Modifier and Type | Field and Description |
---|---|
Atom |
atom1 |
Atom |
atom2 |
short |
colix |
short |
mad |
static int |
myVisibilityFlag |
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_PYMOL_MULT, BOND_PYMOL_SINGLE, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, FLAG_AROMATIC_DEFINED, FLAG_AROMATIC_DOUBLE, FLAG_AROMATIC_STRICT, FLAG_IGNORE_STEREOCHEMISTRY, FLAG_NO_AROMATIC, 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() |
(package private) short |
getColix1() |
(package private) short |
getColix2() |
int |
getCovalentOrder() |
float |
getEnergy() |
java.lang.String |
getIdentity() |
(package private) java.lang.String |
getOrderName() |
(package private) java.lang.String |
getOrderNumberAsString() |
Atom |
getOtherAtom(Atom thisAtom) |
Node |
getOtherAtomNode(Node thisAtom) |
(package private) float |
getRadius() |
int |
getShapeVisibilityFlags() |
int |
getValence() |
boolean |
is(int bondType) |
(package private) boolean |
isAromatic() |
boolean |
isCovalent() |
boolean |
isHydrogen() |
static boolean |
isOrderH(int order) |
(package private) boolean |
isPartial() |
(package private) boolean |
isPymolStyle() |
(package private) boolean |
isStereo() |
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
public Atom atom1
public Atom atom2
public short mad
public short colix
public int shapeVisibilityFlags
public static final int myVisibilityFlag
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 Edge
public boolean isHydrogen()
isHydrogen
in class Edge
public static boolean isOrderH(int order)
boolean isStereo()
boolean isPartial()
boolean isAromatic()
boolean isPymolStyle()
public void setPaletteID(byte pid)
pid
- public float getEnergy()
public int getValence()
void deleteAtomReferences()
public void setColix(short colix)
public void setTranslucent(boolean isTranslucent, float translucentLevel)
public void setOrder(int order)
public Atom getAtom1()
public Atom getAtom2()
public int getAtomIndex1()
getAtomIndex1
in class Edge
public int getAtomIndex2()
getAtomIndex2
in class Edge
float getRadius()
public int getCovalentOrder()
getCovalentOrder
in class Edge
java.lang.String getOrderName()
java.lang.String getOrderNumberAsString()
short getColix1()
short getColix2()
public void setIndex(int i)
public boolean is(int bondType)
public Node getOtherAtomNode(Node thisAtom)
getOtherAtomNode
in class Edge
public java.lang.String toString()
toString
in class java.lang.Object