public class PhosphorusMonomer extends Monomer
Modifier and Type | Field and Description |
---|---|
protected boolean |
isPurine |
protected boolean |
isPyrimidine |
private static float |
MAX_ADJACENT_PHOSPHORUS_DISTANCE |
protected static byte |
P |
private static byte[] |
phosphorusOffsets |
bioPolymer, monomerIndex, offsets
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
Modifier | Constructor and Description |
---|---|
protected |
PhosphorusMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets) |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
(package private) Atom |
getP() |
byte |
getProteinStructureType() |
Quaternion |
getQuaternion(char qType) |
(package private) javax.vecmath.Point3f |
getQuaternionFrameCenter(char qType) |
java.lang.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,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes) |
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
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
protected static final byte P
private static final byte[] phosphorusOffsets
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
protected boolean isPurine
protected boolean isPyrimidine
protected PhosphorusMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
Atom getP()
boolean isPhosphorusMonomer()
public boolean isPyrimidine()
isPyrimidine
in class Group
public java.lang.Object getStructure()
getStructure
in class Group
public byte getProteinStructureType()
getProteinStructureType
in class Monomer
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter
in class Monomer
public Quaternion getQuaternion(char qType)
getQuaternion
in class Group
javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class Monomer
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class Group