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

Field Summary

Fields

Modifier and Type	Field and Description
(package private) BioPolymer	bioPolymer
(package private) int	monomerIndex
protected byte[]	offsets

Fields inherited from class org.jmol.modelset.Group

chain, firstAtomIndex, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	Monomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)

Method Summary

Methods

Modifier and Type	Method and Description
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()
(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)
(package private) Atom	getInitiatorAtom()
Atom	getLeadAtom()
int	getMonomerIndex()
(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)
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)
boolean	isHelix()
boolean	isLeadAtom(int atomIndex)
boolean	isSheet()
protected static byte[]	scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)
(package private) void	setBioPolymer(BioPolymer polymer, int index)
void	setProteinStructureId(int id)
(package private) void	setStructure(ProteinStructure proteinstructure)
(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

Field Detail

bioPolymer

BioPolymer bioPolymer

offsets

protected final byte[] offsets

monomerIndex

int monomerIndex

Constructor Detail

Monomer

protected Monomer(Chain chain,
       java.lang.String group3,
       int seqcode,
       int firstAtomIndex,
       int lastAtomIndex,
       byte[] interestingAtomOffsets)

Method Detail

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