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
           
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, omega, phi, psi, shapeVisibilityFlags, straightness
 
Constructor Summary
protected PhosphorusMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
 byte getProteinStructureType()
           
 java.lang.Object getStructure()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isDna()
           
(package private)  boolean isPhosphorusMonomer()
           
 boolean isPurine()
           
 boolean isPyrimidine()
           
 boolean isRna()
           
(package private) static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes, Atom[] atoms)
           
 
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getInitiatorAtom, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getProteinStructure, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getTerminatorAtom, getWingAtom, getWingAtomPoint, isHelix, isNucleic, isProtein, isSheet, resetHydrogenPoint, scanForOffsets, setBioPolymer, setStructure, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getMinZ, getModel, getModelIndex, getOmega, getPhi, getProteinStructureID, getPsi, getQuaternion, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setMinZ, 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

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,
                            java.lang.String group3,
                            int seqcode,
                            int firstAtomIndex,
                            int lastAtomIndex,
                            byte[] offsets)
Method Detail

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   java.lang.String group3,
                                   int seqcode,
                                   int firstIndex,
                                   int lastIndex,
                                   int[] specialAtomIndexes,
                                   Atom[] atoms)

isPhosphorusMonomer

boolean isPhosphorusMonomer()

isDna

public boolean isDna()
Overrides:
isDna in class Monomer

isRna

public boolean isRna()
Overrides:
isRna in class Monomer

isPurine

public boolean isPurine()
Overrides:
isPurine in class Group

isPyrimidine

public boolean isPyrimidine()
Overrides:
isPyrimidine in class Group

getStructure

public java.lang.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