chemaxon.checkers

Enum StructureCheckerErrorType

java.lang.Object

java.lang.Enum<StructureCheckerErrorType>

chemaxon.checkers.StructureCheckerErrorType

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<StructureCheckerErrorType>

@PublicAPI
public enum StructureCheckerErrorType
extends java.lang.Enum<StructureCheckerErrorType>

Enum containing possible error types for structure checkers.

Since:

Marvin 5.3

Version:

5.7

Author:

Attila Szabo

Enum Constant Summary

Enum Constants

Enum Constant and Description
ABBREVIATED_GROUP Error type represents that abbreviated groups had found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED Error type represents that only contracted abbreviated groups had found in the molecule
ABBREVIATED_GROUP_WITH_ONLY_EXPANDED Error type represents that only expanded abbreviated groups had found in the molecule
ABSENT_CHIRAL_FLAG Error type represents that molecule is chiral, but flag is not added to the molecule
ABSOLUTE_STEREO_CONFIGURATION Error type represents molecules in which all asymmetric centers have absolute stereo configuration
ALIAS Error type represents that alias values had found in the molecule
ALIAS_ATOM Error type represents that alias value that could be converted to an element had found in the molecule
ALIAS_GROUP Error type represents that alias value that could be converted to an abbreviated group had found in the molecule
ALIAS_NONE Error type represents that alias value had found in the molecule
AROMATICITY Error type represents that aromaticity problem had found in the molecule
ATOM_MAP Error type represents that atom maps had found in the molecule
ATOM_QUERY_PROPERTY Error type representing that an atom has a query property set.
ATOM_TYPE Error type represents that atom with the specified symbol had found in the molecule
ATOM_VALUE Error type represents that atom values had found in the molecule
ATROPISOMER Error type represents that atropisomers are found in the molecule
ATTACHED_DATA Error type represents that attached data had found in the molecule
BOND_ANGLE Error type represents that bond angle problem had found in the molecule
BOND_LENGTH Error type represents that bond length problem had found in the molecule
BRACKETS Error type representing that the molecule contains brackets (S-groups).
CHIRAL_FLAG Error type represents molecules marked with "absolute stereo" flag.
CIRCULAR_RGROUP_REFERENCE Error type represents that molecule with circular R-group definition found
COVALENT_COUNTER_ION Error type represents that incorrectly drawn covalent counter ion had found in the molecule
CROSSED_DOUBLE_BOND Error type represents that crossed double bond had found in the molecule
DOODLE Error type represents that molecule with serious scanning or drawing issue had found
DOUBLE_BOND_STEREO Error type represents that molecule contains either double bonds which are not valid
EMPTY Error type represents that molecule structure was empty
EXPLICIT_H Error type represents that explicit hydrogen had found in the molecule
EXPLICIT_LONE_PAIR Error type represents that explicit lone pair had found in the molecule
EXTERNAL Error type for externally developed StructureChecker classes
EZ_DOUBLE_BOND Error type represents that molecule contains double bonds, that can be cis or trans
INCORRECT_TETRAHEDRAL_STEREO Represents incorrect/impossible arrangement of wedge bond around chiral centers.
INVALID_CHIRAL_FLAG Error type represents that stereo center with no enhanced stereo property had found in the molecule
INVALID_COORD_SYSTEM Error type represents that invalid coordination system had found in the molecule
INVALID_REACTION_MAP Error type represents that invalid mapping had found in the molecule (represents a reaction)
INVALID_RGROUP Error type represents that molecule with invalid rgroup had found
