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Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Package Functions | Package Attributes | Private Member Functions | Private Attributes | Static Private Attributes

org::jmol::modelset::Atom Class Reference

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

Public Member Functions

void addDisplayedBackbone (int backboneVisibilityFlag, boolean isVisible)
 Atom (int modelIndex, int atomIndex, float x, float y, float z, float radius, BitSet atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, char alternateLocationID)
short calculateMad (Viewer viewer, RadiusData rd)
void delete (BitSet bsBonds)
boolean equals (Object obj)
Atom findAromaticNeighbor (int notAtomIndex)
float getADPMinMax (boolean isMax)
char getAlternateLocationID ()
short getAtomicAndIsotopeNumber ()
byte getAtomID ()
String getAtomName ()
int getAtomNumber ()
int getAtomSite ()
BitSet getAtomSymmetry ()
String getAtomType ()
int getBfactor100 ()
Bond getBond (Atom atomOther)
int getBondedAtomIndex (int bondIndex)
float getBondingRadiusFloat ()
Bond[] getBonds ()
int getCellTranslation (int cellNNN, int[] cellRange, int nOps)
char getChainID ()
int getClickabilityFlags ()
short getColix ()
int getCovalentBondCount ()
int getCovalentHydrogenCount ()
float getCovalentRadiusFloat ()
boolean getCrossLinkLeadAtomIndexes (List vReturn)
float getDimensionValue (int dimension)
JmolEdge[] getEdges ()
short getElementNumber ()
String getElementSymbol (boolean withIsotope)
String getElementSymbol ()
Object[] getEllipsoid ()
int getFormalCharge ()
Point3f getFractionalUnitCoord (boolean asCartesian)
float getFractionalUnitDistance (Point3f pt, Point3f ptTemp1, Point3f ptTemp2)
Group getGroup ()
String getGroup1 (char c0)
String getGroup3 (boolean allowNull)
short getGroupID ()
int getGroupIndex ()
float getGroupParameter (int tok)
String getGroupType ()
int getImplicitHydrogenCount ()
int getIndex ()
String getInfo ()
char getInsertionCode ()
short getIsotopeNumber ()
int getModelFileIndex ()
int getModelFileNumber ()
int getModelIndex ()
int getModelNumber ()
int getMoleculeNumber ()
int getMonomerIndex ()
int getNBackbonesDisplayed ()
int getOccupancy100 ()
int getOffsetResidueAtom (String name, int offset)
byte getPaletteID ()
float getPartialCharge ()
int getPolymerIndexInModel ()
int getPolymerLength ()
byte getProteinStructureSubType ()
String getProteinStructureTag ()
byte getProteinStructureType ()
float getRadius ()
int getRasMolRadius ()
int getResno ()
int getSelectedGroupCountWithinChain ()
int getSelectedGroupIndexWithinChain ()
int getSelectedMonomerCountWithinPolymer ()
int getSelectedMonomerIndexWithinPolymer ()
int getShapeVisibilityFlags ()
int getStrucNo ()
String getStructureId ()
int getSurfaceDistance100 ()
int getSymmetryTranslation (int symop, int[] cellRange, int nOps)
int getValence ()
float getVanderwaalsRadiusFloat (Viewer viewer, int iType)
float getVibrationCoord (char ch)
Vector3f getVibrationVector ()
int hashCode ()
boolean hasVibration ()
boolean isBonded (Atom atomOther)
boolean isCarbohydrate ()
boolean isClickable ()
boolean isCrossLinked (JmolNode node)
boolean isDeleted ()
boolean isDna ()
boolean isHetero ()
boolean isInFrame ()
boolean isLeadAtom ()
boolean isNucleic ()
boolean isProtein ()
boolean isPurine ()
boolean isPyrimidine ()
boolean isRna ()
boolean isShapeVisible (int shapeVisibilityFlag)
boolean isTranslucent ()
boolean isVisible (int flags)
void set (float x, float y, float z)
void setAtomicAndIsotopeNumber (int n)
void setBonds (Bond[] bonds)
void setClickable (int flag)
void setColixAtom (short colixAtom)
void setGroupBits (BitSet bs)
void setMadAtom (Viewer viewer, RadiusData rd)
void setPaletteID (byte paletteID)
boolean setRadius (float radius)
final void setShapeVisibility (int shapeVisibilityFlag, boolean isVisible)
final void setShapeVisibilityFlags (int flag)
void setTranslucent (boolean isTranslucent, float translucentLevel)
void setValence (int nBonds)
String toString ()

Static Public Member Functions

static float atomPropertyFloat (Viewer viewer, Atom atom, int tokWhat)
static int atomPropertyInt (Atom atom, int tokWhat)
static String atomPropertyString (Atom atom, int tokWhat)
static Tuple3f atomPropertyTuple (Atom atom, int tok)

Public Attributes

byte atomID
int index
short madAtom
short modelIndex = -1
short screenDiameter = -1
int screenX
int screenY
int screenZ

Static Public Attributes

static final int RADIUS_MAX = 16

Package Functions

void addDisplayedBond (int stickVisibilityFlag, boolean isVisible)
void clearBonds ()
void deleteBond (Bond bond)
Chain getChain ()
int getCurrentBondCount ()
String getIdentity (boolean allInfo)
String getIdentityXYZ (boolean allInfo)
String getInfoXYZ (boolean useChimeFormat)
String getModelNumberForLabel ()
int getSeqcode ()
String getSeqcodeString ()
int getSeqNumber ()
String getSymmetryOperatorList ()
int getTargetValence ()
float getVolume (Viewer viewer, int iType)
boolean isAlternateLocationMatch (String strPattern)
boolean isCursorOnTopOf (int xCursor, int yCursor, int minRadius, Atom competitor)
boolean isGroup3 (String group3)
boolean isWithinStructure (byte type)
void setFormalCharge (int charge)
void setFractionalCoord (Point3f ptNew, boolean asAbsolute)
void setFractionalCoord (int tok, float fValue, boolean asAbsolute)
void setFractionalCoord (Point3f pt, Point3f ptNew, boolean asAbsolute)
void setGroup (Group group)
void setVibrationVector ()

Package Attributes

char alternateLocationID
int atomSite
Bond[] bonds
int clickabilityFlags
short colixAtom
Group group
int nBackbonesDisplayed = 0
int nBondsDisplayed = 0
byte paletteID = JmolConstants.PALETTE_CPK
int shapeVisibilityFlags

Private Member Functions

void deleteBond (int i)
Point3f getFractionalCoord (boolean asAbsolute)
float getFractionalCoord (char ch, boolean asAbsolute)
float getFractionalUnitCoord (char ch)
int getVdwType (int iType)

Private Attributes

short atomicAndIsotopeNumber
BitSet atomSymmetry
byte formalChargeAndFlags
float userDefinedVanDerWaalRadius
byte valence

Static Private Attributes

static final byte FLAG_MASK = 3
static final byte IS_HETERO_FLAG = 2
static final byte VIBRATION_VECTOR_FLAG = 1

Detailed Description

Definition at line 46 of file Atom.java.


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

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