checkers

Missing Atom Map Checker (missingatommap)

• Checker searches for missing atom maps.
• Fixer offers mapping all atoms in the sketch (mapmolecule).

Example:

Missing Atom Map Checker (missingatommap)	Warning:	Fix
		Map Atoms (mapmolecule)
Detect atoms without atom maps

List of checkers

Missing R-group Checker (missingrgroup)

• Checker searches for undefined R-groups.
• Fixer: no fixer is available for this checker.

Example:

Missing R-group Reference Checker (missingrgroup)	Warning:	Fix
Detect undefined R-groups

List of checkers

Molecule Charge Checker (moleculecharge)

• Checker searches molecules in which total charge is not zero.
• Fixer offers removing the charge by adding or removing hydrogens (neutralize).

Example:

Molecule Charge Checker (moleculecharge)	Warning:	Fix
		Neutralize (neutralize)
Detect Charged Molecule

Note: Charge is not checked in reactions. Charged molecules where no hydrogens can be removed are to be corrected manually.

List of checkers

Multicenter Checker (multicenter)

• Checker searches for multicenter drawing.
• Fixer offers removing the multicenter from the molecule (removeatom).

Example:

Multicenter Checker (multicenter)	Warning:	Fix
		Delete Atom (removeatom)
Detect Multicenter drawing

List of checkers

Multicomponent Checker (multicomponent)

• Checker searches for multiple components in the drawing.
• Fixer: no fixer is available for this checker.

Example:

Multicomponent Checker (multicomponent)	Warning:	Fix
Detect disconnected fragments

List of checkers

Multiple Stereocenter Checker (multiplestereocenter)

• Checker searches for molecules having multiple stereocenters.
• Fixer: no fixer is available for this checker.

Example:

Multiple Stereocenter Checker (multiplestereocenter)	Warning:	Fix
Detect Multiple Stereocenter

List of checkers

OCR Error Checker (ocr)

• Checker searches for structures imported incorrectly from optical character recognition procedure.
• Fixer: no fixer is available for this checker.

Example:

OCR Error (ocr)	Warning:	Fix
Detecting OCR errors

List of checkers

Overlapping Atoms Checker (overlappingAtoms)

• Checker searches for overlapping atoms, i.e., atoms closer than the pre-set percentage of the default atom radius.
• Fixer offers cleaning the structures by 2D clean (clean).

Example:

Overlapping Atoms Checker (overlappingAtoms)	Warning:	Fix
		Clean (clean)
Detect Overlapping Atoms

List of checkers

Overlapping Bonds Checker (overlappingBonds)

• Checker searches for overlapping bonds: bonds crossing each other or bonds closer to each other than the set minimal value.
• Fixer offers cleaning the structure by:
  1. 2D clean or (clean);
  2. partial clean (partialclean).

Example:

Overlapping Bonds Checker (overlappingBonds)	Warning:	Fix
		Clean (clean)
Detect Overlapping Bonds

Note: Bridged polycycles are cleaned as far as their structure allows it, and the overlapping bonds warning will remain.

List of checkers

Pseudo Atom Checker (pseudoatom)

• Checker searches for pseudo atoms in the molecule.
• Fixer offers:
  1. converting to abbreviated group if the name is in the abbreviated group list (e.g., Et for ethyl) ^* (pseudotogroup);
  2. converting to carbon atom (converttocarbon);
  3. deleting atom (removeatom).

Example:

Pseudo Atom Checker (pseudoatom)	Warning:	Fix
		Convert Pseudo Atom to Group (pseudotogroup)	Convert to Carbon (converttocarbon)	Delete Atom (removeatom)
Detect Pseudo Atom
Detect Pseudo Atom

^*Note: User defined abbreviated groups are also available to be applied as recognizable abbreviated group set.

List of checkers

Query Atom Checker (queryatom)

• Checker searches for query atoms and atom query properties.
• Fixer offers converting query atom to carbon atom ^* (converttocarbon).

