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 javax.vecmath.Point3f |
ptTemp |
alphaOffsets, nitrogenHydrogenPoint, proteinStructure
bioPolymer, monomerIndex, offsets
chain, firstAtomIndex, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
Modifier | Constructor and Description |
---|---|
private |
AminoMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets) |
Modifier and Type | Method and Description |
---|---|
(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.
|
(package private) Atom |
getCarbonylCarbonAtom() |
Atom |
getCarbonylOxygenAtom() |
(package private) javax.vecmath.Point3f |
getExplicitNH() |
(package private) Atom |
getInitiatorAtom() |
boolean |
getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint,
javax.vecmath.Vector3f vNH,
boolean jmolHPoint,
boolean dsspIgnoreHydrogens) |
Atom |
getNitrogenAtom() |
(package private) javax.vecmath.Point3f |
getNitrogenHydrogenPoint() |
java.lang.String |
getProteinStructureTag() |
Quaternion |
getQuaternion(char qType) |
(package private) javax.vecmath.Point3f |
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 |
isBondedCorrectly(int offset1,
int offset2,
int firstAtomIndex,
byte[] offsets,
Atom[] atoms) |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isWithinStructure(EnumStructure type) |
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, getProteinStructure, getProteinStructureSubType, getProteinStructureType, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, setProteinStructureId, setProteinStructureType, setStructure, validateAndAllocate
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getGroups, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, 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 final javax.vecmath.Point3f ptTemp
private static final float beta
private AminoMonomer(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 firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
private static boolean isBondedCorrectly(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()
javax.vecmath.Point3f getNitrogenHydrogenPoint()
javax.vecmath.Point3f getExplicitNH()
public boolean getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint, javax.vecmath.Vector3f vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class AlphaMonomer
public Quaternion getQuaternion(char qType)
getQuaternion
in class AlphaMonomer
public boolean isWithinStructure(EnumStructure type)
isWithinStructure
in class Group
public java.lang.String getStructureId()
getStructureId
in class Monomer
public java.lang.String getProteinStructureTag()
getProteinStructureTag
in class Group