org.jmol.modelsetbio
Class NucleicMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.PhosphorusMonomer
org.jmol.modelsetbio.NucleicMonomer
public class NucleicMonomer
- extends PhosphorusMonomer
Field Summary |
(package private) Point3f |
baseCenter
|
private static byte |
C1P
|
private static byte |
C2
|
private static byte |
C3Pr
|
private static byte |
C4
|
private static byte |
C4P
|
private static byte |
C5
|
(package private) static byte |
C6
|
private static byte |
C8
|
private static byte |
H3T
|
private static byte |
H5T
|
private boolean |
hasRnaO2Prime
|
private static byte[] |
heavyAtomIndexes
|
(package private) static byte[] |
interestingNucleicAtomIDs
|
private static byte |
N1
|
private static byte |
N2
|
private static byte |
N3
|
private static byte |
N4
|
private static byte |
N6
|
private static byte |
N7
|
private static byte |
N9
|
private static byte |
NP
|
private static byte |
O1P
|
private static byte |
O2
|
private static byte |
O2P
|
private static byte |
O2Pr
|
private static byte |
O3Pr
|
private static byte |
O4
|
private static byte |
O5Pr
|
private static byte |
O6
|
private static byte[] |
ring5OffsetIndexes
|
private static byte[] |
ring6OffsetIndexes
|
Constructor Summary |
NucleicMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
Method Summary |
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. |
void |
getBaseRing6Points(Point3f[] ring6Points)
|
(package private) Atom |
getC1P()
|
(package private) Atom |
getC2()
|
(package private) Atom |
getC4P()
|
boolean |
getCrossLinkLeadAtomIndexes(List vReturn)
|
boolean |
getEdgePoints(Point3f[] pts)
|
Object |
getHelixData(int tokType,
char qType,
int mStep)
|
(package private) Atom |
getN0()
|
(package private) Atom |
getN1()
|
(package private) Atom |
getN2()
|
(package private) Atom |
getN3()
|
(package private) Atom |
getN4()
|
(package private) Atom |
getN6()
|
(package private) Atom |
getO2()
|
(package private) Atom |
getO4()
|
(package private) Atom |
getO6()
|
byte |
getProteinStructureType()
|
Quaternion |
getQuaternion(char qType)
|
(package private) Point3f |
getQuaternionFrameCenter(char qType)
|
(package private) Atom |
getTerminatorAtom()
|
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer)
|
boolean |
isCrossLinked(Group g)
|
boolean |
isDna()
|
boolean |
isGuanine()
|
boolean |
isNucleicMonomer()
|
boolean |
isPurine()
|
boolean |
isPyrimidine()
|
boolean |
isRna()
|
boolean |
maybeGetBaseRing5Points(Point3f[] ring5Points)
|
void |
setModelClickability()
|
static Monomer |
validateAndAllocate(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes)
|
Methods inherited from class org.jmol.modelsetbio.Monomer |
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getProteinStructure, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isHelix, isLeadAtom, isProtein, isSheet, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, updateOffsetsForAlternativeLocations |
Methods inherited from class org.jmol.modelset.Group |
getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, toString |
C6
static final byte C6
- See Also:
- Constant Field Values
O2Pr
private static final byte O2Pr
- See Also:
- Constant Field Values
C5
private static final byte C5
- See Also:
- Constant Field Values
N1
private static final byte N1
- See Also:
- Constant Field Values
C2
private static final byte C2
- See Also:
- Constant Field Values
N3
private static final byte N3
- See Also:
- Constant Field Values
C4
private static final byte C4
- See Also:
- Constant Field Values
O2
private static final byte O2
- See Also:
- Constant Field Values
N7
private static final byte N7
- See Also:
- Constant Field Values
C8
private static final byte C8
- See Also:
