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java.lang.Objectorg.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.AlphaMonomer
public class AlphaMonomer
Field Summary | |
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(package private) static byte[] |
alphaOffsets
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protected javax.vecmath.Point3f |
nitrogenHydrogenPoint
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protected ProteinStructure |
proteinStructure
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Fields inherited from class org.jmol.modelsetbio.Monomer |
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bioPolymer, monomerIndex, offsets |
Fields inherited from class org.jmol.modelset.Group |
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chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags |
Constructor Summary | |
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AlphaMonomer(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets)
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Method Summary | |
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Atom |
getAtom(byte specialAtomID)
|
javax.vecmath.Point3f |
getAtomPoint(byte specialAtomID)
|
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep)
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ProteinStructure |
getProteinStructure()
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byte |
getProteinStructureSubType()
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byte |
getProteinStructureType()
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Quaternion |
getQuaternion(char qType)
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(package private) javax.vecmath.Point3f |
getQuaternionFrameCenter(char qType)
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int |
getStrucNo()
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java.lang.Object |
getStructure()
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(package private) boolean |
isAlphaMonomer()
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(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer)
|
boolean |
isHelix()
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boolean |
isProtein()
|
boolean |
isSheet()
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void |
setProteinStructureId(int id)
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int |
setProteinStructureType(byte iType,
int monomerIndexCurrent)
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(package private) void |
setStructure(ProteinStructure proteinStructure)
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(package private) static Monomer |
validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstIndex,
int lastIndex,
int[] specialAtomIndexes)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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static final byte[] alphaOffsets
protected ProteinStructure proteinStructure
protected javax.vecmath.Point3f nitrogenHydrogenPoint
Constructor Detail |
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AlphaMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
Method Detail |
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public boolean isProtein()
isProtein
in class Monomer
static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
boolean isAlphaMonomer()
public ProteinStructure getProteinStructure()
getProteinStructure
in class Monomer
public java.lang.Object getStructure()
getStructure
in class Group
void setStructure(ProteinStructure proteinStructure)
setStructure
in class Monomer
public void setProteinStructureId(int id)
setProteinStructureId
in class Monomer
public byte getProteinStructureType()
getProteinStructureType
in class Monomer
public byte getProteinStructureSubType()
getProteinStructureSubType
in class Group
public int getStrucNo()
getStrucNo
in class Group
public boolean isHelix()
isHelix
in class Monomer
public boolean isSheet()
isSheet
in class Monomer
public int setProteinStructureType(byte iType, int monomerIndexCurrent)
setProteinStructureType
in class Group
iType
- monomerIndexCurrent
- a pointer to the current ProteinStructure
public final Atom getAtom(byte specialAtomID)
public final javax.vecmath.Point3f getAtomPoint(byte specialAtomID)
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter
in class Monomer
javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class Monomer
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class Group
public Quaternion getQuaternion(char qType)
getQuaternion
in class Group
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