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, proteinStructurebackboneBlockVis, bioPolymer, monomerIndex, offsetschain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList| Modifier | Constructor and Description |
|---|---|
protected |
AminoMonomer() |
| Modifier and Type | Method and Description |
|---|---|
private void |
clear(javajs.util.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.
|
javajs.util.BS |
getBSSideChain() |
Atom |
getCarbonylCarbonAtom() |
Atom |
getCarbonylOxygenAtom() |
Atom |
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, validateAndAllocateAcheckOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, toStringprivate 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 Grouppublic Atom getCarbonylCarbonAtom()
public Atom getCarbonylOxygenAtom()
getCarbonylOxygenAtom in class GroupAtom getInitiatorAtom()
getInitiatorAtom in class MonomerAtom getTerminatorAtom()
getTerminatorAtom in class Monomerboolean hasOAtom()
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter in class AlphaMonomervoid findNearestAtomIndex(int x,
int y,
Atom[] closest,
short madBegin,
short madEnd)
MonomerfindNearestAtomIndex in class Monomerpublic void resetHydrogenPoint()
javajs.util.P3 getNitrogenHydrogenPoint()
public Atom 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 AlphaMonomerpublic javajs.util.Quat getQuaternion(char qType)
getQuaternion in class AlphaMonomerpublic java.lang.String getStructureId()
getStructureId in class Monomerpublic java.lang.String getProteinStructureTag()
getProteinStructureTag in class Grouppublic javajs.util.BS getBSSideChain()
getBSSideChain in class Groupprivate void clear(javajs.util.BS bs,
Atom a,
boolean andH)