public class AminoMonomer extends AlphaMonomer
Modifier and Type | Field and Description |
---|---|
private static float |
beta |
private static byte |
C |
private static byte |
CA |
(package private) static byte[] |
interestingAminoAtomIDs |
private static byte |
N |
(package private) boolean |
nhChecked |
private static byte |
O |
private static byte |
OT |
private javajs.util.P3 |
ptTemp |
alphaOffsets, nitrogenHydrogenPoint, proteinStructure
bioPolymer, monomerIndex, offsets
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, htGroup, lastAtomIndex, leadAtomIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
Modifier | Constructor and Description |
---|---|
protected |
AminoMonomer() |
Modifier and Type | Method and Description |
---|---|
private void |
clear(BS bs,
Atom a,
boolean andH) |
(package private) void |
findNearestAtomIndex(int x,
int y,
Atom[] closest,
short madBegin,
short madEnd)
Selects LeadAtom when this Monomer is clicked iff it is
closer to the user.
|
BS |
getBSSideChain() |
(package private) Atom |
getCarbonylCarbonAtom() |
Atom |
getCarbonylOxygenAtom() |
javajs.util.P3 |
getExplicitNH() |
(package private) Atom |
getInitiatorAtom() |
boolean |
getNHPoint(javajs.util.P3 aminoHydrogenPoint,
javajs.util.V3 vNH,
boolean jmolHPoint,
boolean dsspIgnoreHydrogens) |
Atom |
getNitrogenAtom() |
(package private) javajs.util.P3 |
getNitrogenHydrogenPoint() |
java.lang.String |
getProteinStructureTag() |
javajs.util.Quat |
getQuaternion(char qType) |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qType) |
java.lang.String |
getStructureId() |
(package private) Atom |
getTerminatorAtom() |
(package private) boolean |
hasOAtom() |
(package private) boolean |
isAminoMonomer() |
private static boolean |
isBondedCorrectly(int firstAtomIndex,
byte[] offsets,
Atom[] atoms) |
private static boolean |
isBondedCorrectlyRange(int offset1,
int offset2,
int firstAtomIndex,
byte[] offsets,
Atom[] atoms) |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
void |
resetHydrogenPoint() |
(package private) static Monomer |
validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes,
Atom[] atoms) |
getAtom, getAtomPoint, getHelixData, getProteinStructureSubType, getProteinStructureType, getQuaternionAlpha, getQuaternionFrameCenterAlpha, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, isWithinStructure, setProteinStructureType, setStrucNo, setStructure, validateAndAllocateA
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLinkGroup, getCrossLinkLead, getGroup1, getGroup1b, getGroupParameter, getGroups, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getGroup3, getGroupInfo, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, scaleToScreen, selectAtoms, setGroup, setShapeVisibility, toString
private static final byte CA
private static final byte O
private static final byte N
private static final byte C
private static final byte OT
static final byte[] interestingAminoAtomIDs
boolean nhChecked
private static final float beta
private javajs.util.P3 ptTemp
static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
private static boolean isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
boolean isAminoMonomer()
public Atom getNitrogenAtom()
getNitrogenAtom
in class Group
Atom getCarbonylCarbonAtom()
public Atom getCarbonylOxygenAtom()
getCarbonylOxygenAtom
in class Group
Atom getInitiatorAtom()
getInitiatorAtom
in class Monomer
Atom getTerminatorAtom()
getTerminatorAtom
in class Monomer
boolean hasOAtom()
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter
in class AlphaMonomer
void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Monomer
findNearestAtomIndex
in class Monomer
public void resetHydrogenPoint()
javajs.util.P3 getNitrogenHydrogenPoint()
public javajs.util.P3 getExplicitNH()
public boolean getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
javajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class AlphaMonomer
public javajs.util.Quat getQuaternion(char qType)
getQuaternion
in class AlphaMonomer
public java.lang.String getStructureId()
getStructureId
in class Monomer
public java.lang.String getProteinStructureTag()
getProteinStructureTag
in class Group
public BS getBSSideChain()
getBSSideChain
in class Group