org.openscience.cdk
Class CDKConstants

java.lang.Object
  org.openscience.cdk.CDKConstants

@TestClass(value="org.openscience.cdk.CDKConstantsTest")
public class CDKConstants
extends java.lang.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

Belongs to CDK module:

core

Source code:

revision 12456

Field Summary

static java.lang.String	ALL_RINGS A set of all rings computed for this molecule.
static java.lang.String	ANNOTATIONS A List of annotation remarks.
static java.lang.String	AUTONOMNAME The IUPAC compatible name generated with AutoNom.
static java.lang.String	BEILSTEINRN The Beilstein Registry Number.
static IBond.Order	BONDORDER_DOUBLE A bond of degree 2.0.
static IBond.Order	BONDORDER_QUADRUPLE
static IBond.Order	BONDORDER_SINGLE A bond of degree 1.0.
static IBond.Order	BONDORDER_TRIPLE A bond of degree 3.0.
static java.lang.String	CASRN The CAS Registry Number.
static java.lang.String	CHEMICAL_GROUP_CONSTANT Used as property key for indicating the chemical group of a certain atom type.
static java.lang.String	COMMENT A String comment.
static java.lang.String	DESCRIPTION A description for a IChemObject.
static int	DUMMY_POINTER Flag used for JUnit testing the pointer functionality.
static java.lang.String	ESSENTIAL_RINGS The essential rings computed for this molecule.
static java.lang.String	FORMULA The Molecular Formula Identifier.
static int	HYBRIDIZATION_SP1 A geometry of neighboring atoms when an s orbital is hybridized with one p orbital.
static int	HYBRIDIZATION_SP2 A geometry of neighboring atoms when an s orbital is hybridized with two p orbitals.
static int	HYBRIDIZATION_SP3 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals.
static int	HYBRIDIZATION_SP3D1 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with one d orbital.
static int	HYBRIDIZATION_SP3D2 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with two d orbitals.
static int	HYBRIDIZATION_SP3D3 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with three d orbitals.
static int	HYBRIDIZATION_SP3D4 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with four d orbitals.
static int	HYBRIDIZATION_SP3D5 A geometry of neighboring atoms when an s orbital is hybridized with three p orbitals with five d orbitals.
static int	HYBRIDIZATION_UNSET A undefined hybridization.
static java.lang.String	INCHI The IUPAC International Chemical Identifier.
static int	IS_HYDROGENBOND_ACCEPTOR Sets to true if the atom is an hydrogen bond acceptor.
static int	IS_HYDROGENBOND_DONOR Sets to true if the atom is an hydrogen bond donor.
static int	ISALIPHATIC Flag that is set if a chemobject is part of an aliphatic chain.
static int	ISAROMATIC Flag is set if chemobject is part of an aromatic system.
static int	ISCONJUGATED Flag is set if chemobject is part of a conjugated system.
static int	ISINRING Flag that is set when the chemobject is part of a ring.
static int	ISNOTINRING Flag that is set when the chemobject is part of a ring.
static java.lang.String	ISOTROPIC_SHIELDING The Isotropic Shielding, usually calculated by a quantum chemistry program like Gaussian.
static int	ISPLACED Flag that is set if the chemobject is placed (somewhere).
static java.lang.String	LONE_PAIR_COUNT Used as property key for indicating the HOSE code for a certain atom type.
static int	MAPPED Flag is set if a chemobject is mapped to another chemobject.
static int	MAX_FLAG_INDEX Maximum flags array index.
static int	MAX_POINTER_INDEX Maximum pointers array index.
static java.lang.String	NAMES A List of names.
static java.lang.String	NMRSHIFT_CARBON Carbon NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	NMRSHIFT_DEUTERIUM Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	NMRSHIFT_FLUORINE Fluorine NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	NMRSHIFT_HYDROGEN Hydrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	NMRSHIFT_NITROGEN Nitrogen NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	NMRSHIFT_PHOSPORUS Phosphorus NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.
static java.lang.String	PART_OF_RING_OF_SIZE Used as property key for indicating the ring size of a certain atom type.
static java.lang.String	PI_BOND_COUNT Used as property key for indicating the HOSE code for a certain atom type.
static int	REACTIVE_CENTER Flag is set if a chemobject has reactive center.
static java.lang.String	RELEVANT_RINGS The relevant rings computed for this molecule.
static java.lang.String	REMARK A remark for a IChemObject.
static java.lang.String	RING_CONNECTIONS This property indicates how many ring bonds are connected to the given atom.
static java.lang.String	RING_SIZES This property will contain an ArrayList of Integers.
static java.lang.String	SMALLEST_RINGS A smallest set of smallest rings computed for this molecule.
static java.lang.String	SMILES The Daylight SMILES.
static java.lang.String	SPHERICAL_MATCHER Used as property key for indicating the HOSE code for a certain atom type.
static int	STEREO_ATOM_PARITY_MINUS A negative atom parity.
static int	STEREO_ATOM_PARITY_PLUS A positive atom parity.
static int	STEREO_ATOM_PARITY_UNDEFINED A undefined atom parity.
static int	STEREO_BOND_DOWN A bonds which end is below the drawing plane.
static int	STEREO_BOND_DOWN_INV A bonds which end is below the drawing plane.
static int	STEREO_BOND_NONE A bonds for which there is no stereochemistry.
static int	STEREO_BOND_UNDEFINED A bonds for which the stereochemistry is undefined.
static int	STEREO_BOND_UP A bonds which end is above the drawing plane.
static int	STEREO_BOND_UP_INV A bonds which start is above the drawing plane.
static java.lang.String	TITLE The title for a IChemObject.
static java.lang.String	TOTAL_CONNECTIONS
static java.lang.String	TOTAL_H_COUNT
static java.lang.Object	UNSET
static int	VISITED Flag is set if chemobject has been visited.

