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, offsets
chain, 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, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, 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, toString
static 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 Monomer
public java.lang.Object getStructure()
getStructure
in class Group
void setStructure(ProteinStructure proteinStructure)
setStructure
in class Monomer
public void setProteinStructureId(int id)
setProteinStructureId
in class Monomer
public EnumStructure getProteinStructureType()
getProteinStructureType
in class Monomer
public EnumStructure getProteinStructureSubType()
getProteinStructureSubType
in class Group
public int getStrucNo()
getStrucNo
in class Group
public int setProteinStructureType(EnumStructure type, int monomerIndexCurrent)
setProteinStructureType
in class Group
type
- 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 Monomer
javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class Monomer
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class Group
public Quaternion getQuaternion(char qType)
getQuaternion
in class Group