Package org.openscience.cdk

Class CDKConstants

  • public class CDKConstants
extends Object
    An interface providing predefined values for a number of constants used throughout the CDK. Classes using these constants should not implement this interface, but use it like: 
       IBond.Order singleBondOrder = CDKConstants.BONDORDER_SINGLE;
    Source code:
    main
    Belongs to CDK module:
    core
    Keywords:
    bond order, stereochemistry

    • Field Detail

      • UNSET

        public static final Object UNSET

      • BONDORDER_SINGLE

        public static final IBond.Order BONDORDER_SINGLE
        Deprecated.
        Use IBond.Order SINGLE directly.
        A bond of degree 1.0.

      • BONDORDER_DOUBLE

        public static final IBond.Order BONDORDER_DOUBLE
        Deprecated.
        Use IBond.Order DOUBLE directly.
        A bond of degree 2.0.

      • BONDORDER_TRIPLE

        public static final IBond.Order BONDORDER_TRIPLE
        Deprecated.
        Use IBond.Order TRIPLE directly.
        A bond of degree 3.0.

      • BONDORDER_QUADRUPLE

        public static final IBond.Order BONDORDER_QUADRUPLE
        Deprecated.
        Use IBond.Order QUADRUPLE directly.
        A bond of degree 4.0.

      • STEREO_ATOM_PARITY_PLUS

        public static final int STEREO_ATOM_PARITY_PLUS
        A positive atom parity.
        See Also:
        Constant Field Values

      • STEREO_ATOM_PARITY_MINUS

        public static final int STEREO_ATOM_PARITY_MINUS
        A negative atom parity.
        See Also:
        Constant Field Values

      • STEREO_ATOM_PARITY_UNDEFINED

        public static final int STEREO_ATOM_PARITY_UNDEFINED
        A undefined atom parity.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_UNSET

        public static final int HYBRIDIZATION_UNSET
        A undefined hybridization.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP1

        public static final int HYBRIDIZATION_SP1
        A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP2

        public static final int HYBRIDIZATION_SP2
        A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3

        public static final int HYBRIDIZATION_SP3
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3D1

        public static final int HYBRIDIZATION_SP3D1
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3D2

        public static final int HYBRIDIZATION_SP3D2
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3D3

        public static final int HYBRIDIZATION_SP3D3
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3D4

        public static final int HYBRIDIZATION_SP3D4
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.
        See Also:
        Constant Field Values

      • HYBRIDIZATION_SP3D5

        public static final int HYBRIDIZATION_SP3D5
        A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.
        See Also:
        Constant Field Values

      • NMRSHIFT_CARBON

        public static final String NMRSHIFT_CARBON
        Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_HYDROGEN

        public static final String NMRSHIFT_HYDROGEN
        Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_NITROGEN

        public static final String NMRSHIFT_NITROGEN
        Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_PHOSPORUS

        public static final String NMRSHIFT_PHOSPORUS
        Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_FLUORINE

        public static final String NMRSHIFT_FLUORINE
        Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_DEUTERIUM

        public static final String NMRSHIFT_DEUTERIUM
        Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSHIFT_SULFUR

        public static final String NMRSHIFT_SULFUR
        Sulfur NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSIGNAL_MULTIPLICITY

        public static final String NMRSIGNAL_MULTIPLICITY
        NMR signal multiplicity constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSIGNAL_INTENSITY

        public static final String NMRSIGNAL_INTENSITY
        NMR signal intensity constant for use as a key in the IChemObject.physicalProperties hashtable.
        See Also:
        ChemObject, Constant Field Values

      • NMRSPECTYPE_1D

        public static final String NMRSPECTYPE_1D
        NMR spectrum type constant for use as key for an arbitrary 1-dimensional NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_1D_DEPT90

        public static final String NMRSPECTYPE_1D_DEPT90
        NMR spectrum type constant for use as key for a 1-dimensional DEPT90 NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_1D_DEPT135

        public static final String NMRSPECTYPE_1D_DEPT135
        NMR spectrum type constant for use as key for a 1-dimensional DEPT135 NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_2D_HSQC

        public static final String NMRSPECTYPE_2D_HSQC
        NMR spectrum type constant for use as key for a 2-dimensional HSQC NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_2D_HHCOSY

        public static final String NMRSPECTYPE_2D_HHCOSY
        NMR spectrum type constant for use as key for a 2-dimensional H,H-COSY NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_2D_INADEQUATE

        public static final String NMRSPECTYPE_2D_INADEQUATE
        NMR spectrum type constant for use as key for a 2-dimensional INADEQUATE NMR experiment.
        See Also:
        Constant Field Values

