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,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
Methods inherited from class org.jmol.modelsetbio.Monomer |
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getHelixData2, getInitiatorAtom, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getProteinStructure, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getTerminatorAtom, getUniqueID, getWingAtom, getWingAtomPoint, isHelix, isLeadAtom, isNucleic, isProtein, isSheet, resetHydrogenPoint, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, updateOffsetsForAlternativeLocations |
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, getStructureId, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, 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 |
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,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
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