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org::jmol::modelset::Bond Class Reference

Inheritance diagram for org::jmol::modelset::Bond:
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List of all members.

Classes

class  BondSet

Public Member Functions

 Bond (Atom atom1, Atom atom2, int order, short mad, short colix)
Atom getAtom1 ()
Atom getAtom2 ()
int getAtomIndex1 ()
int getAtomIndex2 ()
short getColix ()
int getCovalentOrder ()
float getEnergy ()
String getIdentity ()
int getIndex ()
short getMad ()
int getOrder ()
Atom getOtherAtom (Atom thisAtom)
JmolNode getOtherAtom (JmolNode thisAtom)
int getShapeVisibilityFlags ()
boolean is (int bondType)
boolean isCovalent ()
boolean isHydrogen ()
void setColix (short colix)
void setIndex (int i)
void setMad (short mad)
void setOrder (int order)
void setPaletteID (byte pid)
void setShapeVisibilityFlags (int shapeVisibilityFlags)
void setTranslucent (boolean isTranslucent, float translucentLevel)

Static Public Member Functions

static boolean isHydrogen (int order)

Static Public Attributes

static final int BOND_AROMATIC = 0x203
static final int BOND_AROMATIC_DOUBLE = 0x202
static final int BOND_AROMATIC_MASK = 0x200
static final int BOND_AROMATIC_SINGLE = 0x201
static final int BOND_COVALENT_DOUBLE = 2
static final int BOND_COVALENT_MASK = 0x3FF
static final int BOND_COVALENT_QUADRUPLE = 4
static final int BOND_COVALENT_SINGLE = 1
static final int BOND_COVALENT_TRIPLE = 3
static final int BOND_H_CALC = 2 << 11
static final int BOND_H_CALC_MASK = 0xE << 11
static final int BOND_H_MINUS_3 = 7 << 11
static final int BOND_H_MINUS_4 = 8 << 11
static final int BOND_H_NUCLEOTIDE = 9 << 11
static final int BOND_H_PLUS_2 = 3 << 11
static final int BOND_H_PLUS_3 = 4 << 11
static final int BOND_H_PLUS_4 = 5 << 11
static final int BOND_H_PLUS_5 = 6 << 11
static final int BOND_H_REGULAR = 1 << 11
static final int BOND_HBOND_SHIFT = 11
static final int BOND_HYDROGEN_MASK = 0xF << 11
static final int BOND_NEW = 0x20000
static final int BOND_ORDER_ANY = 0xFFFF
static final int BOND_ORDER_NULL = 0x1FFFF
static final int BOND_ORDER_UNSPECIFIED = 0x11
static final int BOND_PARTIAL01 = 0x21
static final int BOND_PARTIAL12 = 0x42
static final int BOND_PARTIAL23 = 0x61
static final int BOND_PARTIAL32 = 0x64
static final int BOND_PARTIAL_MASK = 0xE0
static final int BOND_STEREO_FAR = 0x411
static final int BOND_STEREO_MASK = 0x400
static final int BOND_STEREO_NEAR = 0x401
static final int BOND_STRUT = 0x8000
static final int BOND_SULFUR_MASK = 0x100

Package Functions

void deleteAtomReferences ()
short getColix1 ()
short getColix2 ()
String getOrderName ()
String getOrderNumberAsString ()
float getRadius ()
int getValence ()
boolean isAromatic ()
boolean isPartial ()
boolean isStereo ()
boolean isTranslucent ()
final void setShapeVisibility (int shapeVisibilityFlag, boolean isVisible)

Package Attributes

Atom atom1
Atom atom2
short colix
int index = -1
short mad
int order
int shapeVisibilityFlags

Static Package Attributes

static final int myVisibilityFlag = JmolConstants.getShapeVisibilityFlag(JmolConstants.SHAPE_STICKS)

Detailed Description

Definition at line 37 of file Bond.java.


The documentation for this class was generated from the following file:

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