INVALID_STEREO Deprecated.
INVALID_WEDGE Deprecated.
ISOTOPE Error type represents that isotpoe atom had found in the molecule
METALLOCENE Error type represents that incorrectly drawn metallocene had found in the molecule
METALLOCENE_AMBIGUOUS Error type represents that incorrectly drawn metallocenes had found in the molecule
MISSING_ATOM_MAP Error type represents that atom with no atom map had found in the molecule
MISSING_RGROUP Error type represents that molecule with missing R-group definition found
MOLECULE_CHARGE Error type represents that the sum charge of the molecule wasn't zero
MULTI_CENTER Error type representing that invalid R-group definition is in the molecule
MULTI_COMPONENT Error type represents that molecule had contained multiple components
MULTIPLE_STEREO_CENTER Error type represents that molecule contains multiple stereo centers
NO_ERROR Error type for results sign no error.
NON_STANDARD_WEDGE_SHEME Wedge configuration around a chiral center doesn't follow IUPAC recommendations.
NON_STEREO_WEDGE_BOND The wedge is connected to a non-stereo atom.
OVERLAPPING_ATOMS Error type represents that overlapping atoms had found in the molecule
OVERLAPPING_BONDS Error type represents that overlapping bonds had found in the molecule
PSEUDO Error type represents that atom with pseudo property could be converted to abbreviated group had found in the molecule
PSEUDO_NO_GROUP Error type represents that atom with pseudo property had found in the molecule
QUERY_ATOM Error type represents that atom with query properties had found in the molecule
QUERY_BOND Error type represents that bond with query properties had found in the molecule
RACEMATE Error type representing asymmetric atom without specific stereo configuration.
RADICAL Error type represents that atom with radical had found in the molecule
RARE_ELEMENT Error type represents that rare element had found in the molecule
RATOM Error type representing that the molecule contains R-atom.
REACTING_CENTER_BOND_MARK Error type represents that molecule contains reacting center bond marks.
RELATIVE_STEREO Error type represents that molecules having multiple stereogenic center groups
RGROUP_ATTACHMENT_ERROR Error type representing invalid attachments in R-group definitions.
RGROUP_BRIDGE_RATOM Error type representing invalid R-atoms corresponding to R-group bridge definitions.
SMALL_RING Error type represents that small ring error had found in the molecule
SOLVENT Error type represents that solvent had found in the molecule
SOLVENT_AMBIGOUS Error type represents that more than one type of solvents had found in the molecule
STAR Error type represents that star atom had found in the molecule
STEREO_CARE_BOX Error type representing stereo search markers in the molecule
STEREO_INVERSION_RETENTION_MARK Error type representing stereo inversion/retention marks in the molecule/reaction
STRAIGHT_DOUBLE_BOND Error type represents molecules containing "either" double bonds.
SUBSTRUCTURE Error type represents that the needed substructure had found
SUBSTRUCTURE_NOFIX Error type represents that the needed substructure had found but no data will be available for the fix in the result
THREE_DIM Error type represents that 3d coordinates had found in the molecule
UNBALANCED_REACTION Error type representing reactions scheme having more atoms on one side of the reaction arrow than on the other.
UNUSED_RGROUP Error type represents that molecule with unused R-group definition found
VALENCE Error type represents that valence error had found in the molecule
VALENCE_PROPERTY Error type representing that an atom has a valence property set.
WIGGLY Error type represents that wiggly bond had found in the molecule
WIGGLY_BOND_TETRAHEDRAL Error type represents molecules having wiggly bonds on tetrahedral stereo centers

