org.jmol.modelsetbio
Class AminoMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
org.jmol.modelsetbio.AminoMonomer
public class AminoMonomer
- extends AlphaMonomer
Field Summary |
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
|
Constructor Summary |
private |
AminoMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
Method Summary |
(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()
|
(package private) javax.vecmath.Point3f |
getCarbonylCarbonAtomPoint()
|
(package private) Atom |
getCarbonylOxygenAtom()
|
(package private) javax.vecmath.Point3f |
getCarbonylOxygenAtomPoint()
|
(package private) Atom |
getInitiatorAtom()
|
boolean |
getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint,
javax.vecmath.Vector3f vNH)
|
(package private) Atom |
getNitrogenAtom()
|
(package private) javax.vecmath.Point3f |
getNitrogenAtomPoint()
|
(package private) javax.vecmath.Point3f |
getNitrogenHydrogenPoint()
|
Quaternion |
getQuaternion(char qType)
|
(package private) javax.vecmath.Point3f |
getQuaternionFrameCenter(char qType)
|
(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)
|
void |
resetHydrogenPoint()
|
(package private) static Monomer |
validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes,
Atom[] atoms)
|
Methods inherited from class org.jmol.modelsetbio.AlphaMonomer |
getAtom, getAtomPoint, getProteinStructure, getProteinStructureID, getProteinStructureType, getStructure, isAlphaMonomer, isHelix, isSheet, setProteinStructureType, setStructure |
Methods inherited from class org.jmol.modelsetbio.Monomer |
checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getWingAtom, getWingAtomPoint, isDna, isNucleic, isProtein, isRna, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations |
Methods inherited from class org.jmol.modelset.Group |
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getMinZ, getModel, getModelIndex, getOmega, getPhi, getPsi, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setMinZ, setModelSet, setOmega, setPhi, setPsi, setShapeVisibility, setStraightness, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
CA
private static final byte CA
- See Also:
- Constant Field Values
O
private static final byte O
- See Also:
- Constant Field Values
N
private static final byte N
- See Also:
- Constant Field Values
C
private static final byte C
- See Also:
- Constant Field Values
OT
private static final byte OT
- See Also:
- Constant Field Values
interestingAminoAtomIDs
static final byte[] interestingAminoAtomIDs
nhChecked
boolean nhChecked
ptTemp
private final javax.vecmath.Point3f ptTemp
beta
private static final float beta
- See Also:
- Constant Field Values
AminoMonomer
private AminoMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
validateAndAllocate
static Monomer validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes,
Atom[] atoms)
isBondedCorrectly
private static boolean isBondedCorrectly(int offset1,
int offset2,
int firstAtomIndex,
byte[] offsets,
Atom[] atoms)
isBondedCorrectly
private static boolean isBondedCorrectly(int firstAtomIndex,
byte[] offsets,
Atom[] atoms)
isAminoMonomer
boolean isAminoMonomer()
getNitrogenAtom
Atom getNitrogenAtom()
getNitrogenAtomPoint
javax.vecmath.Point3f getNitrogenAtomPoint()
getCarbonylCarbonAtom
Atom getCarbonylCarbonAtom()
getCarbonylCarbonAtomPoint
javax.vecmath.Point3f getCarbonylCarbonAtomPoint()
getCarbonylOxygenAtom
Atom getCarbonylOxygenAtom()
getCarbonylOxygenAtomPoint
javax.vecmath.Point3f getCarbonylOxygenAtomPoint()
getInitiatorAtom
Atom getInitiatorAtom()
- Overrides:
getInitiatorAtom
in class Monomer
getTerminatorAtom
Atom getTerminatorAtom()
- Overrides:
getTerminatorAtom
in class Monomer
hasOAtom
boolean hasOAtom()
isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Overrides:
isConnectedAfter
in class AlphaMonomer
findNearestAtomIndex
void findNearestAtomIndex(int x,
int y,
Atom[] closest,
short madBegin,
short madEnd)
- Description copied from class:
Monomer
- Selects LeadAtom when this Monomer is clicked iff it is
closer to the user.
- Overrides:
findNearestAtomIndex
in class Monomer
resetHydrogenPoint
public void resetHydrogenPoint()
- Overrides:
resetHydrogenPoint
in class Monomer
getNitrogenHydrogenPoint
javax.vecmath.Point3f getNitrogenHydrogenPoint()
getNHPoint
public boolean getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint,
javax.vecmath.Vector3f vNH)
getQuaternionFrameCenter
javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in class Monomer
getQuaternion
public Quaternion getQuaternion(char qType)
- Overrides:
getQuaternion
in class Group