Example:

Query Atom Checker (queryatom)	Warning:	Fix
		Convert to Carbon (converttocarbon)
Find Query Atoms

^*Note: Fixer "Convert to Carbon" will not remove any atom query property found by the "Query Atom" checker, but converts related atoms to carbon atoms.
Suggestion: To overcome the unwanted conversion of atoms having atom query property to carbon, apply checker "Atom Query Property" and its fixer before "Query Atom" checker.

List of checkers

Query Bond Checker (querybond)

• Checker searches for query bonds.
• Fixer offers converting query bond to single bond (converttosinglebond).

Example:

Query Bond Checker (querybond)	Warning:	Fix
		Convert to Single Bond (converttosinglebond)
Find Query Bonds

Note: Fixer "Convert to Single Bond" will not effect topology query bonds found by "Query Bond" checker.

List of checkers

R-atom Checker (ratom)

• Checker searches for R-atoms. Tick options for searching:
  • All (:all=true);
  • Disconnected (:disconnected=true);
  • Generic (:generic=true);
  • Linker (:linker=true);
  • Nested R-atoms (:nested=true).
• Fixer: no fixer is available for this checker.

Example:

R-atom Checker (ratom)	Warning:	Fix
Find All R-atoms (:all=true)
Find Disconnected R-atoms (:disconnected=true)
Find Generic R-atoms (:generic=true)
Find Linker R-atoms (:linker=true)
Find Nested R-atoms (:nested=true)

List of checkers

R-group Attachment Error Checker (rgroupattachmenterror)

• Checker searches for missing attachment points among R-group elements.
• Fixer offers adding R-group attachment points only in unambiguous cases (fixrgroupattachment).

Example:

R-group Attachment Error Checker (rgroupattachmenterror)	Warning:	Fix
		Add attachment point (fixrgroupattachment)
Find missing attachment points

List of checkers

Deprecated - R-group Reference Error Checker

• Checker searches for:
  • Unused R-group;
  • Missing R-group;
  • Circular R-group references.
• Fixer: no fixer is available for this checker.

Note: R-group Reference Error Checker has been split into three separate checkers: Circular R-group Reference; Missing R-group Reference, or Unused R-group Reference checker.
Example:

R-group Reference Error Checker	Warning:
Find Unused R-group references
Find Missing R-group references
Find Circular R-group references

List of checkers

Racemate Checker (racemate)

• Checker searches for chiral centers without set configuration.
• Fixer: no fixer is available for this checker.

Example:

Racemate Checker (racemate)	Warning:	Fix
Find unmarked chiral centers

List of checkers

Radical Checker (radical)

• Checker searches for radical information on molecules .
• Fixer offers removing the radical information (removeradical).

Example:

Radical Checker (radical)	Warning:	Fix
		Remove Radical (removeradical)
Find Radical Information

List of checkers

Rare Element Checker (rareelement)

• Checker searches for rare elements in the structures. Atoms generally present in organic compounds are: H, Li, Na, K, Mg, Ca, B, C, N, O, F, Cl, Br, I, Al, P, S, Cr, Mn, Fe, Co, Ni, Cu, Zn. Any elements outside this selection are considered rare elements.
• Fixer: no fixer is available for this checker.

Example:

Rare element Checker (rareelement)	Warning:	Fix
Find Rare element

List of checkers

Reaction Map Error Checker (reactionmaperror)

• Checker searches for incomplete reaction map. A reaction with two or less atom maps (both on the reactant and the product side) is considered an incompletely mapped reaction.
• Fixer offers mapping the reaction (mapreaction).

Example:

Reaction Map Error Checker (reactionmap)	Warning:	Fix
		Mapping (mapreaction)
Find incomplete reaction map

List of checkers

Relative Stereo Checker (relativestereo)

• Checker searches for multiple enchanced stereogenic center flags.
• Fixer: no fixer is available for this checker.

