List of available checkers and their fixers

Checkers

• Abbreviated Group
• Alias
• Aromaticity Error
• Atom Map
• Atom Query Property
• Atom Value
• Attached Data
• Bond Angle
• Bond Length
• Chiral Flag Error
• Coordination System Error
• Covalent Counterion

• Crossed Double-Bond
• Empty Structure
• Explicit Hydrogen
• Explicit Lone Pairs
• Isotope
• Metallocene
• Missing Atom Map
• Molecule Charge
• Multicenter
• Multicomponent
• 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
• Ring Strain Error

• Solvent
• Star Atom
• Substructure
• Three dimension(3D)
• Valence Property
• Valence Error
• Wedge Error
• Wiggly Double Bond

 

Abbreviated Group Checker

• Checker detects abbreviated groups in the structure:
  • contracted;
  • expanded; or
  • both.
• Fixer offers:
  • ungroup abbreviated groups;
  • expand abbreviated groups;
  • contract abbreviated groups.

Example:

Abbreviated Group Checker	Warning:	Fix
		Ungroup	Contract Group	Expand Group
Detect Expanded Groups
Detect Contracted Groups
Detect All Groups

Note: If attachment point is not connected to any atom, ungrouping removes attachment points of abbreviated group and adds an implicit hydrogen.

List of checkers

Alias Checker

• Checker detects aliases in structure.
• Fixer offers:
  • converting alias to atom if the alias value corresponds to an element (e.g. Ar);
  • converting alias to abbreviated group if the alias values corresponds to a group in the abbreviated group list;
  • removing alias (revealing the atom under the alias); or
  • deleting alias atom.

Example:

Alias Checker	Warning:	Fix
		Convert to Atom	Convert Alias to Group	Remove Alias	Delete Atom
Detect Alias

Notes: "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.
Alias only covers the atom, and fixer removes this alias from the original atom.

List of checkers

Aromaticity Error Checker

• Checker detects 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:
  • rearomatizing or;
  • dearomatizing the aromatic system.

Example:

Aromaticity Error checker	Warning:	Fix
		Rearomatize	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

• Checker detects atom maps.
• Fixer offers removing atom maps.

Example:

Atom Map Checker	Warning:	Fix
		Remove Atom Map
Detect Atom Map

List of checkers

Atom Query Property Checker

• Checker detects atoms having query properties. Tick options for searching:
  • Hydrogen Count
  • Connection Count
  • Ring Bond Count
  • Ring Count
  • Implicit Hydrogen Count
  • Smallest Ring Size
  • Aromaticity
  • Substitution Count
  • Unsaturation
  • Explicit Connection Count
  atom query properties.
• Fixer offers removing the identified query properties.

Example:

Atom Query Property Checker	Warning:	Fix
		Removing query property
Detect Atom Query Property

List of checkers

Atom Value Checker

• Checker detects atom values.
• Fixer offers removing atom values or deleting the atom with value.

Example:

Atom Value Checker	Warning:	Fix
		Remove Atom Value	Delete Atom
Detect Atom Value

List of checkers

Attached Data Checker

• Checker detects attached data.
• Fixer offers removing attached data or deleting the atom with attached data.

Example:

Attached Data Checker	Warning:	Fix
		Remove Attached Data	Delete Atom
Detect Attached Data

List of checkers

Bond Angle Checker

• Checker detects 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 2D clean.

Example:

Bond Angle Checker	Warning:	Fix
		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

• Checker detects bond lengths different than the default setting.
• Fixer offers cleaning the structures by 2D clean.

Example:

Bond Length Checker	Warning:	Fix
		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.

List of checkers

Chiral Flag Error Checker

• Checker detects 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.

Example:

Chiral Flag Error Checker	Warning:	Fix
		Fix Chiral Flag
Detect invalid chiral flag

List of checkers

Coordination System Error Checker

• Checker detects 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 or the multicenter

Example:

Coordination System Error Checker	Warning:	Fix
		Delete bond
Detect coordinative bond
Detect coordinative bond

List of checkers

Covalent Counterion Checker

• Checker detects covalently bound counter ions.
• Fixer offers changing the structure to the ionic form.