Constructor Summary

CDKConstants()

Method Summary

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

UNSET

public static final java.lang.Object UNSET

BONDORDER_SINGLE

public static final IBond.Order BONDORDER_SINGLE

A bond of degree 1.0.

BONDORDER_DOUBLE

public static final IBond.Order BONDORDER_DOUBLE

A bond of degree 2.0.

BONDORDER_TRIPLE

public static final IBond.Order BONDORDER_TRIPLE

A bond of degree 3.0.

BONDORDER_QUADRUPLE

public static final IBond.Order BONDORDER_QUADRUPLE

STEREO_BOND_UP

public static final int STEREO_BOND_UP

A bonds which end is above the drawing plane.

See Also:

Constant Field Values

STEREO_BOND_UP_INV

public static final int STEREO_BOND_UP_INV

A bonds which start is above the drawing plane.

See Also:

Constant Field Values

STEREO_BOND_UNDEFINED

public static final int STEREO_BOND_UNDEFINED

A bonds for which the stereochemistry is undefined.

See Also:

Constant Field Values

STEREO_BOND_NONE

public static final int STEREO_BOND_NONE

A bonds for which there is no stereochemistry.

See Also:

Constant Field Values

STEREO_BOND_DOWN

public static final int STEREO_BOND_DOWN

A bonds which end is below the drawing plane. The bond is draw from the first to the second bond atom.

See Also:

Constant Field Values

STEREO_BOND_DOWN_INV

public static final int STEREO_BOND_DOWN_INV

A bonds which end is below the drawing plane. The bond is draw from the second to the first bond atom.

See Also:

Constant Field Values

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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.String NMRSHIFT_DEUTERIUM

Deuterium NMR shift constant for use as a key in the IChemObject.physicalProperties hashtable.

See Also:

ChemObject, 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

MAX_FLAG_INDEX

public static final int MAX_FLAG_INDEX

Maximum flags array index.

See Also:

Constant Field Values

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

TITLE

public static final java.lang.String TITLE

The title for a IChemObject.

See Also:

Constant Field Values

REMARK

public static final java.lang.String REMARK

A remark for a IChemObject.

See Also:

Constant Field Values

COMMENT

public static final java.lang.String COMMENT

A String comment.

See Also:

Constant Field Values

NAMES

public static final java.lang.String NAMES

A List of names.

See Also:

Constant Field Values

ANNOTATIONS

public static final java.lang.String ANNOTATIONS

A List of annotation remarks.

See Also:

Constant Field Values

DESCRIPTION

public static final java.lang.String DESCRIPTION

A description for a IChemObject.

See Also:

Constant Field Values

SMILES

public static final java.lang.String SMILES

The Daylight SMILES.

See Also:

Constant Field Values

INCHI

public static final java.lang.String INCHI

The IUPAC International Chemical Identifier.

See Also:

Constant Field Values

FORMULA

public static final java.lang.String FORMULA

The Molecular Formula Identifier.

See Also:

Constant Field Values

AUTONOMNAME

public static final java.lang.String AUTONOMNAME

The IUPAC compatible name generated with AutoNom.

See Also:

Constant Field Values

BEILSTEINRN

public static final java.lang.String BEILSTEINRN

The Beilstein Registry Number.

See Also:

Constant Field Values

CASRN

public static final java.lang.String CASRN

The CAS Registry Number.

See Also:

Constant Field Values

ALL_RINGS

public static final java.lang.String ALL_RINGS

A set of all rings computed for this molecule.

See Also:

Constant Field Values

SMALLEST_RINGS

public static final java.lang.String SMALLEST_RINGS

A smallest set of smallest rings computed for this molecule.

See Also:

Constant Field Values

ESSENTIAL_RINGS

public static final java.lang.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 java.lang.String RELEVANT_RINGS

The relevant rings computed for this molecule. The concept of relevant Rings is defined in SSSRFinder

See Also:

Constant Field Values

RING_SIZES

public static final java.lang.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 java.lang.String RING_CONNECTIONS

This property indicates how many ring bonds are connected to the given atom.

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Constant Field Values

TOTAL_CONNECTIONS

public static final java.lang.String TOTAL_CONNECTIONS

See Also:

Constant Field Values

TOTAL_H_COUNT

public static final java.lang.String TOTAL_H_COUNT

See Also:

Constant Field Values

ISOTROPIC_SHIELDING

public static final java.lang.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

PART_OF_RING_OF_SIZE

public static final java.lang.String PART_OF_RING_OF_SIZE

Used as property key for indicating the ring size of a certain atom type.

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Constant Field Values

CHEMICAL_GROUP_CONSTANT

public static final java.lang.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 java.lang.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 java.lang.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 java.lang.String LONE_PAIR_COUNT

Used as property key for indicating the HOSE code for a certain atom type.

See Also:

Constant Field Values

Constructor Detail

CDKConstants

public CDKConstants()