Example:

Relative Stereo Checker (relativestereo)	Warning:	Fix
Find relative stereo configuration

List of checkers

Ring Strain Error Checker (ringstrainerror)

• Checker searches for:
  • trans double bonds in bridged rings;
  • cumulated double bonds in rings;
  • triple bonds in rings.
• Fixer: no fixer is available for this checker.

Example:

Ring Strain Error Checker (ringstrainerror)	Warning:	Fix
Detect trans double bonds
Detect cumulated double bonds
Detect triple bonds

List of checkers

Solvent Checker (solvent)

• Checker searches for fragments in the molecule file defined as solvent molecules if more than one fragment is present. The list is customizable and is stored in a configuration file.
• Fixer offers removing solvent fragment(s) (removeatom).

Example:

Solvent Checker (solvent)	Warning:	Fix
		Delete Atom (removeatom)
Find Solvent Molecules
Find Solvent Molecules

Note: In case there are only solvent molecules in the input structure, Solvent Checker detects the solvents but no fixer is offered.

The default solvents are: water, methanol, ethanol, propan-1-ol propan-2-ol, butan-1-ol, formic acid, acetic acid, pentane, hexane, benzene, methylbenzene, ethoxyethane, trichloromathane, ethyl acetate, dichloromethane, propan-2-one, acetonitrile, N-methylacetamide, methanesulfonylmethane, oxolane, heptane, 2-mezhylpropan-2-ol, butan-2-one, cyclohexane, cycloheptane, 1,2-dichloroethane, 2-(propan-2-yloxy)propane, 1,2-dimethoxyethane, N,N-dimethylacetamide, pyridine, 1,2-dimethylbenzene, 2-methyoxy-2-methylpropane

List of checkers

Star Atom Checker (staratom)

• Checker searches for star atoms, inserted as Special node from the Advanced tab of the Periodic Table.
• Fixer offers:
  1. converting star atom to carbon atom (converttocarbon);
  2. removing the star atom (removeatom).

Example:

Star Atom Checker (staratom)	Warning:	Fix
		Convert to Carbon (converttocarbon)	Delete Atom (removeatom)
Find Star Atom

List of checkers

Stereo Care Box Checker (stereocarebox)

• Checker searches for stereo care boxes placed on query bonds.
• Fixer offers removing care boxes from bonds (removestereocarebox).

Example:

Stereo Care Box Checker (stereocarebox)	Warning:	Fix
		Remove Stereo Care Box (removestereocarebox)
Find Stereo Care Box

List of checkers

Stereo Inversion Retention Mark (stereoinversionretentionmark)

• Checker searches for stereo inversion/retention marks both on single molecules and on molecules taking part in reactions.
• Fixer removes stereo inversion/retention marks both from molecules and reactions. (removestereoinversionretentionmark).

Example:

Stereo Inversion Retention Mark (stereoinversionretentionmark)	Warning:	Fix
		Remove Stereo Inversion Retention Mark (removestereoinversionretentionmark)
Detect inversion/retention mark
Detect inversion/retention mark

List of checkers

Straight Double Bond Checker (straightdoublebond)

• Checker searches for undefined double bond stereo representations.
• Fixer offers:
  1. changing crossed double bond to wiggly double bond type (converttowigglydoublebond);
  2. changing wiggly double bond to crossed double bond type (converttocrosseddoublebond).

Example:

Straight Double Bond Checker (straightdoublebond)	Warning:	Fix
		Convert to Crossed Double Bond (converttocrosseddoublebond)	Convert to Wiggly Double Bond (converttowigglydoublebond)
Find Straight Double Bond

List of checkers

Substructure Checker (substructure:[smarts])

• Checker searches for SMARTS defined substructures. Substructure Checkers can be set individually.
• Fixer: when the substructure is specified as reaction SMARTS or SMIRKS, the checker works as fixer as well.

Example:

Substructure Checker	Warning:	Fix
		O=N=O>>[O-][N+]=O
Checker setting: SMARTS: O=N=O>>[O-][N+]=O

Note: You can rename "substructure checker" in Structure Checker GUI. Click on the name field of the configured checker and rename it by typing a new name.

