Enum StructureCheckerErrorType

    • Enum Constant Summary

      Enum Constants 
      Enum Constant 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
    • 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
      • 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
      • 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.
      • 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
      • 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
      • 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

        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
      • 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​(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:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null