Package org.openscience.cdk.silent
Class AtomType
java.lang.Object
org.openscience.cdk.silent.ChemObject
org.openscience.cdk.silent.Element
org.openscience.cdk.silent.Isotope
org.openscience.cdk.silent.AtomType
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
- Direct Known Subclasses:
Atom
The base class for atom types. Atom types are typically used to describe the
behaviour of an atom of a particular element in different environment like
sp3
hybridized carbon C3, etc., in some molecular modelling applications.
- Author:
- steinbeck
- See Also:
- Source code:
- main
- Belongs to CDK module:
- silent
- Keywords:
- atom, type
- Created on:
- 2001-08-08
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected Integer
The electron Valency of this atom with CDKConstants.UNSET as default.protected Integer
The formal charge of the atom with CDKConstants.UNSET as default.protected Integer
The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.protected IAtomType.Hybridization
The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.Fields inherited from class org.openscience.cdk.silent.Isotope
exactMass, naturalAbundance
Fields inherited from class org.openscience.cdk.silent.Element
atomicNumber
Fields inherited from interface org.openscience.cdk.interfaces.IElement
Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr
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Constructor Summary
ConstructorsConstructorDescriptionConstructor for the AtomType object.Constructor for the AtomType object.Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope. -
Method Summary
Modifier and TypeMethodDescriptionclone()
Clones thisIChemObject
.boolean
Compares a atom type with this atom type.Gets the id attribute of the AtomType object.Gets the bondOrderSum attribute of the AtomType object.Returns the covalent radius for this AtomType.Returns the formal charge of this atom.Returns the formal neighbour count of this atom.Returns the hybridization of this atom.Gets the MaxBondOrder attribute of the AtomType object.Gets the the exact electron valency of the AtomType object.void
setAtomTypeName
(String identifier) Sets the if attribute of the AtomType object.void
setBondOrderSum
(Double bondOrderSum) Sets the the exact bond order sum attribute of the AtomType object.void
setCovalentRadius
(Double radius) Sets the covalent radius for this AtomType.void
setFormalCharge
(Integer charge) Sets the formal charge of this atom.void
setFormalNeighbourCount
(Integer count) Sets the formal neighbour count of this atom.void
setHybridization
(IAtomType.Hybridization hybridization) Sets the hybridization of this atom.void
setMaxBondOrder
(IBond.Order maxBondOrder) Sets the MaxBondOrder attribute of the AtomType object.void
setValency
(Integer valency) Sets the the exact electron valency of the AtomType object.toString()
A string representation of this isotope.Methods inherited from class org.openscience.cdk.silent.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
Methods inherited from class org.openscience.cdk.silent.Element
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from class org.openscience.cdk.silent.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Field Details
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formalCharge
The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String)
andAtomType(String, String)
) will explicitly set this field to 0 -
hybridization
The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default. -
electronValency
The electron Valency of this atom with CDKConstants.UNSET as default. -
formalNeighbourCount
The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitely connected atoms, including implicit hydrogens.
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Constructor Details
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AtomType
Constructor for the AtomType object. Defaults to a zero formal charge. All other fields are set toCDKConstants.UNSET
.- Parameters:
elementSymbol
- Symbol of the atom
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AtomType
Constructor for the AtomType object. Defaults to a zero formal charge.- Parameters:
identifier
- An id for this atom type, like C3 for sp3 carbonelementSymbol
- The element symbol identifying the element to which this atom type applies
-
AtomType
Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope. It does not copy the listeners and properties. If the element is an instanceof IAtomType, then the maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name are copied too.- Parameters:
element
- IIsotope to copy information from
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Method Details
-
setAtomTypeName
Sets the if attribute of the AtomType object.- Specified by:
setAtomTypeName
in interfaceIAtomType
- Parameters:
identifier
- The new AtomTypeID value. Null if unset.- See Also:
-
setMaxBondOrder
Sets the MaxBondOrder attribute of the AtomType object.- Specified by:
setMaxBondOrder
in interfaceIAtomType
- Parameters:
maxBondOrder
- The new MaxBondOrder value- See Also:
-
setBondOrderSum
Sets the the exact bond order sum attribute of the AtomType object.- Specified by:
setBondOrderSum
in interfaceIAtomType
- Parameters:
bondOrderSum
- The new bondOrderSum value- See Also:
-
getAtomTypeName
Gets the id attribute of the AtomType object.- Specified by:
getAtomTypeName
in interfaceIAtomType
- Returns:
- The id value
- See Also:
-
getMaxBondOrder
Gets the MaxBondOrder attribute of the AtomType object.- Specified by:
getMaxBondOrder
in interfaceIAtomType
- Returns:
- The MaxBondOrder value
- See Also:
-
getBondOrderSum
Gets the bondOrderSum attribute of the AtomType object.- Specified by:
getBondOrderSum
in interfaceIAtomType
- Returns:
- The bondOrderSum value
- See Also:
-
setFormalCharge
Sets the formal charge of this atom.- Specified by:
setFormalCharge
in interfaceIAtomType
- Parameters:
charge
- The formal charge- See Also:
-
getFormalCharge
Returns the formal charge of this atom.- Specified by:
getFormalCharge
in interfaceIAtomType
- Returns:
- the formal charge of this atom
- See Also:
-
setFormalNeighbourCount
Sets the formal neighbour count of this atom.- Specified by:
setFormalNeighbourCount
in interfaceIAtomType
- Parameters:
count
- The neighbour count- See Also:
-
getFormalNeighbourCount
Returns the formal neighbour count of this atom.- Specified by:
getFormalNeighbourCount
in interfaceIAtomType
- Returns:
- the formal neighbour count of this atom
- See Also:
-
setHybridization
Sets the hybridization of this atom.- Specified by:
setHybridization
in interfaceIAtomType
- Parameters:
hybridization
- The hybridization- See Also:
-
getHybridization
Returns the hybridization of this atom.- Specified by:
getHybridization
in interfaceIAtomType
- Returns:
- the hybridization of this atom
- See Also:
-
compare
Compares a atom type with this atom type. -
setCovalentRadius
Sets the covalent radius for this AtomType.- Specified by:
setCovalentRadius
in interfaceIAtomType
- Parameters:
radius
- The covalent radius for this AtomType- See Also:
-
getCovalentRadius
Returns the covalent radius for this AtomType.- Specified by:
getCovalentRadius
in interfaceIAtomType
- Returns:
- The covalent radius for this AtomType
- See Also:
-
setValency
Sets the the exact electron valency of the AtomType object.- Specified by:
setValency
in interfaceIAtomType
- Parameters:
valency
- The new valency value- See Also:
-
getValency
Gets the the exact electron valency of the AtomType object.- Specified by:
getValency
in interfaceIAtomType
- Returns:
- The valency value
- See Also:
-
clone
Description copied from class:ChemObject
Clones thisIChemObject
. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.- Specified by:
clone
in interfaceIChemObject
- Overrides:
clone
in classIsotope
- Returns:
- The cloned object
- Throws:
CloneNotSupportedException
- if the IChemObject cannot be cloned
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toString
Description copied from class:Isotope
A string representation of this isotope.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classIsotope
- Returns:
- A string representation of this isotope
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