public class AlphaMonomer extends Monomer
| Modifier and Type | Field and Description |
|---|---|
(package private) static byte[] |
alphaOffsets |
protected P3 |
nitrogenHydrogenPoint |
protected ProteinStructure |
proteinStructure |
bioPolymer, monomerIndex, offsetschain, firstAtomIndex, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, seqcode, shapeVisibilityFlags| Modifier | Constructor and Description |
|---|---|
protected |
AlphaMonomer() |
| Modifier and Type | Method and Description |
|---|---|
Atom |
getAtom(byte specialAtomID) |
P3 |
getAtomPoint(byte specialAtomID) |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
ProteinStructure |
getProteinStructure() |
EnumStructure |
getProteinStructureSubType() |
EnumStructure |
getProteinStructureType() |
Quaternion |
getQuaternion(char qType) |
protected Quaternion |
getQuaternionAlpha(char qType) |
(package private) P3 |
getQuaternionFrameCenter(char qType) |
protected P3 |
getQuaternionFrameCenterAlpha(char qType) |
int |
getStrucNo() |
java.lang.Object |
getStructure() |
(package private) boolean |
isAlphaMonomer() |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isHelix() |
boolean |
isProtein() |
boolean |
isSheet() |
int |
setProteinStructureType(EnumStructure type,
int monomerIndexCurrent) |
void |
setStrucNo(int n) |
(package private) void |
setStructure(ProteinStructure proteinStructure) |
(package private) static Monomer |
validateAndAllocateA(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes) |
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLead, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3For, getGroupID, getGroupIdFor, getGroupIndex, getGroupInfo, getGroupParameter, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroup, setGroupIndex, setGroupParameter, setModelSet, setShapeVisibility, toStringstatic final byte[] alphaOffsets
protected ProteinStructure proteinStructure
protected P3 nitrogenHydrogenPoint
static Monomer validateAndAllocateA(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
boolean isAlphaMonomer()
public ProteinStructure getProteinStructure()
getProteinStructure in class Monomerpublic java.lang.Object getStructure()
getStructure in class Groupvoid setStructure(ProteinStructure proteinStructure)
setStructure in class Monomerpublic void setStrucNo(int n)
setStrucNo in class Monomerpublic EnumStructure getProteinStructureType()
getProteinStructureType in class Monomerpublic EnumStructure getProteinStructureSubType()
getProteinStructureSubType in class Grouppublic int getStrucNo()
getStrucNo in class Grouppublic int setProteinStructureType(EnumStructure type, int monomerIndexCurrent)
setProteinStructureType in class Grouptype - monomerIndexCurrent - a pointer to the current ProteinStructurepublic final Atom getAtom(byte specialAtomID)
public final P3 getAtomPoint(byte specialAtomID)
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter in class MonomerP3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter in class Monomerprotected P3 getQuaternionFrameCenterAlpha(char qType)
public java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
getHelixData in class Grouppublic Quaternion getQuaternion(char qType)
getQuaternion in class Groupprotected Quaternion getQuaternionAlpha(char qType)