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 boolean |
calcBioParameters()
|
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 |
getBioPolymerIndexInModel()
|
int |
getBioPolymerLength()
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(package private) void |
getConformation(Atom[] atoms,
java.util.BitSet bsConformation,
int conformationIndex)
clear out bits that are not associated with the nth conformation
counting for each residue from the beginning of the file listing |
protected boolean |
getCrossLink(int i,
java.util.List<java.lang.Integer> vReturn)
|
private boolean |
getCrossLink(int i,
java.util.List<java.lang.Integer> vReturn,
Group group)
|
boolean |
getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn)
|
protected java.lang.Object |
getHelixData2(int tokType,
char qType,
int mStep)
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(package private) Atom |
getInitiatorAtom()
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Atom |
getLeadAtom()
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int |
getMonomerIndex()
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(package private) void |
getMonomerSequenceAtoms(java.util.BitSet bsInclude,
java.util.BitSet bsResult)
|
java.util.Map<java.lang.String,java.lang.Object> |
getMyInfo()
|
ProteinStructure |
getProteinStructure()
|
EnumStructure |
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)
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java.lang.String |
getStructureId()
|
(package private) Atom |
getTerminatorAtom()
|
java.lang.String |
getUniqueID()
|
Atom |
getWingAtom()
|
boolean |
haveParameters()
|
(package private) abstract boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer)
|
boolean |
isConnectedPrevious()
|
boolean |
isCrossLinked(Group g)
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boolean |
isHelix()
|
boolean |
isLeadAtom(int atomIndex)
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boolean |
isSheet()
|
protected static byte[] |
scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs)
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(package private) void |
setBioPolymer(BioPolymer polymer,
int index)
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void |
setProteinStructureId(int id)
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(package private) void |
setStructure(ProteinStructure proteinstructure)
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(package private) void |
updateOffsetsForAlternativeLocations(Atom[] atoms,
java.util.BitSet bsSelected)
|
Methods inherited from class org.jmol.modelset.Group |
addAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, getStructure, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isProtein, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, 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
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
getMonomerIndex
public int getMonomerIndex()
- Overrides:
getMonomerIndex
in class Group
getBioPolymerIndexInModel
public int getBioPolymerIndexInModel()
- Overrides:
getBioPolymerIndexInModel
in class Group
scanForOffsets
protected static byte[] scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs)
setStructure
void setStructure(ProteinStructure proteinstructure)
- Parameters:
proteinstructure
-
getProteinStructure
public ProteinStructure getProteinStructure()
getProteinStructureType
public EnumStructure getProteinStructureType()
- Overrides:
getProteinStructureType
in class Group
isHelix
public boolean isHelix()
isSheet
public boolean isSheet()
setProteinStructureId
public void setProteinStructureId(int id)
- Overrides:
setProteinStructureId
in class Group
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)
isLeadAtom
public boolean isLeadAtom(int atomIndex)
- Overrides:
isLeadAtom
in class Group
- Returns:
- T/F
getLeadAtom
public final Atom getLeadAtom()
- Overrides:
getLeadAtom
in class Group
getWingAtom
public final Atom getWingAtom()
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
-
calcBioParameters
protected boolean calcBioParameters()
- Overrides:
calcBioParameters
in class Group
haveParameters
public boolean haveParameters()
- Overrides:
haveParameters
in class Group
getMyInfo
public java.util.Map<java.lang.String,java.lang.Object> getMyInfo()
getStructureId
public java.lang.String getStructureId()
- Overrides:
getStructureId
in class Group
getConformation
void getConformation(Atom[] atoms,
java.util.BitSet bsConformation,
int conformationIndex)
- clear out bits that are not associated with the nth conformation
counting for each residue from the beginning of the file listing
- Parameters:
atoms
- bsConformation
- conformationIndex
- will be >= 0
updateOffsetsForAlternativeLocations
final void updateOffsetsForAlternativeLocations(Atom[] atoms,
java.util.BitSet bsSelected)
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)
- Parameters:
qtype
-
- Returns:
- center
getHelixData2
protected java.lang.Object getHelixData2(int tokType,
char qType,
int mStep)
getUniqueID
public java.lang.String getUniqueID()
isCrossLinked
public boolean isCrossLinked(Group g)
- Overrides:
isCrossLinked
in class Group
- Returns:
- T/F
getCrossLinkLeadAtomIndexes
public boolean getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn)
- Overrides:
getCrossLinkLeadAtomIndexes
in class Group
- Returns:
- T/F
getCrossLink
protected boolean getCrossLink(int i,
java.util.List<java.lang.Integer> vReturn)
getCrossLink
private boolean getCrossLink(int i,
java.util.List<java.lang.Integer> vReturn,
Group group)
isConnectedPrevious
public boolean isConnectedPrevious()
- Overrides:
isConnectedPrevious
in class Group