@Deprecated public class ChiralityAtom extends SMARTSAtom
IAtomType.Hybridization
atomicNumber, charge, electronValency, exactMass, formalCharge, formalNeighbourCount, fractionalPoint3d, hybridization, hydrogenCount, naturalAbundance, point2d, point3d, stereoParity, symbol
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
Constructor and Description |
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ChiralityAtom(IChemObjectBuilder builder)
Deprecated.
Creates a new instance
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Modifier and Type | Method and Description |
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boolean |
chiralityMatches(IAtom target,
int tParity,
int permParity)
Deprecated.
Check if the atom-based chirality of the target matches.
|
int |
getDegree()
Deprecated.
|
boolean |
isClockwise()
Deprecated.
|
boolean |
isUnspecified()
Deprecated.
|
boolean |
matches(IAtom atom)
Deprecated.
Returns true of the given
atom matches this IQueryAtom. |
void |
setClockwise(boolean clockwise)
Deprecated.
|
void |
setDegree(int degree)
Deprecated.
|
void |
setUnspecified(boolean unspecified)
Deprecated.
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bonds, clone, equals, getAtomicNumber, getAtomTypeName, getBond, getBondCount, getBondOrderSum, getCharge, getContainer, getCovalentRadius, getExactMass, getExpression, getFormalCharge, getFormalNeighbourCount, getFractionalPoint3d, getHybridization, getImplicitHydrogenCount, getIndex, getMapIdx, getMassNumber, getMaxBondOrder, getNaturalAbundance, getPoint2d, getPoint3d, getStereoParity, getSymbol, getValency, hashCode, isAromatic, isInRing, setAtomicNumber, setAtomTypeName, setBondOrderSum, setCharge, setCovalentRadius, setExactMass, setExpression, setFormalCharge, setFormalNeighbourCount, setFractionalPoint3d, setHybridization, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setMassNumber, setMaxBondOrder, setNaturalAbundance, setPoint2d, setPoint3d, setStereoParity, setSymbol, setValency
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
finalize, getClass, notify, notifyAll, toString, wait, wait, wait
bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
getBuilder
public ChiralityAtom(IChemObjectBuilder builder)
public int getDegree()
public void setDegree(int degree)
public boolean isUnspecified()
public void setUnspecified(boolean unspecified)
public boolean isClockwise()
public void setClockwise(boolean clockwise)
public boolean matches(IAtom atom)
QueryAtom
atom
matches this IQueryAtom.matches
in interface IQueryAtom
matches
in class SMARTSAtom
atom
- IAtom to match againstpublic boolean chiralityMatches(IAtom target, int tParity, int permParity)
SMARTSAtom.matches(IAtom)
.
Currently the only atom-based chirality allowed is tetrahedral stereo-
chemistry. ThechiralityMatches
in class SMARTSAtom
target
- the matched target (required to verify 'OR'
conditions)tParity
- the parity (winding) of the target centre,
0=unspecified, 1=clockwise and -1=anticlockwisepermParity
- permutation parity of the query neighbors (will be
multiplied by the query parity)Copyright © 2021. All rights reserved.