ambit2.core.groups
Class AbstractGroup
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.PseudoAtom
ambit2.core.groups.AbstractGroup
- All Implemented Interfaces:
- ISGroup, java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<ISGroup>, org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtomType, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IElement, org.openscience.cdk.interfaces.IIsotope, org.openscience.cdk.interfaces.IPseudoAtom
- Direct Known Subclasses:
- ComponentGroup, ContainerGroup, DataGroup, GenericGroup, MonomerGroup, MultipleGroup, StructureRepeatingUnit, SuperAtom
public abstract class AbstractGroup
- extends org.openscience.cdk.PseudoAtom
- implements ISGroup
- See Also:
- Serialized Form
Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType |
org.openscience.cdk.interfaces.IAtomType.Hybridization |
Field Summary |
protected java.util.List<org.openscience.cdk.interfaces.IAtom> |
atoms
|
protected java.util.List<org.openscience.cdk.interfaces.IBond> |
bonds
|
protected int |
number
|
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, symbol |
Method Summary |
org.openscience.cdk.interfaces.IAtom |
addAtom(org.openscience.cdk.interfaces.IAtom atom)
|
org.openscience.cdk.interfaces.IBond |
addBond(org.openscience.cdk.interfaces.IBond bond)
|
void |
addBondsConnected2Atoms(org.openscience.cdk.interfaces.IAtomContainer mol,
java.util.List<org.openscience.cdk.interfaces.IAtom> atoms,
java.util.List<org.openscience.cdk.interfaces.IBond> bonds)
|
void |
addBrackets(double x1,
double y1,
double x2,
double y2)
|
int |
compareTo(ISGroup o)
|
boolean |
equals(java.lang.Object obj)
|
void |
finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
does nothing |
java.lang.Iterable<org.openscience.cdk.interfaces.IAtom> |
getAtoms(boolean expanded)
|
java.lang.Iterable<org.openscience.cdk.interfaces.IBond> |
getBonds(boolean expanded)
|
int |
getNumber()
|
java.lang.String |
getSubscript()
|
boolean |
isExpanded(org.openscience.cdk.interfaces.IBond bond)
|
static boolean |
isGroupVisible(org.openscience.cdk.interfaces.IChemObject c)
|
static void |
setGroupVisible(org.openscience.cdk.interfaces.IChemObject c,
boolean visible)
|
void |
setNumber(int number)
|
void |
setSubscript(java.lang.String subscript)
text of Sgroup subscript. |
Methods inherited from class org.openscience.cdk.PseudoAtom |
clone, getLabel, setCharge, setExactMass, setFormalCharge, setHydrogenCount, setLabel, setStereoParity, toString |
Methods inherited from class org.openscience.cdk.Atom |
compare, getCharge, getFractionalPoint3d, getHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setHydrogenCount, setPoint2d, setPoint3d, setStereoParity |
Methods inherited from class org.openscience.cdk.AtomType |
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, getVanderwaalsRadius, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency, setVanderwaalsRadius |
Methods inherited from class org.openscience.cdk.Isotope |
getExactMass, getMassNumber, getNaturalAbundance, setMassNumber, setNaturalAbundance |
Methods inherited from class org.openscience.cdk.Element |
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol |
Methods inherited from class org.openscience.cdk.ChemObject |
addListener, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy |
Methods inherited from class java.lang.Object |
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.openscience.cdk.interfaces.IAtom |
getCharge, getFractionalPoint3d, getHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setHydrogenCount, setPoint2d, setPoint3d, setStereoParity |
Methods inherited from interface org.openscience.cdk.interfaces.IAtomType |
getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, getVanderwaalsRadius, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency, setVanderwaalsRadius |
Methods inherited from interface org.openscience.cdk.interfaces.IIsotope |
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance |
Methods inherited from interface org.openscience.cdk.interfaces.IElement |
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol |
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject |
addListener, clone, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString |
atoms
protected java.util.List<org.openscience.cdk.interfaces.IAtom> atoms
bonds
protected java.util.List<org.openscience.cdk.interfaces.IBond> bonds
number
protected int number
AbstractGroup
public AbstractGroup()
AbstractGroup
public AbstractGroup(java.lang.String label)
AbstractGroup
public AbstractGroup(java.lang.String label,
int number)
getNumber
public int getNumber()
- Specified by:
getNumber
in interface ISGroup
setNumber
public void setNumber(int number)
- Specified by:
setNumber
in interface ISGroup
compareTo
public int compareTo(ISGroup o)
- Specified by:
compareTo
in interface java.lang.Comparable<ISGroup>
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in class java.lang.Object
addAtom
public org.openscience.cdk.interfaces.IAtom addAtom(org.openscience.cdk.interfaces.IAtom atom)
- Specified by:
addAtom
in interface ISGroup
addBond
public org.openscience.cdk.interfaces.IBond addBond(org.openscience.cdk.interfaces.IBond bond)
- Specified by:
addBond
in interface ISGroup
finalizeAtomList
public void finalizeAtomList(org.openscience.cdk.interfaces.IAtomContainer mol)
- does nothing
- Specified by:
finalizeAtomList
in interface ISGroup
setSubscript
public void setSubscript(java.lang.String subscript)
- Description copied from interface:
ISGroup
- text of Sgroup subscript. See
SGroupMDL2000Helper.SGROUP_LINE.M__SMT
.
- Specified by:
setSubscript
in interface ISGroup
getSubscript
public java.lang.String getSubscript()
- Specified by:
getSubscript
in interface ISGroup
addBrackets
public void addBrackets(double x1,
double y1,
double x2,
double y2)
- Specified by:
addBrackets
in interface ISGroup
getAtoms
public java.lang.Iterable<org.openscience.cdk.interfaces.IAtom> getAtoms(boolean expanded)
- Specified by:
getAtoms
in interface ISGroup
getBonds
public java.lang.Iterable<org.openscience.cdk.interfaces.IBond> getBonds(boolean expanded)
- Specified by:
getBonds
in interface ISGroup
isExpanded
public boolean isExpanded(org.openscience.cdk.interfaces.IBond bond)
setGroupVisible
public static void setGroupVisible(org.openscience.cdk.interfaces.IChemObject c,
boolean visible)
isGroupVisible
public static boolean isGroupVisible(org.openscience.cdk.interfaces.IChemObject c)
addBondsConnected2Atoms
public void addBondsConnected2Atoms(org.openscience.cdk.interfaces.IAtomContainer mol,
java.util.List<org.openscience.cdk.interfaces.IAtom> atoms,
java.util.List<org.openscience.cdk.interfaces.IBond> bonds)