public class QueryBond extends QueryChemObject implements IQueryBond
IBond.Display, IBond.Order, IBond.Stereo
Modifier and Type | Field and Description |
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protected int |
atomCount
Number of atoms contained by this object.
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protected IAtom[] |
atoms
A list of atoms participating in this query bond.
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protected Integer |
electronCount
Number of electrons in the ElectronContainer.
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protected IBond.Order |
order
The bond order of this query bond.
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protected IBond.Stereo |
stereo
A descriptor the stereochemical orientation of this query bond.
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Constructor and Description |
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QueryBond(IAtom[] atoms,
IBond.Order order,
IChemObjectBuilder builder)
Constructs a multi-center query bond, with a specified order and no stereo information.
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QueryBond(IAtom[] atoms,
IChemObjectBuilder builder)
Constructs a multi-center query bond, with undefined order and no stereo information.
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QueryBond(IAtom beg,
IAtom end,
Expr.Type type)
Constructs an query bond from an expression type.
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QueryBond(IAtom beg,
IAtom end,
Expr.Type type,
int val)
Constructs an query bond from an expression type and value.
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QueryBond(IAtom beg,
IAtom end,
Expr expr)
Constructs an query bond from an expression.
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QueryBond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo,
IChemObjectBuilder builder)
Constructs a query bond with a given order and stereo orientation from an array
of atoms.
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QueryBond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IChemObjectBuilder builder)
Constructs a query bond with a given order.
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QueryBond(IAtom atom1,
IAtom atom2,
IChemObjectBuilder builder)
Constructs a query bond with a single query bond order..
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QueryBond(IChemObjectBuilder builder)
Constructs an empty query bond.
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Modifier and Type | Method and Description |
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Iterable<IAtom> |
atoms()
Returns the Iterator to atoms making up this query bond.
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IQueryBond |
clone()
Clones this query bond object, including clones of the atoms between which the
query bond is defined.
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boolean |
compare(Object object)
Compares a query bond with this query bond.
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boolean |
contains(IAtom atom)
Returns true if the given atom participates in this query bond.
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boolean |
equals(Object obj) |
javax.vecmath.Point2d |
get2DCenter()
Returns the geometric 2D center of the query bond.
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javax.vecmath.Point3d |
get3DCenter()
Returns the geometric 3D center of the query bond.
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IAtom |
getAtom(int position)
Returns an Atom from this query bond.
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int |
getAtomCount()
Returns the number of Atoms in this Bond.
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IAtom |
getBegin()
Access the begin (or first) atom of the bond.
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IAtom |
getConnectedAtom(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.
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IAtom[] |
getConnectedAtoms(IAtom atom)
Returns all the atoms in the bond connected to the given atom.
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IAtomContainer |
getContainer() |
IBond.Display |
getDisplay()
Not used for query bonds.
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Integer |
getElectronCount()
Returns the number of electrons in this bond
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IAtom |
getEnd()
Access the end (or second) atom of the bond.
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Expr |
getExpression()
Access the bond expression predicate associated with this query bond.
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int |
getIndex() |
IBond.Order |
getOrder()
Returns the query bond order of this query bond.
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IAtom |
getOther(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.This
method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined
and the more correct
IBond.getConnectedAtoms(IAtom) should be used. |
IBond.Stereo |
getStereo()
Returns the stereo descriptor for this query bond.
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int |
hashCode() |
boolean |
isAromatic()
Access whether this bond has been marked as aromatic.
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boolean |
isConnectedTo(IBond bond)
Checks whether a query bond is connected to another one.
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boolean |
isInRing()
Access whether this bond has been flagged as in a ring.
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boolean |
matches(IBond bond)
Returns true of the given
bond matches this IQueryBond. |
void |
setAtom(IAtom atom,
int position)
Sets an atom in this query bond.
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void |
setAtoms(IAtom[] atoms)
Sets the array of atoms making up this query bond.
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void |
setDisplay(IBond.Display display)
Not used for query bonds.
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void |
setElectronCount(Integer electronCount)
Sets the number of electrons in this bond
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void |
setExpression(Expr expr)
Set the bond expression for this query bond.
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void |
setIsAromatic(boolean arom)
Mark this bond as being aromatic.
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void |
setIsInRing(boolean ring)
Mark this bond as being in a ring.
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void |
setOrder(IBond.Order order)
Sets the bond order of this query bond.
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void |
setStereo(IBond.Stereo stereo)
Sets the stereo descriptor for this query bond.
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String |
toString()
Returns a one line string representation of this query bond.
