Structure
NucleicMonomer
public class PhosphorusMonomer extends Monomer
Modifier and Type | Field | Description |
---|---|---|
private static float |
MAX_ADJACENT_PHOSPHORUS_DISTANCE |
|
protected static byte |
P |
|
private static byte[] |
phosphorusOffsets |
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
bioPolymer, monomerIndex, offsets
Modifier | Constructor | Description |
---|---|---|
protected |
PhosphorusMonomer() |
Modifier and Type | Method | 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) |
addAtoms, 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, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toString
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, updateOffsetsForAlternativeLocations
protected static final byte P
private static final byte[] phosphorusOffsets
private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
public final boolean isNucleic()
Group
static Monomer validateAndAllocateP(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
public boolean isDna()
Group
public boolean isRna()
Group
public boolean isPurine()
Group
public boolean isPyrimidine()
Group
isPyrimidine
in class Group
public Structure 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