public class PharmacophoreQueryAtom extends Atom implements IQueryAtom
PharmacophoreQueryBond
and an
QueryAtomContainer
.PharmacophoreQueryBond
,
QueryAtomContainer
,
PharmacophoreMatcher
,
Serialized FormIAtomType.Hybridization
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
electronValency, formalCharge, formalNeighbourCount, hybridization
exactMass, naturalAbundance
atomicNumber
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 |
---|
PharmacophoreQueryAtom(String symbol,
String smarts)
Creat a new query pharmacophore group
|
Modifier and Type | Method and Description |
---|---|
String |
getSmarts()
Get the SMARTS pattern for this pharmacophore group.
|
String |
getSymbol()
Returns the element symbol of this element.
|
boolean |
matches(IAtom atom)
Checks whether this query atom matches a target atom.
|
void |
setSymbol(String symbol)
Sets the element symbol of this element.
|
String |
toString()
String representation of this pharmacophore group.
|
bonds, clone, compare, equals, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, hashCode, 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, setAtomicNumber
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
finalize, getClass, notify, notifyAll, 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, setAtomicNumber
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
getBuilder
public String getSymbol()
getSymbol
in interface IElement
getSymbol
in class Element
Element.setSymbol(java.lang.String)
public void setSymbol(String symbol)
setSymbol
in interface IElement
setSymbol
in class Element
symbol
- The element symbol to be assigned to this atomElement.getSymbol()
public String getSmarts()
public boolean matches(IAtom atom)
matches
in interface IQueryAtom
atom
- A target pharmacophore grouppublic String toString()
toString
in interface IChemObject
toString
in class Atom
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