- Constant Field Values
N9
private static final byte N9
- See Also:
- Constant Field Values
O4
private static final byte O4
- See Also:
- Constant Field Values
O6
private static final byte O6
- See Also:
- Constant Field Values
N4
private static final byte N4
- See Also:
- Constant Field Values
NP
private static final byte NP
- See Also:
- Constant Field Values
N6
private static final byte N6
- See Also:
- Constant Field Values
N2
private static final byte N2
- See Also:
- Constant Field Values
H5T
private static final byte H5T
- See Also:
- Constant Field Values
O5Pr
private static final byte O5Pr
- See Also:
- Constant Field Values
H3T
private static final byte H3T
- See Also:
- Constant Field Values
O3Pr
private static final byte O3Pr
- See Also:
- Constant Field Values
C3Pr
private static final byte C3Pr
- See Also:
- Constant Field Values
O1P
private static final byte O1P
- See Also:
- Constant Field Values
O2P
private static final byte O2P
- See Also:
- Constant Field Values
C1P
private static final byte C1P
- See Also:
- Constant Field Values
C4P
private static final byte C4P
- See Also:
- Constant Field Values
interestingNucleicAtomIDs
static final byte[] interestingNucleicAtomIDs
hasRnaO2Prime
private boolean hasRnaO2Prime
ring6OffsetIndexes
private static final byte[] ring6OffsetIndexes
ring5OffsetIndexes
private static final byte[] ring5OffsetIndexes
heavyAtomIndexes
private static final byte[] heavyAtomIndexes
baseCenter
Point3f baseCenter
NucleicMonomer
NucleicMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
validateAndAllocate
public static Monomer validateAndAllocate(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes)
isNucleicMonomer
public boolean isNucleicMonomer()
isDna
public boolean isDna()
- Overrides:
isDna
in class PhosphorusMonomer
isRna
public boolean isRna()
- Overrides:
isRna
in class PhosphorusMonomer
isPurine
public boolean isPurine()
- Overrides:
isPurine
in class PhosphorusMonomer
isPyrimidine
public boolean isPyrimidine()
- Overrides:
isPyrimidine
in class PhosphorusMonomer
isGuanine
public boolean isGuanine()
getProteinStructureType
public byte getProteinStructureType()
- Overrides:
getProteinStructureType
in class PhosphorusMonomer
getC1P
Atom getC1P()
getC2
Atom getC2()
getC4P
Atom getC4P()
getN1
Atom getN1()
getN3
Atom getN3()
getN2
Atom getN2()
getN4
Atom getN4()
getN6
Atom getN6()
getO2
Atom getO2()
getO4
Atom getO4()
getO6
Atom getO6()
getTerminatorAtom
Atom getTerminatorAtom()
- Overrides:
getTerminatorAtom
in class Monomer
getBaseRing6Points
public void getBaseRing6Points(Point3f[] ring6Points)
maybeGetBaseRing5Points
public boolean maybeGetBaseRing5Points(Point3f[] ring5Points)
isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Overrides:
isConnectedAfter
in class PhosphorusMonomer
findNearestAtomIndex
public 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
setModelClickability
public void setModelClickability()
getN0
Atom getN0()
getHelixData
public Object getHelixData(int tokType,
char qType,
int mStep)
- Overrides:
getHelixData
in class PhosphorusMonomer
- Returns:
- helix data of some sort
getQuaternionFrameCenter
Point3f getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in class PhosphorusMonomer
- Returns:
- center
getQuaternion
public Quaternion getQuaternion(char qType)
- Overrides:
getQuaternion
in class PhosphorusMonomer
- Returns:
- quaternion
isCrossLinked
public boolean isCrossLinked(Group g)
- Overrides:
isCrossLinked
in class Monomer
- Returns:
- T/F
getCrossLinkLeadAtomIndexes
public boolean getCrossLinkLeadAtomIndexes(List vReturn)
- Overrides:
getCrossLinkLeadAtomIndexes
in class Monomer
- Returns:
- T/F
getEdgePoints
public boolean getEdgePoints(Point3f[] pts)