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

org::jmol::modelsetbio::NucleicMonomer Class Reference

Inheritance diagram for org::jmol::modelsetbio::NucleicMonomer:
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List of all members.

Public Member Functions

void findNearestAtomIndex (int x, int y, Atom[] closest, short madBegin, short madEnd)
void getBaseRing6Points (Point3f[] ring6Points)
BioPolymer getBioPolymer ()
int getBioPolymerIndexInModel ()
int getBioPolymerLength ()
Atom getCarbonylOxygenAtom ()
final char getChainID ()
boolean getCrossLinkLeadAtomIndexes (List vReturn)
boolean getEdgePoints (Point3f[] pts)
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)
final Atom getLeadAtom ()
Model getModel ()
int getModelIndex ()
final ModelSet getModelSet ()
int getMonomerIndex ()
Map getMyInfo ()
Atom getNitrogenAtom ()
ProteinStructure getProteinStructure ()
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 ()
String getUniqueID ()
final Atom getWingAtom ()
boolean haveParameters ()
boolean isCarbohydrate ()
boolean isConnectedPrevious ()
boolean isCrossLinked (Group g)
boolean isDna ()
boolean isGuanine ()
boolean isHelix ()
boolean isLeadAtom (int atomIndex)
final boolean isNucleic ()
boolean isNucleicMonomer ()
boolean isProtein ()
boolean isPurine ()
boolean isPyrimidine ()
boolean isRna ()
boolean isSelected (BitSet bs)
boolean isSheet ()
boolean isWithinStructure (byte type)
boolean maybeGetBaseRing5Points (Point3f[] ring5Points)
final int selectAtoms (BitSet bs)
void setGroupIndex (int groupIndex)
void setGroupParameter (int tok, float f)
void setModelClickability ()
void setModelSet (ModelSet modelSet)
void setProteinStructureId (int id)
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)
static Monomer validateAndAllocate (Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)

Public Attributes

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

Protected Member Functions

boolean calcBioParameters ()
final Atom getAtomFromOffsetIndex (int offsetIndex)
boolean getCrossLink (int i, List vReturn)
Object getHelixData2 (int tokType, char qType, int mStep)
final Atom getSpecialAtom (byte[] interestingIDs, byte specialAtomID)
final Point3f getSpecialAtomPoint (byte[] interestingIDs, byte specialAtomID)
boolean isAtomHidden (int atomIndex)
boolean isCursorOnTopOf (Atom atom, int x, int y, int radius, Atom champ)
int scaleToScreen (int Z, int mar)

Static Protected Member Functions

static final boolean checkOptional (byte[]offsets, byte atom, int firstAtomIndex, int index)
static byte[] scanForOffsets (int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)

Protected Attributes

Chain chain
short groupID
boolean isAmino
boolean isPurine
boolean isPyrimidine
final byte[] offsets

Static Protected Attributes

static final byte P = 0

Package Functions

Atom getC1P ()
Atom getC2 ()
Atom getC4P ()
void getConformation (Atom[] atoms, BitSet bsConformation, int conformationIndex)
final String getGroup3 ()
Atom getInitiatorAtom ()
final void getMonomerSequenceAtoms (BitSet bsInclude, BitSet bsResult)
Atom getN0 ()
Atom getN1 ()
Atom getN2 ()
Atom getN3 ()
Atom getN4 ()
Atom getN6 ()
Atom getO2 ()
Atom getO4 ()
Atom getO6 ()
Atom getP ()
Point3f getQuaternionFrameCenter (char qType)
Atom getTerminatorAtom ()
boolean isConnectedAfter (Monomer possiblyPreviousMonomer)
final boolean isGroup3 (String group3)
boolean isHetero ()
boolean isPhosphorusMonomer ()
 NucleicMonomer (Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
void setBioPolymer (BioPolymer polymer, int index)
void setStructure (ProteinStructure proteinstructure)
final void updateOffsetsForAlternativeLocations (Atom[] atoms, BitSet bsSelected)

Static Package Functions

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

Package Attributes

Point3f baseCenter
BioPolymer bioPolymer
int monomerIndex
int selectedIndex
int seqcode

Static Package Attributes

static final byte C6 = 1
static short group3NameCount = 0
static String[] group3Names = new String[128]
static final byte[] interestingNucleicAtomIDs

Private Attributes

boolean hasRnaO2Prime

Static Private Attributes

static final byte C1P = 25
static final byte C2 = 5
static final byte C3Pr = 22
static final byte C4 = 7
static final byte C4P = 26
static final byte C5 = 3
static final byte C8 = 10
static final byte H3T = 20
static final byte H5T = 18
static final byte[] heavyAtomIndexes
static final byte N1 = 4
static final byte N2 = 17
static final byte N3 = 6
static final byte N4 = 14
static final byte N6 = 16
static final byte N7 = 9
static final byte N9 = 11
static final byte NP = 15
static final byte O1P = 23
static final byte O2 = 8
static final byte O2P = 24
static final byte O2Pr = 2
static final byte O3Pr = 21
static final byte O4 = 12
static final byte O5Pr = 19
static final byte O6 = 13
static final byte[] ring5OffsetIndexes = {C5, N7, C8, N9, C4}
static final byte[] ring6OffsetIndexes = {C5, C6, N1, C2, N3, C4}

Detailed Description

Definition at line 39 of file NucleicMonomer.java.


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

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