public class PhosphorusMonomer extends Monomer
| Modifier and Type | Field and Description |
|---|---|
private static float |
MAX_ADJACENT_PHOSPHORUS_DISTANCE |
protected static byte |
P |
private static byte[] |
phosphorusOffsets |
backboneBlockVis, bioPolymer, monomerIndex, offsetschain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, 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) |
STR |
getProteinStructureType() |
javajs.util.Quat |
getQuaternion(char qType) |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qType) |
protected javajs.util.Quat |
getQuaternionP() |
Structure |
getStructure() |
protected boolean |
isCA2(Monomer possiblyPreviousMonomer) |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isDna()
group ID-based definition
|
boolean |
isNucleic()
group ID-based definition
|
boolean |
isPurine()
group ID-based definition
|
boolean |
isPyrimidine()
group ID-based definition
|
boolean |
isRna()
group ID-based definition
|
(package private) static Monomer |
validateAndAllocateP(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes) |
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, setStrucNo, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDnaByID, isNucleicMonomer, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toStringprotected static final byte P
private static final byte[] phosphorusOffsets
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
public final boolean isNucleic()
Groupstatic Monomer validateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
public boolean isDna()
Grouppublic boolean isRna()
Grouppublic boolean isPurine()
Grouppublic boolean isPyrimidine()
GroupisPyrimidine in class Grouppublic Structure getStructure()
getStructure in class Grouppublic STR getProteinStructureType()
getProteinStructureType in class Monomerboolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter in class Monomerprotected boolean isCA2(Monomer possiblyPreviousMonomer)
public javajs.util.Quat getQuaternion(char qType)
getQuaternion in class Groupprotected javajs.util.Quat getQuaternionP()
javajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter in class Monomerpublic java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
getHelixData in class Group