Class PharmacophoreQueryAtom
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.Element
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- org.openscience.cdk.Isotope
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- org.openscience.cdk.AtomType
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- org.openscience.cdk.Atom
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- org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IQueryAtom
public class PharmacophoreQueryAtom extends Atom implements IQueryAtom
Represents a query pharmacophore group. This class is meant to be used to construct pharmacophore queries in conjunction withPharmacophoreQueryBond
and anQueryAtomContainer
.- Author:
- Rajarshi Guha
- See Also:
PharmacophoreQueryBond
,QueryAtomContainer
,PharmacophoreMatcher
, Serialized Form- Source code:
- main
- Belongs to CDK module:
- pcore
- Keywords:
- pharmacophore, 3D isomorphism
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
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Fields inherited from class org.openscience.cdk.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
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Fields inherited from class org.openscience.cdk.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
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Fields inherited from class org.openscience.cdk.Isotope
exactMass, naturalAbundance
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Fields inherited from class org.openscience.cdk.Element
atomicNumber
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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
Constructors Constructor Description PharmacophoreQueryAtom(String symbol, String smarts)
Creat a new query pharmacophore group
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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.-
Methods inherited from class org.openscience.cdk.Atom
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
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Methods inherited from class org.openscience.cdk.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
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Methods inherited from class org.openscience.cdk.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Methods inherited from class org.openscience.cdk.Element
getAtomicNumber, setAtomicNumber
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Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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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
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Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, setAtomicNumber
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Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Method Detail
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getSymbol
public String getSymbol()
Returns the element symbol of this element.- Specified by:
getSymbol
in interfaceIElement
- Overrides:
getSymbol
in classElement
- Returns:
- The element symbol of this element. Null if unset.
- See Also:
Element.setSymbol(java.lang.String)
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setSymbol
public void setSymbol(String symbol)
Sets the element symbol of this element.- Specified by:
setSymbol
in interfaceIElement
- Overrides:
setSymbol
in classElement
- Parameters:
symbol
- The element symbol to be assigned to this atom- See Also:
Element.getSymbol()
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getSmarts
public String getSmarts()
Get the SMARTS pattern for this pharmacophore group.- Returns:
- The SMARTS pattern
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matches
public boolean matches(IAtom atom)
Checks whether this query atom matches a target atom. Currently a query pharmacophore atom will match a target pharmacophore group if the symbols of the two groups match. This is based on the assumption that pharmacophore groups with the same symbol will have the same SMARTS pattern.- Specified by:
matches
in interfaceIQueryAtom
- Parameters:
atom
- A target pharmacophore group- Returns:
- true if the current query group has the same symbol as the target group
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toString
public String toString()
String representation of this pharmacophore group.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classAtom
- Returns:
- String representation of this pharmacophore group
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