public class AlphaMonomer extends Monomer
Modifier and Type | Field and Description |
---|---|
(package private) static byte[] |
alphaOffsets |
protected javajs.util.P3 |
nitrogenHydrogenPoint |
ProteinStructure |
proteinStructure |
bioPolymer, monomerIndex, offsets
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, htGroup, lastAtomIndex, leadAtomIndex, 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() |
java.lang.Object |
getStructure() |
(package private) boolean |
isAlphaMonomer() |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isHelix() |
boolean |
isProtein() |
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) |
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLinkGroup, getCrossLinkLead, getGroup1, getGroup1b, getGroupParameter, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, scaleToScreen, selectAtoms, setGroup, setShapeVisibility, toString
static final byte[] alphaOffsets
public ProteinStructure proteinStructure
protected javajs.util.P3 nitrogenHydrogenPoint
static Monomer validateAndAllocateA(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
boolean isAlphaMonomer()
public java.lang.Object getStructure()
getStructure
in class Group
void setStructure(ProteinStructure ps)
public void setStrucNo(int n)
setStrucNo
in class Monomer
public STR getProteinStructureType()
getProteinStructureType
in class Monomer
public STR getProteinStructureSubType()
getProteinStructureSubType
in class Group
public int getStrucNo()
getStrucNo
in class Group
public int setProteinStructureType(STR type, int monomerIndexCurrent)
setProteinStructureType
in class Group
type
- 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 Monomer
javajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class Monomer
public boolean isWithinStructure(STR type)
isWithinStructure
in class Group
protected javajs.util.P3 getQuaternionFrameCenterAlpha(char qType)
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class Group
public javajs.util.Quat getQuaternion(char qType)
getQuaternion
in class Group
protected javajs.util.Quat getQuaternionAlpha(char qType)