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org::jmol::modelset::AtomCollection Class Reference

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

Classes

class  AtomSorter

Public Member Functions

Point3f[][] calculateHydrogens (BitSet bs, int[] nTotal, boolean doAll, boolean justCarbon, List vConnect)
Point3f[] calculateSurface (BitSet bsSelected, float envelopeRadius)
float calculateVolume (BitSet bs, int iType)
void clearBfactorRange ()
BitSet findAtomsInRectangle (Rectangle rect, BitSet bsModels)
String getAtomChain (int i)
short getAtomColix (int i)
int getAtomCount ()
float[] getAtomicCharges ()
String getAtomicPropertyState (int taintWhat, BitSet bsSelected)
void getAtomicPropertyState (StringBuffer commands, byte type, BitSet bs, String label, float[] fData)
int getAtomIndexFromAtomNumber (int atomNumber, BitSet bsVisibleFrames)
int[] getAtomIndices (BitSet bs)
String getAtomInfo (int i, String format)
String getAtomInfoXYZ (int i, boolean useChimeFormat)
int getAtomModelIndex (int i)
String getAtomName (int i)
int getAtomNumber (int i)
Point3f getAtomPoint3f (int i)
List getAtomPointVector (BitSet bs)
float getAtomRadius (int i)
String getAtomSequenceCode (int i)
BitSet getAtomsWithin (float distance, Point4f plane)
String[] getAtomTypes ()
float getAtomVdwRadius (int i, int iType)
int getBfactor100Hi ()
int getBfactor100Lo ()
short[] getBFactors ()
BitSet getClickableSet ()
int getElementNumber (int i)
String getElementSymbol (int i)
Object[] getEllipsoid (int i)
Object getHelixData (BitSet bs, int tokType)
String getHybridizationAndAxes (int atomIndex, Vector3f z, Vector3f x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ)
float[] getIonicRadii ()
float getMaxVanderwaalsRadius ()
float[] getPartialCharges ()
Quaternion getQuaternion (int i, char qtype)
int getSurfaceDistanceMax ()
BitSet getTaintedAtoms (byte type)
float getVibrationCoord (int atomIndex, char c)
Vector3f getVibrationVector (int atomIndex, boolean forceNew)
BitSet getVisibleSet ()
boolean isAtomHidden (int iAtom)
boolean modelSetHasVibrationVectors ()
void setAtomCoord (BitSet bs, int tokType, Object xyzValues)
void setAtomCoord (int atomIndex, float x, float y, float z)
void setAtomCoordRelative (int atomIndex, float x, float y, float z)
void setAtomData (int type, String name, String dataString, boolean isDefault)
void setAtomProperty (BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
void setBsHidden (BitSet bs)
void setFormalCharges (BitSet bs, int formalCharge)
void setHaveStraightness (boolean TF)
void setPreserveState (boolean TF)
void setTaintedAtoms (BitSet bs, byte type)
void taint (BitSet bsAtoms, byte type)
void unTaintAtoms (BitSet bs, byte type)

Static Public Member Functions

static int getUserSettableType (String dataType)

Public Attributes

Atom[] atoms
Vector3f[] vibrationVectors
Viewer viewer

Static Public Attributes

final static byte TAINT_ATOMNAME = 0
final static byte TAINT_ATOMNO = 12
final static byte TAINT_ATOMTYPE = 1
final static byte TAINT_COORD = 2
final static byte TAINT_ELEMENT = 3
static final byte TAINT_FORMALCHARGE = 4
final static byte TAINT_MAX = 13

Protected Member Functions

void deleteModelAtoms (int firstAtomIndex, int nAtoms, BitSet bs)
void fillAtomData (AtomData atomData, int mode)
void findMaxRadii ()
void findNearestAtomIndex (int x, int y, Atom[] closest, BitSet bsNot)
BitSet getAtomBits (int tokType, Object specInfo)
BitSet getChainBits (char chain)
String getChimeInfo (int tok, BitSet bs)
boolean getHaveStraightness ()
float getRadiusVdwJmol (Atom atom)
BitSet getSeqcodeBits (int seqcode, boolean returnEmpty)
void mergeAtomArrays (AtomCollection mergeModelSet)
void releaseModelSet ()
void setAtomCoordRelative (BitSet bs, float x, float y, float z)
void setAtomName (int atomIndex, String name)
boolean setAtomNumber (int atomIndex, int atomno)
void setAtomType (int atomIndex, String type)
boolean setBFactor (int atomIndex, float bfactor)
void setElement (Atom atom, int atomicNumber)
void setEllipsoid (int atomIndex, Object[] ellipsoid)
boolean setIonicRadius (int atomIndex, float radius)
boolean setOccupancy (int atomIndex, int occupancy)
boolean setPartialCharge (int atomIndex, float partialCharge)
void setVibrationVector (int atomIndex, float x, float y, float z)
void taint (int atomIndex, byte type)

Protected Attributes

Bspf bspf
Object[][] ellipsoids
Graphics3D g3d
boolean haveStraightness
float maxBondingRadius = Float.MIN_VALUE
boolean preserveState = true
int[] surfaceDistance100s
BitSet[] tainted

Package Functions

String getElementName (int i)
int getSurfaceDistance100 (int atomIndex)
boolean isCursorOnTopOf (Atom contender, int x, int y, int radius, Atom champion)

Static Package Functions

 [static initializer]

Package Attributes

int atomCount
String[] atomNames
int[] atomSerials
String[] atomTypes
short[] bfactor100s
float[] ionicRadii
byte[] occupancies
float[] partialCharges

Private Member Functions

void calcBfactorRange (BitSet bs)
void calcSurfaceDistances ()
BitSet findNotAttached (int nAttached, int[][] angles, int[] ptrs, int nPtrs)
Atom[] getAttached (Atom atom, int nMax, boolean doSort)
String getHybridizationAndAxesD (int atomIndex, Vector3f z, Vector3f x, String lcaoType)
BitSet getIdentifierOrNull (String identifier)
BitSet getSpecName (String name)
BitSet getSpecNameOrNull (String name, boolean checkStar)
boolean isAtomNameMatch (Atom atom, String strPattern, boolean checkStar)
boolean isTainted (int atomIndex, byte type)
void loadCoordinates (String data, boolean isVibrationVectors, boolean doTaint)
void setAtomVibrationVector (int atomIndex, float x, float y, float z)
void setBf (int i)
void setVibrationVector (int atomIndex, int tok, float fValue)
void untaint (int atomIndex, byte type)

Private Attributes

int bfactor100Hi
int bfactor100Lo
final BitSet bsEmpty = new BitSet()
final BitSet bsFoundRectangle = new BitSet()
BitSet bsHidden = new BitSet()
BitSet bsSurface
boolean hasBfactorRange
float maxVanderwaalsRadius = Float.MIN_VALUE
int nSurfaceAtoms
int surfaceDistanceMax

Static Private Attributes

static final float almost180 = (float) Math.PI * 0.95f
static final int minimumPixelSelectionRadius = 6
static final float sqrt3_2 = (float) (Math.sqrt(3) / 2)
final static byte TAINT_IONICRADIUS = 5
final static byte TAINT_OCCUPANCY = 6
final static byte TAINT_PARTIALCHARGE = 7
final static byte TAINT_TEMPERATURE = 8
final static byte TAINT_VALENCE = 9
final static byte TAINT_VANDERWAALS = 10
final static byte TAINT_VIBRATION = 11
final static String[] userSettableValues
static final Vector3f vRef = new Vector3f(3.14159f, 2.71828f, 1.41421f)

Detailed Description

Definition at line 60 of file AtomCollection.java.


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

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