org.jmol.modelsetbio
Class PhosphorusMonomer

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

public class PhosphorusMonomer
extends Monomer


Field Summary
protected  boolean isPurine
           
protected  boolean isPyrimidine
           
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
           
protected static byte P
           
private static byte[] phosphorusOffsets
           
 
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
 
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
 
Constructor Summary
protected PhosphorusMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
 Object getHelixData(int tokType, char qType, int mStep)
           
(package private)  Atom getP()
           
 byte getProteinStructureType()
           
 Quaternion getQuaternion(char qType)
           
(package private)  Point3f getQuaternionFrameCenter(char qType)
           
 Object getStructure()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isDna()
           
 boolean isNucleic()
           
(package private)  boolean isPhosphorusMonomer()
           
 boolean isPurine()
           
 boolean isPyrimidine()
           
 boolean isRna()
           
(package private) static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
           
 
Methods inherited from class org.jmol.modelsetbio.Monomer
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getProteinStructure, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isProtein, isSheet, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, 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

P

protected static final byte P
See Also:
Constant Field Values

phosphorusOffsets

private static final byte[] phosphorusOffsets

MAX_ADJACENT_PHOSPHORUS_DISTANCE

private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE

isPurine

protected boolean isPurine

isPyrimidine

protected boolean isPyrimidine
Constructor Detail

PhosphorusMonomer

protected PhosphorusMonomer(Chain chain,
                            String group3,
                            int seqcode,
                            int firstAtomIndex,
                            int lastAtomIndex,
                            byte[] offsets)
Method Detail

isNucleic

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

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   String group3,
                                   int seqcode,
                                   int firstIndex,
                                   int lastIndex,
                                   int[] specialAtomIndexes)

getP

Atom getP()

isPhosphorusMonomer

boolean isPhosphorusMonomer()

isDna

public boolean isDna()
Overrides:
isDna in class Group

isRna

public boolean isRna()
Overrides:
isRna in class Group

isPurine

public boolean isPurine()
Overrides:
isPurine in class Group

isPyrimidine

public boolean isPyrimidine()
Overrides:
isPyrimidine in class Group

getStructure

public Object getStructure()
Overrides:
getStructure in class Group

getProteinStructureType

public byte getProteinStructureType()
Overrides:
getProteinStructureType in class Monomer

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
Specified by:
isConnectedAfter in class Monomer

getQuaternion

public Quaternion getQuaternion(char qType)
Overrides:
getQuaternion in class Group
Returns:
quaternion

getQuaternionFrameCenter

Point3f getQuaternionFrameCenter(char qType)
Overrides:
getQuaternionFrameCenter in class Monomer
Returns:
center

getHelixData

public Object getHelixData(int tokType,
                           char qType,
                           int mStep)
Overrides:
getHelixData in class Group
Returns:
helix data of some sort