Package org.openscience.cdk

Class CDKConstants

java.lang.Object
org.openscience.cdk.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;
Keywords:
bond order, stereochemistry

  • Field Details

    • 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:

    • STEREO_ATOM_PARITY_MINUS

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

    • STEREO_ATOM_PARITY_UNDEFINED

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

    • HYBRIDIZATION_UNSET

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

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • NMRSHIFT_CARBON

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

    • NMRSHIFT_HYDROGEN

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

    • NMRSHIFT_NITROGEN

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

    • NMRSHIFT_PHOSPORUS

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

    • NMRSHIFT_FLUORINE

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

    • NMRSHIFT_DEUTERIUM

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

    • NMRSHIFT_SULFUR

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

    • NMRSIGNAL_MULTIPLICITY

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

    • NMRSIGNAL_INTENSITY

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

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • ISPLACED

      @Deprecated public static final int ISPLACED
      Deprecated.
      Now IChemObject.PLACED
      Flag that is set if the chemobject is placed (somewhere).
      See Also:

    • ISINRING

      @Deprecated public static final int ISINRING
      Deprecated.
      Now IChemObject.IN_RING
      Flag that is set when the chemobject is part of a ring.
      See Also:

    • ISNOTINRING

      @Deprecated public static final int ISNOTINRING
      Deprecated.
      Now negated from IChemObject.IN_RING
      Flag that is set when the chemobject is part of a ring.
      See Also:

    • ISALIPHATIC

      @Deprecated public static final int ISALIPHATIC
      Deprecated.
      Now IChemObject.ALIPHATIC but should really use not(AROMATIC)
      Flag that is set if a chemobject is part of an aliphatic chain.
      See Also:

    • VISITED

      @Deprecated public static final int VISITED
      Deprecated.
      Now IChemObject.VISITED
      Flag is set if chemobject has been visited.
      See Also:

    • ISAROMATIC

      @Deprecated public static final int ISAROMATIC
      Deprecated.
      Now IChemObject.AROMATIC
      Flag is set if chemobject is part of an aromatic system
      See Also:

    • ISCONJUGATED

      @Deprecated public static final int ISCONJUGATED
      Deprecated.
      Now IChemObject.CONJUGATED
      Flag is set if chemobject is part of a conjugated system.
      See Also:

    • MAPPED

      @Deprecated public static final int MAPPED
      Deprecated.
      Now IChemObject.MAPPED
      Flag is set if a chemobject is mapped to another chemobject. It is used for example in subgraph isomorphism search.
      See Also:

    • IS_HYDROGENBOND_DONOR

      @Deprecated public static final int IS_HYDROGENBOND_DONOR
      Deprecated.
      Now IChemObject.HYDROGEN_BOND_DONOR
      Sets to true if the atom is an hydrogen bond donor.
      See Also:

    • IS_HYDROGENBOND_ACCEPTOR

      @Deprecated public static final int IS_HYDROGENBOND_ACCEPTOR
      Deprecated.
      Now IChemObject.HYDROGEN_BOND_ACCEPTOR
      Sets to true if the atom is an hydrogen bond acceptor.
      See Also:

    • REACTIVE_CENTER

      @Deprecated public static final int REACTIVE_CENTER
      Deprecated.
      Now IChemObject.REACTIVE_CENTER
      Flag is set if a chemobject has reactive center. It is used for example in reaction.
      See Also:

    • IS_TYPEABLE

      @Deprecated public static final int IS_TYPEABLE
      Deprecated.
      Now IChemObject.TYPEABLE
      Flag is set if an atom could be typed.
      See Also:

    • 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:

    • 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:

    • 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:

    • MAX_POINTER_INDEX

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

    • TITLE

      public static final String TITLE
      The title for a IChemObject.
      See Also:

    • REMARK

      public static final String REMARK
      A remark for a IChemObject.
      See Also:

    • COMMENT

      public static final String COMMENT
      A String comment.
      See Also:

    • NAMES

      public static final String NAMES
      A List of names.
      See Also:

    • ANNOTATIONS

      public static final String ANNOTATIONS
      A List of annotation remarks.
      See Also:

    • DESCRIPTION

      public static final String DESCRIPTION
      A description for a IChemObject.
      See Also:

    • SMILES

      public static final String SMILES
      The Daylight SMILES.
      See Also:

    • INCHI

      public static final String INCHI
      The IUPAC International Chemical Identifier.
      See Also:

    • FORMULA

      public static final String FORMULA
      The Molecular Formula Identifier.
      See Also:

    • AUTONOMNAME

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

    • BEILSTEINRN

      public static final String BEILSTEINRN
      The Beilstein Registry Number.
      See Also:

    • CASRN

      public static final String CASRN
      The CAS Registry Number.
      See Also:

    • ALL_RINGS

      public static final String ALL_RINGS
      A set of all rings computed for this molecule.
      See Also:

    • SMALLEST_RINGS

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

    • 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:

    • 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:

    • COMPONENT_GROUP

      public static final String COMPONENT_GROUP
      See Also:

    • REACTION_ROLE

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

    • 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:

    • RGROUP_MEMBERSHIP

      public static final String RGROUP_MEMBERSHIP
      This property is set on atoms of an RGroup substitute definition to indicate which RGroup the definition is for.
      See Also:

    • Z_ORDER

      public static final Object Z_ORDER
      The Z-Order controls the relative ordering in 2D depictions when bonds overlap/intersect. Some sketch formats (e.g. CDX/CDXML) capture the Z-order as a property.

    • 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:

    • RING_CONNECTIONS

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

    • TOTAL_CONNECTIONS

      public static final String TOTAL_CONNECTIONS
      See Also:

    • TOTAL_H_COUNT

      public static final String TOTAL_H_COUNT
      See Also:

    • 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:

    • 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:

    • ATOM_ATOM_MAPPING

      public static final String ATOM_ATOM_MAPPING
      See Also:

    • 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:

    • 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:

    • SPIN_MULTIPLICITY

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

    • REACTION_CONDITIONS

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

    • REACTION_ARROW

      public static final String REACTION_ARROW
      Arrow display type
      See Also:

    • RENDER_BOUNDS

      public static final Object RENDER_BOUNDS
      Bounds object for when an IChemObject has been generated by another generator.

    • SELECTION

      public static final Object SELECTION
      Used to attach an IChemObjectSelection

    • 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:

    • 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:

    • SPHERICAL_MATCHER

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

    • 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:

    • 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:

    • 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:

  • Constructor Details

    • CDKConstants

      public CDKConstants()