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
           
(package private)  int monomerIndex
           
protected  byte[] offsets
           
 
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
 
Constructor Summary
protected Monomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)
           
 
Method Summary
protected  boolean calcBioParameters()
           
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 getBioPolymerIndexInModel()
           
 int getBioPolymerLength()
           
(package private)  void getConformation(Atom[] atoms, java.util.BitSet bsConformation, int conformationIndex)
          clear out bits that are not associated with the nth conformation counting for each residue from the beginning of the file listing
protected  boolean getCrossLink(int i, java.util.List vReturn)
           
private  boolean getCrossLink(int i, java.util.List vReturn, Group group)
           
 boolean getCrossLinkLeadAtomIndexes(java.util.List vReturn)
           
protected  java.lang.Object getHelixData2(int tokType, char qType, int mStep)
           
(package private)  Atom getInitiatorAtom()
           
 Atom getLeadAtom()
           
 int getMonomerIndex()
           
(package private)  void getMonomerSequenceAtoms(java.util.BitSet bsInclude, java.util.BitSet bsResult)
           
 java.util.Map getMyInfo()
           
 ProteinStructure getProteinStructure()
           
 byte getProteinStructureType()
           
(package private)  javax.vecmath.Point3f getQuaternionFrameCenter(char qtype)
           
 int getSelectedMonomerCount()
           
 int getSelectedMonomerIndex()
           
protected  Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)
           
protected  javax.vecmath.Point3f getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)
           
 java.lang.String getStructureId()
           
(package private)  Atom getTerminatorAtom()
           
 java.lang.String getUniqueID()
           
 Atom getWingAtom()
           
 boolean haveParameters()
           
(package private) abstract  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isConnectedPrevious()
           
 boolean isCrossLinked(Group g)
           
 boolean isHelix()
           
 boolean isLeadAtom(int atomIndex)
           
 boolean isProtein()
           
 boolean isSheet()
           
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(Atom[] atoms, java.util.BitSet bsSelected)
           
 
Methods inherited from class org.jmol.modelset.Group
getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, getStructure, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, 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

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

getMonomerIndex

public int getMonomerIndex()
Overrides:
getMonomerIndex in class Group

getBioPolymerIndexInModel

public int getBioPolymerIndexInModel()
Overrides:
getBioPolymerIndexInModel in class Group

scanForOffsets

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

isProtein

public boolean isProtein()
Overrides:
isProtein in class Group

setStructure

void setStructure(ProteinStructure proteinstructure)
Parameters:
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)

isLeadAtom

public boolean isLeadAtom(int atomIndex)
Overrides:
isLeadAtom in class Group
Returns:
T/F

getLeadAtom

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

getWingAtom

public final Atom getWingAtom()

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 -

calcBioParameters

protected boolean calcBioParameters()
Overrides:
calcBioParameters in class Group

haveParameters

public boolean haveParameters()
Overrides:
haveParameters in class Group

getMyInfo

public java.util.Map getMyInfo()

getStructureId

public java.lang.String getStructureId()
Overrides:
getStructureId in class Group

getConformation

void getConformation(Atom[] atoms,
                     java.util.BitSet bsConformation,
                     int conformationIndex)
clear out bits that are not associated with the nth conformation counting for each residue from the beginning of the file listing

Parameters:
atoms -
bsConformation -
conformationIndex - will be >= 0

updateOffsetsForAlternativeLocations

final void updateOffsetsForAlternativeLocations(Atom[] atoms,
                                                java.util.BitSet bsSelected)

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

javax.vecmath.Point3f getQuaternionFrameCenter(char qtype)
Parameters:
qtype -
Returns:
center

getHelixData2

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

getUniqueID

public java.lang.String getUniqueID()

isCrossLinked

public boolean isCrossLinked(Group g)
Overrides:
isCrossLinked in class Group
Returns:
T/F

getCrossLinkLeadAtomIndexes

public boolean getCrossLinkLeadAtomIndexes(java.util.List vReturn)
Overrides:
getCrossLinkLeadAtomIndexes in class Group
Returns:
T/F

getCrossLink

protected boolean getCrossLink(int i,
                               java.util.List vReturn)

getCrossLink

private boolean getCrossLink(int i,
                             java.util.List vReturn,
                             Group group)

isConnectedPrevious

public boolean isConnectedPrevious()
Overrides:
isConnectedPrevious in class Group