org.jmol.modelsetbio
Class PhosphorusMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.PhosphorusMonomer
- Direct Known Subclasses:
- NucleicMonomer
public class PhosphorusMonomer
- extends Monomer
Constructor Summary |
protected |
PhosphorusMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
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 |
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
PhosphorusMonomer
protected PhosphorusMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
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