Example:

Covalent Counterion Checker	Warning:	Fix
		Convert to Ionic Form
Detect Covalent Counterion

List of checkers

Crossed Double Bond Checker

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

Example:

Crossed Double Bond Checker	Warning:	Fix
		Convert to Wiggly Double Bond
Detect crossed double bond

Note: Reverse action is: Wiggly Double Bond Checker.

List of checkers

Empty Structure Checker

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

List of checkers

Explicit Hydrogen Checker

• Checker detects explicit hydrogens. Tick options for searching:
  • lonely
  • isotopic
  • charged
  • radical
  • mapped
  • wedged
  explicit hydrogens.
• Fixer offers removing explicit hydrogens and the selected special atoms.

Example:

Explicit Hydrogen Checker	Warning:	Fix
		Remove Explicit Hydrogen
Detect Explicit Hydrogen

List of checkers

Explicit Lone Pairs Checker

• Checker detects explicitly drawn lone pairs (inserted as Special node from the Advanced tab of MarvinSketch's Periodic Table).
• Fixer offers removing the explicit lone pair.

Example:

Explicit Lone Pairs checker	Warning:	Fix
		Delete Atom
Detect Explicit Lone Pair

List of checkers

Isotope Checker

• Checker detects isotopic atoms.
• Fixer offers changing the isotopic atom to the most abundant natural isotope of that element.

Example:

Isotope Checker	Warning:	Fix
		Convert to Element
Detect Isotopic Atom

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

List of checkers

Metallocene Error Checker

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

Example:

Metallocene Error Checker	Warning:	Fix
		Fix Multiple Metallocenes
Detect Metallcoene

List of checkers

Missing Atom Map Checker

• Checker detects missing atom maps.
• Fixer offers mapping all atoms in the sketch.

Example:

Missing Atom Map Checker	Warning:	Fix
		Map Atoms
Detect atoms without atom maps

List of checkers

Molecule Charge Checker

• Checker detects molecules in which total charge is not zero.
• Fixer offers removing the charge by adding or removing hydrogens.

Example:

Molecule Charge Checker	Warning:	Fix
		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

• Checker detects multicenter scheme.
• Fixer offers removing the multicenter from the molecule.

Example:

Multicenter Checker	Warning:	Fix
		Delete Atom
Detect Multicenter scheme

List of checkers

Multicomponent Checker

• Checker detects multiple components in scheme.
• Fixer: no fixer is available for this checker.

Example:

Multicomponent Checker	Warning:	Fix
Detect disconnected fragments

List of checkers

OCR Error

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

Example:

OCR Error	Warning:	Fix
Detecting OCR errors

List of checkers

Overlapping Atoms Checker

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

Example:

Overlapping Atoms Checker	Warning:	Fix
		Clean
Detect Overlapping Atoms

List of checkers

Overlapping Bonds Checker

• Checker detects overlapping bonds: bonds crossing each other or bonds closer to each other than the set minimal value.
• Fixer offers cleaning the structures by 2D clean.

Example:

Overlapping Bonds Checker	Warning:	Fix
		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

• Checker detects pseudo atoms in the molecule.
• Fixer offers
  • converting to abbreviated group if the name is in the abbreviated group list (e.g. Et for ethyl);
  • converting to a carbon atom;
  • deleting atom.

Example:

Pseudo Atom Checker	Warning:	Fix
		Convert to Carbon	Delete Atom	Convert Pseudo Atom to Group
Detect Pseudo Atom
Detect Pseudo Atom

List of checkers

Query Atom Checker

• Checker detects query atoms.
• Fixer: no fixer is available for this checker.

Example:

Query Atom Checker	Warning:	Fix
Find Query Atoms

List of checkers

Query Bond Checker

• Checker detects query bonds.
• Fixer: no fixer is available for this checker.

Example:

Query Bond Checker	Warning:	Fix
Find Query Bonds

List of checkers

R-atom Checker

• Checker detects R-atoms. Tick options for searching:
  • All;
  • Disconnected;
  • Generic;
  • Linker, or;
  • Nested R-atoms.
• Fixer: no fixer is available for this checker.

