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, group1, group3Names, groupID, groupIndex, htGroup, lastAtomIndex, leadAtomIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
Modifier | Constructor and Description |
---|---|
protected |
PhosphorusMonomer() |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
(package private) Atom |
getP() |
STR |
getProteinStructureType() |
javajs.util.Quat |
getQuaternion(char qType) |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qType) |
protected javajs.util.Quat |
getQuaternionP() |
java.lang.Object |
getStructure() |
protected boolean |
isCA2(Monomer possiblyPreviousMonomer) |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isDna() |
boolean |
isNucleic() |
(package private) boolean |
isPhosphorusMonomer() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
protected PhosphorusMonomer |
set3(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets) |
(package private) static Monomer |
validateAndAllocateP(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes) |
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLinkGroup, getCrossLinkLead, getGroup1, getGroup1b, getGroupParameter, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setStrucNo, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isProtein, isSelected, isWithinStructure, scaleToScreen, selectAtoms, setGroup, 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
static Monomer validateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
protected PhosphorusMonomer set3(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
Atom getP()
boolean isPhosphorusMonomer()
public boolean isPyrimidine()
isPyrimidine
in class Group
public java.lang.Object getStructure()
getStructure
in class Group
public STR getProteinStructureType()
getProteinStructureType
in class Monomer
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter
in class Monomer
protected boolean isCA2(Monomer possiblyPreviousMonomer)
public javajs.util.Quat getQuaternion(char qType)
getQuaternion
in class Group
protected javajs.util.Quat getQuaternionP()
javajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class Monomer
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class Group