org.jmol.modelset
Class Bond
java.lang.Object
org.jmol.util.JmolEdge
org.jmol.modelset.Bond
- Direct Known Subclasses:
- HBond
public class Bond
- extends JmolEdge
Fields inherited from class org.jmol.util.JmolEdge |
argbsHbondType, 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, index, order |
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, wait, wait, wait |
atom1
Atom atom1
atom2
Atom atom2
mad
short mad
colix
short colix
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()
setMad
public void setMad(short mad)
setShapeVisibilityFlags
public void setShapeVisibilityFlags(int shapeVisibilityFlags)
getShapeVisibilityFlags
public int getShapeVisibilityFlags()
setShapeVisibility
void setShapeVisibility(boolean isVisible)
getIdentity
public java.lang.String getIdentity()
isCovalent
public boolean isCovalent()
- Specified by:
isCovalent
in class JmolEdge
isHydrogen
public boolean isHydrogen()
- Specified by:
isHydrogen
in class JmolEdge
isHydrogen
public static boolean isHydrogen(int order)
isStereo
boolean isStereo()
isPartial
boolean isPartial()
isAromatic
boolean isAromatic()
setPaletteID
public void setPaletteID(byte pid)
- Parameters:
pid
-
getEnergy
public float getEnergy()
getValence
int getValence()
deleteAtomReferences
void deleteAtomReferences()
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 class JmolEdge
getAtomIndex2
public int getAtomIndex2()
- Specified by:
getAtomIndex2
in class JmolEdge
getRadius
float getRadius()
getCovalentOrder
public int getCovalentOrder()
- Specified by:
getCovalentOrder
in class JmolEdge
getOrderName
java.lang.String getOrderName()
getOrderNumberAsString
java.lang.String getOrderNumberAsString()
getColix1
short getColix1()
getColix2
short getColix2()
getOtherAtom
public Atom getOtherAtom(Atom thisAtom)
setIndex
public void setIndex(int i)
is
public boolean is(int bondType)
getOtherAtom
public JmolNode getOtherAtom(JmolNode thisAtom)
- Specified by:
getOtherAtom
in class JmolEdge
toString
public java.lang.String toString()
- Overrides:
toString
in class java.lang.Object