org.jmol.modelsetbio
Class Monomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
- Direct Known Subclasses:
- AlphaMonomer, CarbohydrateMonomer, PhosphorusMonomer
public abstract class Monomer
- extends Group
Constructor Summary |
protected |
Monomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] interestingAtomOffsets)
|
Method Summary |
protected static boolean |
checkOptional(byte[] offsets,
byte atom,
int firstAtomIndex,
int index)
|
(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. |
protected Atom |
getAtomFromOffsetIndex(int offsetIndex)
|
BioPolymer |
getBioPolymer()
|
int |
getBioPolymerIndex()
|
int |
getBioPolymerLength()
|
(package private) Atom |
getInitiatorAtom()
|
Atom |
getLeadAtom()
|
(package private) int |
getLeadAtomIndex()
|
(package private) javax.vecmath.Point3f |
getLeadAtomPoint()
|
(package private) void |
getMonomerSequenceAtoms(java.util.BitSet bsInclude,
java.util.BitSet bsResult)
|
java.util.Hashtable |
getMyInfo()
|
(package private) javax.vecmath.Point3f |
getPointAtomPoint()
|
ProteinStructure |
getProteinStructure()
|
byte |
getProteinStructureType()
|
(package private) javax.vecmath.Point3f |
getQuaternionFrameCenter(char qtype)
|
int |
getSelectedMonomerCount()
|
int |
getSelectedMonomerIndex()
|
protected Atom |
getSpecialAtom(byte[] interestingIDs,
byte specialAtomID)
|
protected javax.vecmath.Point3f |
getSpecialAtomPoint(byte[] interestingIDs,
byte specialAtomID)
|
(package private) static java.lang.String |
getStructureTypeName(byte type)
|
(package private) Atom |
getTerminatorAtom()
|
Atom |
getWingAtom()
|
javax.vecmath.Point3f |
getWingAtomPoint()
|
(package private) abstract boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer)
|
boolean |
isDna()
|
boolean |
isHelix()
|
boolean |
isNucleic()
|
boolean |
isProtein()
|
boolean |
isRna()
|
boolean |
isSheet()
|
void |
resetHydrogenPoint()
|
protected static byte[] |
scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs)
|
(package private) void |
setBioPolymer(BioPolymer polymer,
int index)
|
(package private) void |
setStructure(ProteinStructure proteinstructure)
|
(package private) void |
updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected,
int nAltLocInModel)
|
Methods inherited from class org.jmol.modelset.Group |
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getMinZ, getModel, getModelIndex, getOmega, getPhi, getProteinStructureID, getPsi, getQuaternion, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, getStructure, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setMinZ, setModelSet, setOmega, setPhi, setProteinStructureType, setPsi, setShapeVisibility, setStraightness, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
bioPolymer
BioPolymer bioPolymer
offsets
protected final byte[] offsets
monomerIndex
protected int monomerIndex
Monomer
protected Monomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] interestingAtomOffsets)
setBioPolymer
void setBioPolymer(BioPolymer polymer,
int index)
getSelectedMonomerCount
public int getSelectedMonomerCount()
- Overrides:
getSelectedMonomerCount
in class Group
getSelectedMonomerIndex
public int getSelectedMonomerIndex()
- Overrides:
getSelectedMonomerIndex
in class Group
getBioPolymer
public BioPolymer getBioPolymer()
getBioPolymerLength
public int getBioPolymerLength()
- Overrides:
getBioPolymerLength
in class Group
getBioPolymerIndex
public int getBioPolymerIndex()
- Overrides:
getBioPolymerIndex
in class Group
scanForOffsets
protected static byte[] scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs)
isDna
public boolean isDna()
- Overrides:
isDna
in class Group
isRna
public boolean isRna()
- Overrides:
isRna
in class Group
isProtein
public final boolean isProtein()
- Overrides:
isProtein
in class Group
isNucleic
public final boolean isNucleic()
- Overrides:
isNucleic
in class Group
setStructure
void setStructure(ProteinStructure proteinstructure)
getProteinStructure
public ProteinStructure getProteinStructure()
getProteinStructureType
public byte getProteinStructureType()
- Overrides:
getProteinStructureType
in class Group
isHelix
public boolean isHelix()
isSheet
public boolean isSheet()
getAtomFromOffsetIndex
protected final Atom getAtomFromOffsetIndex(int offsetIndex)
getSpecialAtom
protected final Atom getSpecialAtom(byte[] interestingIDs,
byte specialAtomID)
getSpecialAtomPoint
protected final javax.vecmath.Point3f getSpecialAtomPoint(byte[] interestingIDs,
byte specialAtomID)
getLeadAtomIndex
final int getLeadAtomIndex()
getLeadAtom
public final Atom getLeadAtom()
- Overrides:
getLeadAtom
in class Group
getLeadAtomPoint
final javax.vecmath.Point3f getLeadAtomPoint()
getWingAtom
public final Atom getWingAtom()
getWingAtomPoint
public final javax.vecmath.Point3f getWingAtomPoint()
getPointAtomPoint
final javax.vecmath.Point3f getPointAtomPoint()
getInitiatorAtom
Atom getInitiatorAtom()
getTerminatorAtom
Atom getTerminatorAtom()
isConnectedAfter
abstract boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
findNearestAtomIndex
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.
- Parameters:
x
- y
- closest
- madBegin
- madEnd
-
getMyInfo
public java.util.Hashtable getMyInfo()
- Overrides:
getMyInfo
in class Group
getStructureTypeName
static java.lang.String getStructureTypeName(byte type)
updateOffsetsForAlternativeLocations
final void updateOffsetsForAlternativeLocations(java.util.BitSet bsSelected,
int nAltLocInModel)
getMonomerSequenceAtoms
final void getMonomerSequenceAtoms(java.util.BitSet bsInclude,
java.util.BitSet bsResult)
checkOptional
protected static final boolean checkOptional(byte[] offsets,
byte atom,
int firstAtomIndex,
int index)
getQuaternionFrameCenter
javax.vecmath.Point3f getQuaternionFrameCenter(char qtype)
resetHydrogenPoint
public void resetHydrogenPoint()