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,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
|
Methods inherited from class org.jmol.modelsetbio.Monomer |
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getInitiatorAtom, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getQuaternionFrameCenter, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getTerminatorAtom, getWingAtom, getWingAtomPoint, isDna, isNucleic, isProtein, isRna, resetHydrogenPoint, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations |
Methods inherited from class org.jmol.modelset.Group |
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getMinZ, getModel, getModelIndex, getOmega, getPhi, getPsi, getQuaternion, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setMinZ, setModelSet, setOmega, setPhi, setPsi, setShapeVisibility, setStraightness, toString |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
alphaOffsets
static final byte[] alphaOffsets
proteinStructure
private ProteinStructure proteinStructure
nitrogenHydrogenPoint
protected javax.vecmath.Point3f nitrogenHydrogenPoint
AlphaMonomer
AlphaMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
validateAndAllocate
static Monomer validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes,
Atom[] atoms)
isAlphaMonomer
boolean isAlphaMonomer()
getProteinStructure
public ProteinStructure getProteinStructure()
- Overrides:
getProteinStructure
in class Monomer
getStructure
public java.lang.Object getStructure()
- Overrides:
getStructure
in class Group
setStructure
void setStructure(ProteinStructure proteinStructure)
- Overrides:
setStructure
in class Monomer
getProteinStructureType
public byte getProteinStructureType()
- Overrides:
getProteinStructureType
in class Monomer
getProteinStructureID
public int getProteinStructureID()
- Overrides:
getProteinStructureID
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 javax.vecmath.Point3f getAtomPoint(byte specialAtomID)
isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfter
in class Monomer