Method Summary

Modifier and Type	Method and Description
static StructureCheckerErrorType	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static StructureCheckerErrorType[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

ABBREVIATED_GROUP

public static final StructureCheckerErrorType ABBREVIATED_GROUP

Error type represents that abbreviated groups had found in the molecule

ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED

public static final StructureCheckerErrorType ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED

Error type represents that only contracted abbreviated groups had found in the molecule

ABBREVIATED_GROUP_WITH_ONLY_EXPANDED

public static final StructureCheckerErrorType ABBREVIATED_GROUP_WITH_ONLY_EXPANDED

Error type represents that only expanded abbreviated groups had found in the molecule

ABSENT_CHIRAL_FLAG

public static final StructureCheckerErrorType ABSENT_CHIRAL_FLAG

Error type represents that molecule is chiral, but flag is not added to the molecule

ABSOLUTE_STEREO_CONFIGURATION

public static final StructureCheckerErrorType ABSOLUTE_STEREO_CONFIGURATION

Error type represents molecules in which all asymmetric centers have absolute stereo configuration

ALIAS

public static final StructureCheckerErrorType ALIAS

Error type represents that alias values had found in the molecule

ALIAS_ATOM

public static final StructureCheckerErrorType ALIAS_ATOM

Error type represents that alias value that could be converted to an element had found in the molecule

ALIAS_GROUP

public static final StructureCheckerErrorType ALIAS_GROUP

Error type represents that alias value that could be converted to an abbreviated group had found in the molecule

ALIAS_NONE

public static final StructureCheckerErrorType ALIAS_NONE

Error type represents that alias value had found in the molecule

AROMATICITY

public static final StructureCheckerErrorType AROMATICITY

Error type represents that aromaticity problem had found in the molecule

ATOM_MAP

public static final StructureCheckerErrorType ATOM_MAP

Error type represents that atom maps had found in the molecule

ATOM_QUERY_PROPERTY

public static final StructureCheckerErrorType ATOM_QUERY_PROPERTY

Error type representing that an atom has a query property set.

ATOM_TYPE

public static final StructureCheckerErrorType ATOM_TYPE

Error type represents that atom with the specified symbol had found in the molecule

ATOM_VALUE

public static final StructureCheckerErrorType ATOM_VALUE

Error type represents that atom values had found in the molecule

ATROPISOMER

public static final StructureCheckerErrorType ATROPISOMER

Error type represents that atropisomers are found in the molecule

ATTACHED_DATA

public static final StructureCheckerErrorType ATTACHED_DATA

Error type represents that attached data had found in the molecule

BOND_ANGLE

public static final StructureCheckerErrorType BOND_ANGLE

Error type represents that bond angle problem had found in the molecule

BOND_LENGTH

public static final StructureCheckerErrorType BOND_LENGTH

Error type represents that bond length problem had found in the molecule

BRACKETS

public static final StructureCheckerErrorType BRACKETS

Error type representing that the molecule contains brackets (S-groups).

CHIRAL_FLAG

public static final StructureCheckerErrorType CHIRAL_FLAG

Error type represents molecules marked with "absolute stereo" flag.

CIRCULAR_RGROUP_REFERENCE

public static final StructureCheckerErrorType CIRCULAR_RGROUP_REFERENCE

Error type represents that molecule with circular R-group definition found

COVALENT_COUNTER_ION

public static final StructureCheckerErrorType COVALENT_COUNTER_ION

Error type represents that incorrectly drawn covalent counter ion had found in the molecule

CROSSED_DOUBLE_BOND

public static final StructureCheckerErrorType CROSSED_DOUBLE_BOND

Error type represents that crossed double bond had found in the molecule

DOODLE

public static final StructureCheckerErrorType DOODLE

Error type represents that molecule with serious scanning or drawing issue had found

DOUBLE_BOND_STEREO

public static final StructureCheckerErrorType DOUBLE_BOND_STEREO

Error type represents that molecule contains either double bonds which are not valid

EMPTY

public static final StructureCheckerErrorType EMPTY

Error type represents that molecule structure was empty

EXPLICIT_H

public static final StructureCheckerErrorType EXPLICIT_H

Error type represents that explicit hydrogen had found in the molecule

EXPLICIT_LONE_PAIR

public static final StructureCheckerErrorType EXPLICIT_LONE_PAIR

Error type represents that explicit lone pair had found in the molecule

EXTERNAL

public static final StructureCheckerErrorType EXTERNAL

Error type for externally developed StructureChecker classes

EZ_DOUBLE_BOND

public static final StructureCheckerErrorType EZ_DOUBLE_BOND

Error type represents that molecule contains double bonds, that can be cis or trans

