Modifier and Type | Class and Description |
---|---|
static class |
Bond.BondSet |
Modifier and Type | Field and Description |
---|---|
(package private) Atom |
atom1 |
(package private) Atom |
atom2 |
(package private) short |
colix |
(package private) short |
mad |
(package private) static int |
myVisibilityFlag |
(package private) int |
shapeVisibilityFlags |
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 and Description |
---|
Bond(Atom atom1,
Atom atom2,
int order,
short mad,
short colix) |
Modifier and Type | Method and Description |
---|---|
(package private) void |
deleteAtomReferences() |
Atom |
getAtom1() |
Atom |
getAtom2() |
int |
getAtomIndex1() |
int |
getAtomIndex2() |
short |
getColix() |
(package private) short |
getColix1() |
(package private) short |
getColix2() |
int |
getCovalentOrder() |
float |
getEnergy() |
java.lang.String |
getIdentity() |
short |
getMad() |
(package private) java.lang.String |
getOrderName() |
(package private) java.lang.String |
getOrderNumberAsString() |
Atom |
getOtherAtom(Atom thisAtom) |
JmolNode |
getOtherAtom(JmolNode thisAtom) |
(package private) float |
getRadius() |
int |
getShapeVisibilityFlags() |
(package private) int |
getValence() |
boolean |
is(int bondType) |
(package private) boolean |
isAromatic() |
boolean |
isCovalent() |
boolean |
isHydrogen() |
static boolean |
isHydrogen(int order) |
(package private) boolean |
isPartial() |
(package private) boolean |
isStereo() |
(package private) boolean |
isTranslucent() |
void |
setColix(short colix) |
void |
setIndex(int i) |
void |
setMad(short mad) |
void |
setOrder(int order) |
void |
setPaletteID(byte pid) |
(package private) void |
setShapeVisibility(boolean isVisible) |
void |
setShapeVisibilityFlags(int shapeVisibilityFlags) |
void |
setTranslucent(boolean isTranslucent,
float translucentLevel) |
java.lang.String |
toString() |
getArgbHbondType, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder
Atom atom1
Atom atom2
short mad
short colix
int shapeVisibilityFlags
static final int myVisibilityFlag
public short getMad()
public short getColix()
public void setMad(short mad)
public void setShapeVisibilityFlags(int shapeVisibilityFlags)
public int getShapeVisibilityFlags()
void setShapeVisibility(boolean isVisible)
public java.lang.String getIdentity()
public boolean isCovalent()
isCovalent
in class JmolEdge
public boolean isHydrogen()
isHydrogen
in class JmolEdge
public static boolean isHydrogen(int order)
boolean isStereo()
boolean isPartial()
boolean isAromatic()
public void setPaletteID(byte pid)
pid
- public float getEnergy()
int getValence()
void deleteAtomReferences()
public void setColix(short colix)
public void setTranslucent(boolean isTranslucent, float translucentLevel)
boolean isTranslucent()
public void setOrder(int order)
public Atom getAtom1()
public Atom getAtom2()
public int getAtomIndex1()
getAtomIndex1
in class JmolEdge
public int getAtomIndex2()
getAtomIndex2
in class JmolEdge
float getRadius()
public int getCovalentOrder()
getCovalentOrder
in class JmolEdge
java.lang.String getOrderName()
java.lang.String getOrderNumberAsString()
short getColix1()
short getColix2()
public void setIndex(int i)
public boolean is(int bondType)
public JmolNode getOtherAtom(JmolNode thisAtom)
getOtherAtom
in class JmolEdge
public java.lang.String toString()
toString
in class java.lang.Object