      • NMRSPECTYPE_2D_HMBC

        public static final String NMRSPECTYPE_2D_HMBC
        NMR spectrum type constant for use as key for a 2-dimensional HMBC NMR experiment.
        See Also:
        Constant Field Values

      • CIP_DESCRIPTOR

        public static final String CIP_DESCRIPTOR
        Property key to store the CIP descriptor label for an atom / bond. The label is a string.
        See Also:
        Constant Field Values

      • ISPLACED

        public static final int ISPLACED
        Flag that is set if the chemobject is placed (somewhere).
        See Also:
        Constant Field Values

      • ISINRING

        public static final int ISINRING
        Flag that is set when the chemobject is part of a ring.
        See Also:
        Constant Field Values

      • ISNOTINRING

        public static final int ISNOTINRING
        Flag that is set when the chemobject is part of a ring.
        See Also:
        Constant Field Values

      • ISALIPHATIC

        public static final int ISALIPHATIC
        Flag that is set if a chemobject is part of an aliphatic chain.
        See Also:
        Constant Field Values

      • VISITED

        public static final int VISITED
        Flag is set if chemobject has been visited.
        See Also:
        Constant Field Values

      • ISAROMATIC

        public static final int ISAROMATIC
        Flag is set if chemobject is part of an aromatic system.
        See Also:
        Constant Field Values

      • ISCONJUGATED

        public static final int ISCONJUGATED
        Flag is set if chemobject is part of a conjugated system.
        See Also:
        Constant Field Values

      • MAPPED

        public static final int MAPPED
        Flag is set if a chemobject is mapped to another chemobject. It is used for example in subgraph isomorphism search.
        See Also:
        Constant Field Values

      • IS_HYDROGENBOND_DONOR

        public static final int IS_HYDROGENBOND_DONOR
        Sets to true if the atom is an hydrogen bond donor.
        See Also:
        Constant Field Values

      • IS_HYDROGENBOND_ACCEPTOR

        public static final int IS_HYDROGENBOND_ACCEPTOR
        Sets to true if the atom is an hydrogen bond acceptor.
        See Also:
        Constant Field Values

      • REACTIVE_CENTER

        public static final int REACTIVE_CENTER
        Flag is set if a chemobject has reactive center. It is used for example in reaction.
        See Also:
        Constant Field Values

      • IS_TYPEABLE

        public static final int IS_TYPEABLE
        Flag is set if an atom could be typed.
        See Also:
        Constant Field Values

      • SINGLE_OR_DOUBLE

        public static final int SINGLE_OR_DOUBLE
        Flag used for marking uncertainty of the bond order. If used on an
        • IAtomContainer it means that one or several of the bonds have this flag raised (which may indicate aromaticity).
        • IBond it means that it's unclear whether the bond is a single or double bond.
        • IAtom it is a way for the Smiles parser to indicate that this atom was written with a lower case letter, e.g. 'c' rather than 'C'
        See Also:
        Constant Field Values

      • MAX_FLAG_INDEX

        public static final int MAX_FLAG_INDEX
        Maximum flags array index. Please update this if the value exceeds 16 - the flags are currently stored as a single short value (16-bit) in the ChemObject implementations (default, silent and query).
        See Also:
        Constant Field Values

      • FLAG_MASKS

        public static final int[] FLAG_MASKS

      • DUMMY_POINTER

        public static final int DUMMY_POINTER
        Flag used for JUnit testing the pointer functionality.
        See Also:
        Constant Field Values

      • MAX_POINTER_INDEX

        public static final int MAX_POINTER_INDEX
        Maximum pointers array index.
        See Also:
        Constant Field Values

      • AUTONOMNAME

        public static final String AUTONOMNAME
        The IUPAC compatible name generated with AutoNom.
        See Also:
        Constant Field Values

