public class AlphaMonomer extends Monomer
| Modifier and Type | Field and Description |
|---|---|
(package private) static byte[] |
alphaOffsets |
protected javax.vecmath.Point3f |
nitrogenHydrogenPoint |
protected ProteinStructure |
proteinStructure |
bioPolymer, monomerIndex, offsetschain, firstAtomIndex, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags| Constructor and Description |
|---|
AlphaMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets) |
| Modifier and Type | Method and Description |
|---|---|
Atom |
getAtom(byte specialAtomID) |
javax.vecmath.Point3f |
getAtomPoint(byte specialAtomID) |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
ProteinStructure |
getProteinStructure() |
EnumStructure |
getProteinStructureSubType() |
EnumStructure |
getProteinStructureType() |
Quaternion |
getQuaternion(char qType) |
(package private) javax.vecmath.Point3f |
getQuaternionFrameCenter(char qType) |
int |
getStrucNo() |
java.lang.Object |
getStructure() |
(package private) boolean |
isAlphaMonomer() |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isHelix() |
boolean |
isProtein() |
boolean |
isSheet() |
void |
setProteinStructureId(int id) |
int |
setProteinStructureType(EnumStructure type,
int monomerIndexCurrent) |
(package private) void |
setStructure(ProteinStructure proteinStructure) |
(package private) static Monomer |
validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes) |
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setShapeVisibility, toStringstatic final byte[] alphaOffsets
protected ProteinStructure proteinStructure
protected javax.vecmath.Point3f nitrogenHydrogenPoint
AlphaMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
static Monomer validateAndAllocate(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 setProteinStructureId(int id)
setProteinStructureId 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 javax.vecmath.Point3f getAtomPoint(byte specialAtomID)
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter in class Monomerjavax.vecmath.Point3f getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter in class Monomerpublic java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
getHelixData in class Grouppublic Quaternion getQuaternion(char qType)
getQuaternion in class Group