INCORRECT_TETRAHEDRAL_STEREO

public static final StructureCheckerErrorType INCORRECT_TETRAHEDRAL_STEREO

Represents incorrect/impossible arrangement of wedge bond around chiral centers. Type: error

INVALID_CHIRAL_FLAG

public static final StructureCheckerErrorType INVALID_CHIRAL_FLAG

Error type represents that stereo center with no enhanced stereo property had found in the molecule

INVALID_COORD_SYSTEM

public static final StructureCheckerErrorType INVALID_COORD_SYSTEM

Error type represents that invalid coordination system had found in the molecule

INVALID_REACTION_MAP

public static final StructureCheckerErrorType INVALID_REACTION_MAP

Error type represents that invalid mapping had found in the molecule (represents a reaction)

INVALID_RGROUP

public static final StructureCheckerErrorType INVALID_RGROUP

Error type represents that molecule with invalid rgroup had found

INVALID_STEREO

@Deprecated
public static final StructureCheckerErrorType INVALID_STEREO

Deprecated.

Error type represents that a small ring with trans double bond had found in the molecule

INVALID_WEDGE

@Deprecated
public static final StructureCheckerErrorType INVALID_WEDGE

Deprecated.

Error type represents that invalid wedge bond had found in the molecule

ISOTOPE

public static final StructureCheckerErrorType ISOTOPE

Error type represents that isotpoe atom had found in the molecule

METALLOCENE

public static final StructureCheckerErrorType METALLOCENE

Error type represents that incorrectly drawn metallocene had found in the molecule

METALLOCENE_AMBIGUOUS

public static final StructureCheckerErrorType METALLOCENE_AMBIGUOUS

Error type represents that incorrectly drawn metallocenes had found in the molecule

MISSING_ATOM_MAP

public static final StructureCheckerErrorType MISSING_ATOM_MAP

Error type represents that atom with no atom map had found in the molecule

MISSING_RGROUP

public static final StructureCheckerErrorType MISSING_RGROUP

Error type represents that molecule with missing R-group definition found

MOLECULE_CHARGE

public static final StructureCheckerErrorType MOLECULE_CHARGE

Error type represents that the sum charge of the molecule wasn't zero

MULTI_CENTER

public static final StructureCheckerErrorType MULTI_CENTER

Error type representing that invalid R-group definition is in the molecule

MULTI_COMPONENT

public static final StructureCheckerErrorType MULTI_COMPONENT

Error type represents that molecule had contained multiple components

MULTIPLE_STEREO_CENTER

public static final StructureCheckerErrorType MULTIPLE_STEREO_CENTER

Error type represents that molecule contains multiple stereo centers

NO_ERROR

public static final StructureCheckerErrorType NO_ERROR

Error type for results sign no error. Not used anywhere. Just for completeness

NON_STANDARD_WEDGE_SHEME

public static final StructureCheckerErrorType NON_STANDARD_WEDGE_SHEME

Wedge configuration around a chiral center doesn't follow IUPAC recommendations. Type: warning

NON_STEREO_WEDGE_BOND

public static final StructureCheckerErrorType NON_STEREO_WEDGE_BOND

The wedge is connected to a non-stereo atom. Type: error

OVERLAPPING_ATOMS

public static final StructureCheckerErrorType OVERLAPPING_ATOMS

Error type represents that overlapping atoms had found in the molecule

OVERLAPPING_BONDS

public static final StructureCheckerErrorType OVERLAPPING_BONDS

Error type represents that overlapping bonds had found in the molecule

PSEUDO

public static final StructureCheckerErrorType PSEUDO

Error type represents that atom with pseudo property could be converted to abbreviated group had found in the molecule

PSEUDO_NO_GROUP

public static final StructureCheckerErrorType PSEUDO_NO_GROUP

Error type represents that atom with pseudo property had found in the molecule

QUERY_ATOM

public static final StructureCheckerErrorType QUERY_ATOM

Error type represents that atom with query properties had found in the molecule

QUERY_BOND

public static final StructureCheckerErrorType QUERY_BOND

Error type represents that bond with query properties had found in the molecule

RACEMATE

public static final StructureCheckerErrorType RACEMATE

Error type representing asymmetric atom without specific stereo configuration.

