org.jmol.modelsetbio
Class AlphaMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
- Direct Known Subclasses:
- AminoMonomer
public class AlphaMonomer
- extends Monomer
Constructor Summary |
AlphaMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
Methods inherited from class org.jmol.modelsetbio.Monomer |
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, 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, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setShapeVisibility, toString |
alphaOffsets
static final byte[] alphaOffsets
proteinStructure
protected ProteinStructure proteinStructure
nitrogenHydrogenPoint
protected Point3f nitrogenHydrogenPoint
AlphaMonomer
AlphaMonomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
isProtein
public boolean isProtein()
- Overrides:
isProtein
in class Monomer
validateAndAllocate
static Monomer validateAndAllocate(Chain chain,
String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes)
isAlphaMonomer
boolean isAlphaMonomer()
getProteinStructure
public ProteinStructure getProteinStructure()
- Overrides:
getProteinStructure
in class Monomer
getStructure
public Object getStructure()
- Overrides:
getStructure
in class Group
setStructure
void setStructure(ProteinStructure proteinStructure)
- Overrides:
setStructure
in class Monomer
setProteinStructureId
public void setProteinStructureId(int id)
- Overrides:
setProteinStructureId
in class Monomer
getProteinStructureType
public byte getProteinStructureType()
- Overrides:
getProteinStructureType
in class Monomer
getProteinStructureSubType
public byte getProteinStructureSubType()
- Overrides:
getProteinStructureSubType
in class Group
getStrucNo
public int getStrucNo()
- Overrides:
getStrucNo
in class Group
isHelix
public boolean isHelix()
- Overrides:
isHelix
in class Monomer
isSheet
public boolean isSheet()
- Overrides:
isSheet
in class Monomer
setProteinStructureType
public int setProteinStructureType(byte iType,
int monomerIndexCurrent)
- Overrides:
setProteinStructureType
in class Group
- Parameters:
iType
- monomerIndexCurrent
- a pointer to the current ProteinStructure
- Returns:
- a pointer to this ProteinStructure
getAtom
public final Atom getAtom(byte specialAtomID)
getAtomPoint
public final Point3f getAtomPoint(byte specialAtomID)
isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfter
in class Monomer
getQuaternionFrameCenter
Point3f getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in class Monomer
- Returns:
- center
getHelixData
public Object getHelixData(int tokType,
char qType,
int mStep)
- Overrides:
getHelixData
in class Group
- Returns:
- helix data of some sort
getQuaternion
public Quaternion getQuaternion(char qType)
- Overrides:
getQuaternion
in class Group
- Returns:
- quaternion