org.jmol.modelset
Class Bond
java.lang.Object
org.jmol.modelset.Bond
- All Implemented Interfaces:
- JmolEdge
- Direct Known Subclasses:
- HBond
public class Bond
- extends java.lang.Object
- implements JmolEdge
Fields inherited from interface org.jmol.api.JmolEdge |
BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, BOND_COVALENT_SINGLE, BOND_COVALENT_TRIPLE, BOND_H_CALC, BOND_H_CALC_MASK, BOND_H_MINUS_3, BOND_H_MINUS_4, BOND_H_NUCLEOTIDE, BOND_H_PLUS_2, BOND_H_PLUS_3, BOND_H_PLUS_4, BOND_H_PLUS_5, BOND_H_REGULAR, BOND_HBOND_SHIFT, BOND_HYDROGEN_MASK, BOND_NEW, BOND_ORDER_ANY, BOND_ORDER_NULL, BOND_ORDER_UNSPECIFIED, BOND_PARTIAL_MASK, BOND_PARTIAL01, BOND_PARTIAL12, BOND_PARTIAL23, BOND_PARTIAL32, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK |
Constructor Summary |
Bond(Atom atom1,
Atom atom2,
int order,
short mad,
short colix)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
atom1
Atom atom1
atom2
Atom atom2
order
int order
mad
short mad
colix
short colix
index
int index
shapeVisibilityFlags
int shapeVisibilityFlags
myVisibilityFlag
static final int myVisibilityFlag
Bond
public Bond(Atom atom1,
Atom atom2,
int order,
short mad,
short colix)
getMad
public short getMad()
getColix
public short getColix()
getIndex
public int getIndex()
- Specified by:
getIndex
in interface JmolEdge
getShapeVisibilityFlags
public int getShapeVisibilityFlags()
getIdentity
public java.lang.String getIdentity()
isCovalent
public boolean isCovalent()
- Specified by:
isCovalent
in interface JmolEdge
isHydrogen
public boolean isHydrogen()
- Specified by:
isHydrogen
in interface JmolEdge
isHydrogen
public static boolean isHydrogen(int order)
isStereo
boolean isStereo()
isPartial
boolean isPartial()
isAromatic
boolean isAromatic()
setPaletteID
public void setPaletteID(byte pid)
getEnergy
public float getEnergy()
getValence
int getValence()
deleteAtomReferences
void deleteAtomReferences()
setMad
public void setMad(short mad)
setShapeVisibility
final void setShapeVisibility(int shapeVisibilityFlag,
boolean isVisible)
setColix
public void setColix(short colix)
setTranslucent
public void setTranslucent(boolean isTranslucent,
float translucentLevel)
isTranslucent
boolean isTranslucent()
setOrder
public void setOrder(int order)
getAtom1
public Atom getAtom1()
getAtom2
public Atom getAtom2()
getAtomIndex1
public int getAtomIndex1()
- Specified by:
getAtomIndex1
in interface JmolEdge
getAtomIndex2
public int getAtomIndex2()
- Specified by:
getAtomIndex2
in interface JmolEdge
getRadius
float getRadius()
getOrder
public int getOrder()
- Specified by:
getOrder
in interface JmolEdge
getCovalentOrder
public int getCovalentOrder()
- Specified by:
getCovalentOrder
in interface JmolEdge
getOrderName
java.lang.String getOrderName()
getOrderNumberAsString
java.lang.String getOrderNumberAsString()
getColix1
short getColix1()
getColix2
short getColix2()
getOtherAtom
public Atom getOtherAtom(Atom thisAtom)
setShapeVisibilityFlags
public void setShapeVisibilityFlags(int shapeVisibilityFlags)
setIndex
public void setIndex(int i)
is
public boolean is(int bondType)
getOtherAtom
public JmolNode getOtherAtom(JmolNode thisAtom)
- Specified by:
getOtherAtom
in interface JmolEdge