      • SMALLEST_RINGS

        public static final String SMALLEST_RINGS
        A smallest set of smallest rings computed for this molecule.
        See Also:
        Constant Field Values

      • ESSENTIAL_RINGS

        public static final String ESSENTIAL_RINGS
        The essential rings computed for this molecule. The concept of Essential Rings is defined in SSSRFinder
        See Also:
        Constant Field Values

      • RELEVANT_RINGS

        public static final String RELEVANT_RINGS
        The relevant rings computed for this molecule. The concept of relevant Rings is defined in SSSRFinder
        See Also:
        Constant Field Values

      • REACTION_ROLE

        public static final String REACTION_ROLE
        Property used for reactions when converted to/from molecules. It defines what role and atom has an a reaction. Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.
        See Also:
        Constant Field Values

      • REACTION_GROUP

        public static final String REACTION_GROUP
        Property used for reactions when converted to/from molecules. It defines fragment grouping, for example when handling ionic components. Used in. ReactionManipulator.toMolecule and ReactionManipulator.toReaction.
        See Also:
        Constant Field Values

      • RING_SIZES

        public static final String RING_SIZES
        This property will contain an ArrayList of Integers. Each element of the list indicates the size of the ring the given atom belongs to (if it is a ring atom at all).
        See Also:
        Constant Field Values

      • RING_CONNECTIONS

        public static final String RING_CONNECTIONS
        This property indicates how many ring bonds are connected to the given atom.
        See Also:
        Constant Field Values

      • ISOTROPIC_SHIELDING

        public static final String ISOTROPIC_SHIELDING
        The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian. This is a property used for calculating NMR chemical shifts by subtracting the value from the isotropic shielding value of a standard (e.g. TMS).
        See Also:
        Constant Field Values

      • REST_H

        public static final String REST_H
        A property to indicate RestH being true or false. RestH is a term used in RGroup queries: "if this property is applied ('on'), sites labelled with Rgroup rrr may only be substituted with a member of the Rgroup or with H"
        See Also:
        Constant Field Values

      • ACDLABS_LABEL

        public static final String ACDLABS_LABEL
        Atom number/label that can be applied using the Manual Numbering Tool in ACD/ChemSketch.
        See Also:
        Constant Field Values

      • CTAB_SGROUPS

        public static final String CTAB_SGROUPS
        Key to store/fetch CTab Sgroups from Molfiles. Important! - Use at your own risk, property is transitive and may be removed in future with a more specific accessor.
        See Also:
        Constant Field Values

      • SPIN_MULTIPLICITY

        public static final String SPIN_MULTIPLICITY
        Enumeration of all valid radical values.
        See Also:
        Constant Field Values

      • REACTION_CONDITIONS

        public static final String REACTION_CONDITIONS
        Property for reaction objects where the conditions of reactions can be placed.
        See Also:
        Constant Field Values

      • PART_OF_RING_OF_SIZE

        public static final String PART_OF_RING_OF_SIZE
        Used as property key for indicating the ring size of a certain atom type.
        See Also:
        Constant Field Values

      • CHEMICAL_GROUP_CONSTANT

        public static final String CHEMICAL_GROUP_CONSTANT
        Used as property key for indicating the chemical group of a certain atom type.
        See Also:
        Constant Field Values

      • SPHERICAL_MATCHER

        public static final String SPHERICAL_MATCHER
        Used as property key for indicating the HOSE code for a certain atom type.
        See Also:
        Constant Field Values

      • PI_BOND_COUNT

        public static final String PI_BOND_COUNT
        Used as property key for indicating the HOSE code for a certain atom type.
        See Also:
        Constant Field Values

      • LONE_PAIR_COUNT

        public static final String LONE_PAIR_COUNT
        Used as property key for indicating the HOSE code for a certain atom type.
        See Also:
        Constant Field Values

      • SINGLE_ELECTRON_COUNT

        public static final String SINGLE_ELECTRON_COUNT
        Used as property key for indicating the number of single electrons on the atom type.
        See Also:
        Constant Field Values

    • Constructor Detail

      • CDKConstants

        public CDKConstants()