public class AlphaMonomer extends Monomer
| Modifier and Type | Field and Description |
|---|---|
(package private) static byte[] |
alphaOffsets |
protected javajs.util.P3 |
nitrogenHydrogenPoint |
ProteinStructure |
proteinStructure |
backboneBlockVis, bioPolymer, monomerIndex, offsetschain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList| Modifier | Constructor and Description |
|---|---|
protected |
AlphaMonomer() |
| Modifier and Type | Method and Description |
|---|---|
Atom |
getAtom(byte specialAtomID) |
javajs.util.P3 |
getAtomPoint(byte specialAtomID) |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
STR |
getProteinStructureSubType() |
STR |
getProteinStructureType() |
javajs.util.Quat |
getQuaternion(char qType) |
protected javajs.util.Quat |
getQuaternionAlpha(char qType) |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qType) |
protected javajs.util.P3 |
getQuaternionFrameCenterAlpha(char qType) |
int |
getStrucNo() |
Structure |
getStructure() |
(package private) boolean |
isAlphaMonomer() |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isHelix() |
boolean |
isProtein()
group ID-based definition
|
boolean |
isSheet() |
boolean |
isWithinStructure(STR type) |
int |
setProteinStructureType(STR type,
int monomerIndexCurrent) |
void |
setStrucNo(int n) |
(package private) void |
setStructure(ProteinStructure ps) |
(package private) static Monomer |
validateAndAllocateA(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, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, toStringstatic final byte[] alphaOffsets
public ProteinStructure proteinStructure
protected javajs.util.P3 nitrogenHydrogenPoint
public boolean isProtein()
Groupstatic Monomer validateAndAllocateA(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
boolean isAlphaMonomer()
public Structure getStructure()
getStructure in class Groupvoid setStructure(ProteinStructure ps)
public void setStrucNo(int n)
setStrucNo in class Monomerpublic STR getProteinStructureType()
getProteinStructureType in class Monomerpublic STR getProteinStructureSubType()
getProteinStructureSubType in class Grouppublic int getStrucNo()
getStrucNo in class Grouppublic int setProteinStructureType(STR type, int monomerIndexCurrent)
setProteinStructureType in class Grouptype - monomerIndexCurrent - a pointer to the current ProteinStructurepublic final Atom getAtom(byte specialAtomID)
public final javajs.util.P3 getAtomPoint(byte specialAtomID)
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter in class Monomerjavajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter in class Monomerpublic boolean isWithinStructure(STR type)
isWithinStructure in class Groupprotected javajs.util.P3 getQuaternionFrameCenterAlpha(char qType)
public java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
getHelixData in class Grouppublic javajs.util.Quat getQuaternion(char qType)
getQuaternion in class Groupprotected javajs.util.Quat getQuaternionAlpha(char qType)