List of checkers

Three Dimension Checker (3d)

• Checker searches for 3D (Z) coordinates.
• Fixer offers:
  1. cleaning the structures by 2D clean (clean);
  2. setting the atomic z-coordinates to zero (removezcoordinate).

Example:

Three Dimension Checker (3d)	Warning:	Fix
		Clean (clean)	Remove Z-Coordinate (removezcoordinate)
Detect 3D coordinates

List of checkers

Unbalanced Reaction Checker (unbalancedreaction)

• Checker detects reaction scheme with differing total atom numbers or atom types on the two sides of the reaction arrow.
• Fixer: no fixer is available for this checker.

Example:

Unbalanced Reaction Checker (unbalancedreaction)	Warning:	Fix
Detect unbalanced reaction scheme
Approved reaction scheme

List of checkers

Unused R-group Checker (unusedrgroup)

• Checker searches for R-group definitions that are not used.
• Fixer removes unused R-group definitions (fixunusedrgroups).

Example:

Unused R-group Reference Checker (unusedrgroup)	Warning:	Fix
		Remove unused R-group definitions (fixunusedrgroups)
Detect unused R-groups

List of checkers

Valence Error Checker (valenceerror)

• Checker searches for valence errors.
  • Allow traditional N representation: checking this option will allow the presence of pentavalent nitrogen. Details on valence calculation of nitrogen (:allowTraditionalNitrogen=true)
• Fixer offers removing explicit hydrogens if applicable (fixvalence).

Example:

Valence Error Checker (valenceerror)	Warning:	Fix
		Fix Valence (fixvalence)
Detect Valence Error
Detect Valence Error: Allow traditional N representation (:allowTraditionalNitrogen=true)

Note: Valence errors with no removable hydrogens have to be corrected manually.

Current limitation: If an R group definition contains an S group with valence error inside, the checker reports about the problem but no fixer is applied (even if the valence error could be eliminated with H removal).

List of checkers

Valence Property Checker (valenceproperty)

• Checker searches for atoms with marked default and non-default valence properties.
• Fixer offers removing the identified valence properties (removevalenceproperty).

Example:

Valence Property Checker (valenceproperty)	Warning:	Fix
		Remove Valence Property (removevalenceproperty)
Detect Marked Valence Property

List of checkers

Wedge Error Checker (wedgeerror)

• Checker searches for irregular wedge bonds.
• Fixer offers removing all wedge bonds and replacing them with a single bond (wedgeclean).

Example:

Wedge Error Checker (wedgeerror)	Warning:	Fix
		Clean Wedge (wedgeclean)
Detect irregular wedge bond

Note: Some symmetric structures are not recognized by the checker.

List of checkers

Wiggly Bond Checker (wigglybond)

• Checker searches for wiggly bond (molecules with unknown or unspecified configuration) starting from chiral centers.
• Fixer offers changing wiggly bond to single bond (converttosinglebond).

Example:

Wiggly Double Bond Checker (wigglybond)	Warning:	Fix
		Convert to Single Bond (converttosinglebond)
Detect Wiggly Bond

List of checkers

Wiggly Double Bond Checker (wigglydoublebond)

• Checker searches for wiggly double bond (molecules with unknown or unspecified configuration).
• Fixer offers changing wiggly double bond to crossed double bond type (converttocrosseddoublebond).

Example:

Wiggly Double Bond Checker (wigglydoublebond)	Warning:	Fix
		Convert to Crossed Double Bond (converttocrosseddoublebond)
Detect Wiggly Double Bond

Note: Reverse action: Crossed Double Bond checker.

Deprecation

The following action strings are deprecated from version 5.12.0:

Links

Structure Checker GUI

Structure Checker in MarvinSketch

structurechecker Command Line Tool

Examples of structure checking in various ChemAxon products

Structure Checker Developer Guide