Example:

R-atom Checker	Warning:	Fix
Find All R-atoms
Find Disconnected R-atoms
Find Generic R-atoms
Find Linker R-atoms
Find Nested R-atoms

List of checkers

R-group Attachment Error Checker

• Checker detects missing attachment points among R-group elements.
• Fixer offers adding R-group attachment points only in unambiguous cases.

Example:

R-group Attachment Error Checker	Warning:	Fix
		Add attachment point
Find missing attachment points

List of checkers

R-group Reference Error Checker

• Checker detects missing or inconsistent R-group references.
• Fixer: no fixer is available for this checker.

Example:

R-group Reference Error Checker	Warning:	Fix
Find R-group references
Find R-group references

List of checkers

Racemate Checker

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

Example:

Racemate Checker	Warning:	Fix
Find unmarked chiral centers

List of checkers

Radical Checker

• Checker detects radical information on molecules.
• Fixer offers removing the radical information.

Example:

Radical Checker	Warning:	Fix
		Remove Radical
Find Radical Information

List of checkers

Rare Element Checker

• Checker detects 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	Warning:	Fix
Find Rare element

List of checkers

Reaction Map Error Checker

• Checker detects 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.

Example:

Reaction Map Error Checker	Warning:	Fix
		Mapping
Find incomplete reaction map

List of checkers

Ring Strain Error Checker

• Checker detects:
  • 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	Warning:	Fix
Detect trans double bonds
Detect cumulated double bonds
Detect triple bonds

List of checkers

Solvent Checker

• Checker detects 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 fragments in case only one type of solvent is present.

Example:

Solvent Checker	Warning:	Fix
		Delete Atom
Find Solvent Molecules

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

• Checker detects star atoms inserted as Special node from the Advanced tab of the Periodic Table.
• Fixer offers removing the star atom.

Example:

Star Atom Checker	Warning:	Fix
		Convert to Carbon	Delete Atom
Find Star Atom

List of checkers

Stereo Care Box Checker

• Checker detects stereo care boxes placed on query bonds.
• Fixer offers removing care boxes from bonds.

Example:

Stereo Care Box Checker	Warning:	Fix
		Remove Stereo Care Box
Find Stereo Care Box

List of checkers

Substructure Checker

• Checker detects 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: This checker is available only in JChem. The checker can also be accessed from MarvinSketch if MarvinSketch is run from the JChem\bin folder (e.g, c:\Program Files\ChemAxon\Jchem\bin\msketch.bat).

List of checkers

Three Dimension Checker

• Checker detects 3rd dimension (Z) coordinates.
• Fixer offers cleaning the structures by 2D clean or setting the atomic z-coordinates to zero.

Example:

Three Dimension Checker	Warning:	Fix
		Remove Z-Coordinate	Clean
Detect 3D coordinates

List of checkers

Unbalanced Reaction Checker

• 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	Warning:	Fix
Detect unbalanced reaction scheme
Approved reaction scheme

List of checkers

Valence Error Checker

• Checker detects valence errors.
• Fixer offers removing explicit hydrogens if applicable.

Example:

Valence Error Checker	Warning:	Fix
		Fix Valence
Detect Valence Error

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

List of checkers

Valence Property Checker

• Checker detects atoms with marked default and non-default valence properties.
• Fixer offers removing the identified valence properties.

Example:

Valence Property Checker	Warning:	Fix
		Remove Valence Property
Detect Marked Valence Property

List of checkers

Wedge Error Checker

• Checker detects improper wedge bonds.
• Fixer offers removing all wedge bonds and replacing them with a single bond.

Example:

Wedge Error Checker	Warning:	Fix
		Clean Wedge
Detect irregular wedge bond

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

List of checkers

Wiggly Double Bond Checker

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

Example:

Wiggly Double Bond Checker	Warning:	Fix
		Convert to Crossed Double Bond
Detect Wiggly Double Bond

Note: Reverse action: Crossed Double Bond checker.

 

List of checkers

Links

Structure Checker GUI
structurecheck Command Line Application
Structure Checker in MarvinSketch
Structure Checker Developer Guide