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

org::jmol::modelset::Group Class Reference

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

Public Member Functions

int getBioPolymerIndexInModel ()
int getBioPolymerLength ()
Atom getCarbonylOxygenAtom ()
final char getChainID ()
boolean getCrossLinkLeadAtomIndexes (List vReturn)
final char getGroup1 ()
final short getGroupID ()
int getGroupIndex ()
float getGroupParameter (int tok)
Object getHelixData (int tokType, char qType, int mStep)
char getInsertionCode ()
Atom getLeadAtom (Atom atom)
Atom getLeadAtom ()
Model getModel ()
int getModelIndex ()
final ModelSet getModelSet ()
int getMonomerIndex ()
Atom getNitrogenAtom ()
byte getProteinStructureSubType ()
String getProteinStructureTag ()
byte getProteinStructureType ()
Quaternion getQuaternion (char qType)
Quaternion getQuaternionFrame (Atom[] atoms)
final int getResno ()
int getSelectedGroupIndex ()
int getSelectedMonomerCount ()
int getSelectedMonomerIndex ()
final int getSeqcode ()
final String getSeqcodeString ()
final int getSeqNumber ()
int getStrucNo ()
Object getStructure ()
String getStructureId ()
 Group (Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
boolean haveParameters ()
boolean isCarbohydrate ()
boolean isConnectedPrevious ()
boolean isCrossLinked (Group g)
boolean isDna ()
boolean isLeadAtom (int atomIndex)
boolean isNucleic ()
boolean isProtein ()
boolean isPurine ()
boolean isPyrimidine ()
boolean isRna ()
boolean isSelected (BitSet bs)
boolean isWithinStructure (byte type)
final int selectAtoms (BitSet bs)
void setGroupIndex (int groupIndex)
void setGroupParameter (int tok, float f)
void setModelSet (ModelSet modelSet)
void setProteinStructureId (int i)
int setProteinStructureType (byte iType, int monomerIndexCurrent)
final void setShapeVisibility (int visFlag, boolean isVisible)
String toString ()

Static Public Member Functions

static String getGroup3 (short groupID)
static short getGroupID (String group3)
static char getInsertionCode (int seqcode)
static final int getInsertionCodeValue (int seqcode)
static int getSeqcode (int sequenceNumber, char insertionCode)
static String getSeqcodeString (int seqcode)
static final int getSequenceNumber (int seqcode)
static final boolean haveSequenceNumber (int seqcode)
static short lookupGroupID (String group3)

Public Attributes

int firstAtomIndex = -1
int lastAtomIndex
int leadAtomIndex = -1
int shapeVisibilityFlags = 0

Protected Member Functions

boolean calcBioParameters ()
boolean isAtomHidden (int atomIndex)
boolean isCursorOnTopOf (Atom atom, int x, int y, int radius, Atom champ)
int scaleToScreen (int Z, int mar)

Protected Attributes

Chain chain
short groupID
boolean isAmino

Package Functions

final String getGroup3 ()
final boolean isGroup3 (String group3)
boolean isHetero ()

Static Package Functions

 [static initializer]
static synchronized short addGroup3Name (String group3)

Package Attributes

int selectedIndex
int seqcode

Static Package Attributes

static short group3NameCount = 0
static String[] group3Names = new String[128]

Private Attributes

int groupIndex
float mu = Float.NaN
float omega = Float.NaN
float phi = Float.NaN
float psi = Float.NaN
float straightness = Float.NaN
float theta = Float.NaN

Static Private Attributes

static Map htGroup = new Hashtable()
static final int INSERTION_CODE_MASK = 0x7F
static final int SEQUENCE_NUMBER_FLAG = 0x80
static final int SEQUENCE_NUMBER_SHIFT = 8

Detailed Description

Definition at line 41 of file Group.java.

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

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