Class PharmacophoreQueryAtom
java.lang.Object
org.openscience.cdk.ChemObject
org.openscience.cdk.Element
org.openscience.cdk.Isotope
org.openscience.cdk.AtomType
org.openscience.cdk.Atom
org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IQueryAtom
Represents a query pharmacophore group.
This class is meant to be used to construct pharmacophore queries in conjunction
with
PharmacophoreQueryBond
and an
QueryAtomContainer
.- Author:
- Rajarshi Guha
- See Also:
- Source code:
- main
- Belongs to CDK module:
- pcore
- Keywords:
- pharmacophore, 3D isomorphism
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
-
Field Summary
Fields inherited from class org.openscience.cdk.Atom
charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity
Fields inherited from class org.openscience.cdk.AtomType
electronValency, formalCharge, formalNeighbourCount, hybridization
Fields inherited from class org.openscience.cdk.Isotope
exactMass, naturalAbundance
Fields inherited from class org.openscience.cdk.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
-
Constructor Summary
ConstructorsConstructorDescriptionPharmacophoreQueryAtom
(String symbol, String smarts) Creat a new query pharmacophore group -
Method Summary
Modifier and TypeMethodDescriptionGet the SMARTS pattern for this pharmacophore group.Returns the element symbol of this element.boolean
Checks whether this query atom matches a target atom.void
Sets the element symbol of this element.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
Methods inherited from class org.openscience.cdk.AtomType
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency
Methods inherited from class org.openscience.cdk.Isotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
Methods inherited from class org.openscience.cdk.Element
getAtomicNumber, setAtomicNumber
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
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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
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
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, setAtomicNumber
Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
-
Constructor Details
-
PharmacophoreQueryAtom
Creat a new query pharmacophore group- Parameters:
symbol
- The symbol for the groupsmarts
- The SMARTS pattern to be used for matching
-
-
Method Details
-
getSymbol
Returns the element symbol of this element. -
setSymbol
Sets the element symbol of this element. -
getSmarts
Get the SMARTS pattern for this pharmacophore group.- Returns:
- The SMARTS pattern
-
matches
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
-
toString
String representation of this pharmacophore group.- Specified by:
toString
in interfaceIChemObject
- Overrides:
toString
in classAtom
- Returns:
- String representation of this pharmacophore group
-