public class PseudoAtom extends Atom implements Serializable, Cloneable, IPseudoAtom
This should be replaced by the mechanism explained in RFC #8.
Atom,
Serialized FormIAtomType.Hybridizationcharge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParityelectronValency, formalCharge, formalNeighbourCount, hybridizationexactMass, naturalAbundanceatomicNumberAc, 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| Constructor and Description |
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PseudoAtom()
Constructs an empty PseudoAtom.
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PseudoAtom(IElement element)
Constructs an PseudoAtom from a IAtom.
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PseudoAtom(String label)
Constructs an Atom from a String containing an element symbol.
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PseudoAtom(String label,
javax.vecmath.Point2d point2d)
Constructs an Atom from an Element and a Point2d.
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PseudoAtom(String label,
javax.vecmath.Point3d point3d)
Constructs an Atom from an Element and a Point3d.
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| Modifier and Type | Method and Description |
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IPseudoAtom |
clone()
Clones this atom object and its content.
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int |
getAttachPointNum()
Access the attachment point number.
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String |
getLabel()
Returns the label of this PseudoAtom.
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void |
setAttachPointNum(int attachPoint)
Set the attachment point number.
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void |
setLabel(String label)
Sets the label of this PseudoAtom.
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void |
setStereoParity(Integer stereoParity)
Dummy method: the stereo parity is undefined, final.
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String |
toString()
Returns a one line string representation of this Atom.
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bonds, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3dgetAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValencygetExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundancegetAtomicNumber, getSymbol, setAtomicNumber, setSymboladdListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopyfinalize, getClass, notify, notifyAll, wait, wait, waitbonds, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3dgetAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValencygetExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundancegetAtomicNumber, getSymbol, setAtomicNumber, setSymboladdListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setPropertygetBuilderpublic PseudoAtom()
public PseudoAtom(String label)
label - The String describing the PseudoAtompublic PseudoAtom(IElement element)
element - IAtom from which the PseudoAtom is constructedpublic PseudoAtom(String label, javax.vecmath.Point3d point3d)
label - The String describing the PseudoAtompoint3d - The 3D coordinates of the atompublic PseudoAtom(String label, javax.vecmath.Point2d point2d)
label - The String describing the PseudoAtompoint2d - The Pointpublic String getLabel()
getLabel in interface IPseudoAtomsetLabel(java.lang.String)public void setLabel(String label)
setLabel in interface IPseudoAtomlabel - The new label for this PseudoAtomgetLabel()public int getAttachPointNum()
getAttachPointNum in interface IPseudoAtompublic void setAttachPointNum(int attachPoint)
setAttachPointNum in interface IPseudoAtomattachPoint - attach point numberpublic void setStereoParity(Integer stereoParity)
setStereoParity in interface IAtomsetStereoParity in class AtomstereoParity - The stereo parity for this atomfor predefined values.,
Atom.getStereoParity()public String toString()
toString in interface IChemObjecttoString in class Atompublic IPseudoAtom clone() throws CloneNotSupportedException
Atomclone in interface IAtomclone in interface IChemObjectclone in interface IPseudoAtomclone in class AtomCloneNotSupportedException - if the IChemObject cannot be clonedCopyright © 2022. All rights reserved.