RADICAL

public static final StructureCheckerErrorType RADICAL

Error type represents that atom with radical had found in the molecule

RARE_ELEMENT

public static final StructureCheckerErrorType RARE_ELEMENT

Error type represents that rare element had found in the molecule

RATOM

public static final StructureCheckerErrorType RATOM

Error type representing that the molecule contains R-atom.

REACTING_CENTER_BOND_MARK

public static final StructureCheckerErrorType REACTING_CENTER_BOND_MARK

Error type represents that molecule contains reacting center bond marks.

RELATIVE_STEREO

public static final StructureCheckerErrorType RELATIVE_STEREO

Error type represents that molecules having multiple stereogenic center groups

RGROUP_ATTACHMENT_ERROR

public static final StructureCheckerErrorType RGROUP_ATTACHMENT_ERROR

Error type representing invalid attachments in R-group definitions.

RGROUP_BRIDGE_RATOM

@Beta
public static final StructureCheckerErrorType RGROUP_BRIDGE_RATOM

Error type representing invalid R-atoms corresponding to R-group bridge definitions.

SMALL_RING

public static final StructureCheckerErrorType SMALL_RING

Error type represents that small ring error had found in the molecule

SOLVENT

public static final StructureCheckerErrorType SOLVENT

Error type represents that solvent had found in the molecule

SOLVENT_AMBIGOUS

public static final StructureCheckerErrorType SOLVENT_AMBIGOUS

Error type represents that more than one type of solvents had found in the molecule

STAR

public static final StructureCheckerErrorType STAR

Error type represents that star atom had found in the molecule

STEREO_CARE_BOX

public static final StructureCheckerErrorType STEREO_CARE_BOX

Error type representing stereo search markers in the molecule

STEREO_INVERSION_RETENTION_MARK

public static final StructureCheckerErrorType STEREO_INVERSION_RETENTION_MARK

Error type representing stereo inversion/retention marks in the molecule/reaction

STRAIGHT_DOUBLE_BOND

public static final StructureCheckerErrorType STRAIGHT_DOUBLE_BOND

Error type represents molecules containing "either" double bonds.

SUBSTRUCTURE

public static final StructureCheckerErrorType SUBSTRUCTURE

Error type represents that the needed substructure had found

SUBSTRUCTURE_NOFIX

public static final StructureCheckerErrorType SUBSTRUCTURE_NOFIX

Error type represents that the needed substructure had found but no data will be available for the fix in the result

THREE_DIM

public static final StructureCheckerErrorType THREE_DIM

Error type represents that 3d coordinates had found in the molecule

UNBALANCED_REACTION

public static final StructureCheckerErrorType UNBALANCED_REACTION

Error type representing reactions scheme having more atoms on one side of the reaction arrow than on the other.

UNUSED_RGROUP

public static final StructureCheckerErrorType UNUSED_RGROUP

Error type represents that molecule with unused R-group definition found

VALENCE

public static final StructureCheckerErrorType VALENCE

Error type represents that valence error had found in the molecule

VALENCE_PROPERTY

public static final StructureCheckerErrorType VALENCE_PROPERTY

Error type representing that an atom has a valence property set.

WIGGLY

public static final StructureCheckerErrorType WIGGLY

Error type represents that wiggly bond had found in the molecule

WIGGLY_BOND_TETRAHEDRAL

public static final StructureCheckerErrorType WIGGLY_BOND_TETRAHEDRAL

Error type represents molecules having wiggly bonds on tetrahedral stereo centers

Method Detail

values

public static StructureCheckerErrorType[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (StructureCheckerErrorType c : StructureCheckerErrorType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static StructureCheckerErrorType valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null