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addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, matches, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
finalize, getClass, notify, notifyAll, wait, wait, wait
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty
getBuilder
protected IBond.Order order
protected int atomCount
protected IAtom[] atoms
protected IBond.Stereo stereo
protected Integer electronCount
public QueryBond(IAtom beg, IAtom end, Expr expr)
// pi-bond in a ring
Expr e = new Expr(IS_IN_RING);
e.and(new Expr(ALIPHATIC_ORDER, 2));
new QueryBond(beg, end, e);
expr
- the expressionpublic QueryBond(IAtom beg, IAtom end, Expr.Type type)
new QueryBond(beg, end, IS_IN_RING);
type
- the expression typepublic QueryBond(IAtom beg, IAtom end, Expr.Type type, int val)
new QueryBond(beg, end, ALIPHATIC_ORDER, 8);
type
- the expression typeval
- the expression valuepublic QueryBond(IChemObjectBuilder builder)
public QueryBond(IAtom atom1, IAtom atom2, IChemObjectBuilder builder)
atom1
- the first Atom in the query bondatom2
- the second Atom in the query bondpublic QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IChemObjectBuilder builder)
atom1
- the first Atom in the query bondatom2
- the second Atom in the query bondorder
- the query bond orderpublic QueryBond(IAtom[] atoms, IChemObjectBuilder builder)
atoms
- An array of IAtom containing the atoms constituting the query bondpublic QueryBond(IAtom[] atoms, IBond.Order order, IChemObjectBuilder builder)
atoms
- An array of IAtom containing the atoms constituting the query bondorder
- The order of the query bondpublic QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo, IChemObjectBuilder builder)
atom1
- the first Atom in the query bondatom2
- the second Atom in the query bondorder
- the query bond orderstereo
- a descriptor the stereochemical orientation of this query bondpublic Iterable<IAtom> atoms()
atoms
in interface IBond
setAtoms(org.openscience.cdk.interfaces.IAtom[])
public IAtomContainer getContainer()
getContainer
in interface IBond
public void setAtoms(IAtom[] atoms)
public int getAtomCount()
getAtomCount
in interface IBond
public IAtom getAtom(int position)
getAtom
in interface IBond
position
- The position in this query bond where the atom issetAtom(org.openscience.cdk.interfaces.IAtom, int)
public IAtom getBegin()
public IAtom getEnd()
public IAtom getOther(IAtom atom)
IBond.getConnectedAtoms(IAtom)
should be used.
IAtom beg = bond.getBegin();
IAtom end = bond.getEnd();
// bond.getOther(beg) == end
// bond.getOther(end) == beg
public IAtom getConnectedAtom(IAtom atom)
IBond.getConnectedAtoms(IAtom)
should be used.
IAtom beg = bond.getBegin();
IAtom end = bond.getEnd();
// bond.getConnectedAtom(beg) == end
// bond.getConnectedAtom(end) == beg
getConnectedAtom
in interface IBond
atom
- The atom the bond partner is searched ofpublic IAtom[] getConnectedAtoms(IAtom atom)
getConnectedAtoms
in interface IBond
atom
- The atoms the bond partner is searched ofpublic boolean contains(IAtom atom)
public void setAtom(IAtom atom, int position)
setAtom
in interface IBond
atom
- The atom to be setposition
- The position in this query bond where the atom is to be insertedgetAtom(int)
public IBond.Order getOrder()
getOrder
in interface IBond
org.openscience.cdk.CDKConstants
for predefined values.
,
setOrder(org.openscience.cdk.interfaces.IBond.Order)
public void setOrder(IBond.Order order)
setOrder
in interface IBond
order
- The query bond order to be assigned to this query bondorg.openscience.cdk.CDKConstants for predefined values.
,
getOrder()
public IBond.Stereo getStereo()
getStereo
in interface IBond
setStereo(org.openscience.cdk.interfaces.IBond.Stereo)
,
for predefined values.
public void setStereo(IBond.Stereo stereo)
setStereo
in interface IBond
stereo
- The stereo descriptor to be assigned to this query bond.getStereo()
,
for predefined values.
public IBond.Display getDisplay()
getDisplay
in interface IBond
public void setDisplay(IBond.Display display)
setDisplay
in interface IBond
display
- the displaypublic javax.vecmath.Point2d get2DCenter()
get2DCenter
in interface IBond
public javax.vecmath.Point3d get3DCenter()
get3DCenter
in interface IBond
public boolean compare(Object object)
public boolean isConnectedTo(IBond bond)
isConnectedTo
in interface IBond
bond
- bond The query bond which is checked to be connect with this onepublic IQueryBond clone() throws CloneNotSupportedException
clone
in interface IBond
clone
in interface IChemObject
clone
in class QueryChemObject
CloneNotSupportedException
- if the IChemObject cannot be clonedpublic String toString()
toString
in interface IChemObject
toString
in class Object
public Integer getElectronCount()
getElectronCount
in interface IElectronContainer
setElectronCount(java.lang.Integer)
public boolean isAromatic()
isAromatic
in interface IBond
IChemObject.getFlag(int)
,
Aromaticity
public void setIsAromatic(boolean arom)
setIsAromatic
in interface IBond
arom
- aromatic statusIChemObject.setFlag(int, boolean)
public boolean isInRing()
isInRing
in interface IBond
IChemObject.getFlag(int)
,
RingSearch
public void setIsInRing(boolean ring)
setIsInRing
in interface IBond
ring
- ring statusIChemObject.setFlag(int, boolean)
public void setElectronCount(Integer electronCount)
setElectronCount
in interface IElectronContainer
electronCount
- The number of electrons in this electron container.getElectronCount()
public Expr getExpression()
public void setExpression(Expr expr)
expr
- the new bond expressionpublic boolean matches(IBond bond)
bond
matches this IQueryBond.matches
in interface IQueryBond
bond
- IBond to match againstCopyright © 2021. All rights reserved.