org.jmol.modelsetbio
Class Monomer

java.lang.Object
  extended by org.jmol.modelset.Group
      extended by org.jmol.modelsetbio.Monomer
Direct Known Subclasses:
AlphaMonomer, CarbohydrateMonomer, PhosphorusMonomer

public abstract class Monomer
extends Group


Field Summary
(package private)  BioPolymer bioPolymer
           
protected  int monomerIndex
           
protected  byte[] offsets
           
 
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, omega, phi, psi, shapeVisibilityFlags, straightness
 
Constructor Summary
protected Monomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)
           
 
Method Summary
protected static boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)
           
(package private)  void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
          Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
protected  Atom getAtomFromOffsetIndex(int offsetIndex)
           
 BioPolymer getBioPolymer()
           
 int getBioPolymerIndex()
           
 int getBioPolymerLength()
           
protected  java.lang.Object getHelixData2(int tokType, char qType, int mStep)
           
(package private)  Atom getInitiatorAtom()
           
 Atom getLeadAtom()
           
(package private)  int getLeadAtomIndex()
           
(package private)  javax.vecmath.Point3f getLeadAtomPoint()
           
(package private)  void getMonomerSequenceAtoms(java.util.BitSet bsInclude, java.util.BitSet bsResult)
           
 java.util.Hashtable getMyInfo()
           
(package private)  javax.vecmath.Point3f getPointAtomPoint()
           
 ProteinStructure getProteinStructure()
           
 byte getProteinStructureType()
           
(package private)  Atom getQuaternionFrameCenter(char qtype)
           
 int getSelectedMonomerCount()
           
 int getSelectedMonomerIndex()
           
protected  Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)
           
protected  javax.vecmath.Point3f getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)
           
(package private) static java.lang.String getStructureTypeName(byte type)
           
(package private)  Atom getTerminatorAtom()
           
 java.lang.String getUniqueID()
           
 Atom getWingAtom()
           
 javax.vecmath.Point3f getWingAtomPoint()
           
(package private) abstract  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isDna()
           
 boolean isHelix()
           
 boolean isNucleic()
           
 boolean isProtein()
           
 boolean isRna()
           
 boolean isSheet()
           
 void resetHydrogenPoint()
           
protected static byte[] scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)
           
(package private)  void setBioPolymer(BioPolymer polymer, int index)
           
 void setProteinStructureId(int id)
           
(package private)  void setStructure(ProteinStructure proteinstructure)
           
(package private)  void updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected, int nAltLocInModel)
           
 
Methods inherited from class org.jmol.modelset.Group
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getModel, getModelIndex, getOmega, getPhi, getProteinStructureTag, getPsi, getQuaternion, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, getStrucNo, getStructure, getStructureId, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setModelSet, setOmega, setPhi, setProteinStructureType, setPsi, setShapeVisibility, setStraightness, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

bioPolymer

BioPolymer bioPolymer

offsets

protected final byte[] offsets

monomerIndex

protected int monomerIndex
Constructor Detail

Monomer

protected Monomer(Chain chain,
                  java.lang.String group3,
                  int seqcode,
                  int firstAtomIndex,
                  int lastAtomIndex,
                  byte[] interestingAtomOffsets)
Method Detail

setBioPolymer

void setBioPolymer(BioPolymer polymer,
                   int index)

getSelectedMonomerCount

public int getSelectedMonomerCount()
Overrides:
getSelectedMonomerCount in class Group

getSelectedMonomerIndex

public int getSelectedMonomerIndex()
Overrides:
getSelectedMonomerIndex in class Group

getBioPolymer

public BioPolymer getBioPolymer()

getBioPolymerLength

public int getBioPolymerLength()
Overrides:
getBioPolymerLength in class Group

getBioPolymerIndex

public int getBioPolymerIndex()
Overrides:
getBioPolymerIndex in class Group

scanForOffsets

protected static byte[] scanForOffsets(int firstAtomIndex,
                                       int[] specialAtomIndexes,
                                       byte[] interestingAtomIDs)

isDna

public boolean isDna()
Overrides:
isDna in class Group

isRna

public boolean isRna()
Overrides:
isRna in class Group

isProtein

public final boolean isProtein()
Overrides:
isProtein in class Group

isNucleic

public final boolean isNucleic()
Overrides:
isNucleic in class Group

setStructure

void setStructure(ProteinStructure proteinstructure)

getProteinStructure

public ProteinStructure getProteinStructure()

getProteinStructureType

public byte getProteinStructureType()
Overrides:
getProteinStructureType in class Group

isHelix

public boolean isHelix()

isSheet

public boolean isSheet()

setProteinStructureId

public void setProteinStructureId(int id)
Overrides:
setProteinStructureId in class Group

getAtomFromOffsetIndex

protected final Atom getAtomFromOffsetIndex(int offsetIndex)

getSpecialAtom

protected final Atom getSpecialAtom(byte[] interestingIDs,
                                    byte specialAtomID)

getSpecialAtomPoint

protected final javax.vecmath.Point3f getSpecialAtomPoint(byte[] interestingIDs,
                                                          byte specialAtomID)

getLeadAtomIndex

final int getLeadAtomIndex()

getLeadAtom

public final Atom getLeadAtom()
Overrides:
getLeadAtom in class Group

getLeadAtomPoint

final javax.vecmath.Point3f getLeadAtomPoint()

getWingAtom

public final Atom getWingAtom()

getWingAtomPoint

public final javax.vecmath.Point3f getWingAtomPoint()

getPointAtomPoint

final javax.vecmath.Point3f getPointAtomPoint()

getInitiatorAtom

Atom getInitiatorAtom()

getTerminatorAtom

Atom getTerminatorAtom()

isConnectedAfter

abstract boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

findNearestAtomIndex

void findNearestAtomIndex(int x,
                          int y,
                          Atom[] closest,
                          short madBegin,
                          short madEnd)
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.

Parameters:
x -
y -
closest -
madBegin -
madEnd -

getMyInfo

public java.util.Hashtable getMyInfo()
Overrides:
getMyInfo in class Group

getStructureTypeName

static java.lang.String getStructureTypeName(byte type)

updateOffsetsForAlternativeLocations

final void updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected,
                                                int nAltLocInModel)

getMonomerSequenceAtoms

final void getMonomerSequenceAtoms(java.util.BitSet bsInclude,
                                   java.util.BitSet bsResult)

checkOptional

protected static final boolean checkOptional(byte[] offsets,
                                             byte atom,
                                             int firstAtomIndex,
                                             int index)

getQuaternionFrameCenter

Atom getQuaternionFrameCenter(char qtype)

getHelixData2

protected java.lang.Object getHelixData2(int tokType,
                                         char qType,
                                         int mStep)

resetHydrogenPoint

public void resetHydrogenPoint()

getUniqueID

public java.lang.String getUniqueID()