Package org.jmol.modelsetbio
Class AlphaMonomer
- java.lang.Object
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- org.jmol.modelset.Group
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- org.jmol.modelsetbio.Monomer
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- org.jmol.modelsetbio.AlphaMonomer
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- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
AminoMonomer
public class AlphaMonomer extends Monomer
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Field Summary
Fields Modifier and Type Field Description (package private) static byte[]
alphaOffsets
protected javajs.util.P3
nitrogenHydrogenPoint
ProteinStructure
proteinStructure
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Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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Fields inherited from class org.jmol.modelset.Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors Modifier Constructor Description protected
AlphaMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Atom
getAtom(byte specialAtomID)
javajs.util.P3
getAtomPoint(byte specialAtomID)
java.lang.Object
getHelixData(int tokType, char qType, int mStep)
STR
getProteinStructureSubType()
STR
getProteinStructureType()
javajs.util.Quat
getQuaternion(char qType)
protected javajs.util.Quat
getQuaternionAlpha(char qType)
(package private) javajs.util.P3
getQuaternionFrameCenter(char qType)
protected javajs.util.P3
getQuaternionFrameCenterAlpha(char qType)
int
getStrucNo()
Structure
getStructure()
(package private) boolean
isAlphaMonomer()
(package private) boolean
isConnectedAfter(Monomer possiblyPreviousMonomer)
boolean
isHelix()
boolean
isProtein()
group ID-based definitionboolean
isSheet()
boolean
isWithinStructure(STR type)
int
setProteinStructureType(STR type, int monomerIndexCurrent)
void
setStrucNo(int n)
(package private) void
setStructure(ProteinStructure ps)
(package private) static Monomer
validateAndAllocateA(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
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Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, updateOffsetsForAlternativeLocations
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Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, toString
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Field Detail
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alphaOffsets
static final byte[] alphaOffsets
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proteinStructure
public ProteinStructure proteinStructure
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nitrogenHydrogenPoint
protected javajs.util.P3 nitrogenHydrogenPoint
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Method Detail
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isProtein
public boolean isProtein()
Description copied from class:Group
group ID-based definition
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validateAndAllocateA
static Monomer validateAndAllocateA(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
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isAlphaMonomer
boolean isAlphaMonomer()
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getStructure
public Structure getStructure()
- Overrides:
getStructure
in classGroup
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setStructure
void setStructure(ProteinStructure ps)
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setStrucNo
public void setStrucNo(int n)
- Overrides:
setStrucNo
in classMonomer
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureType
in classMonomer
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getProteinStructureSubType
public STR getProteinStructureSubType()
- Overrides:
getProteinStructureSubType
in classGroup
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getStrucNo
public int getStrucNo()
- Overrides:
getStrucNo
in classGroup
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setProteinStructureType
public int setProteinStructureType(STR type, int monomerIndexCurrent)
- Overrides:
setProteinStructureType
in classGroup
- Parameters:
type
-monomerIndexCurrent
- a pointer to the current ProteinStructure- Returns:
- a pointer to this ProteinStructure
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getAtom
public final Atom getAtom(byte specialAtomID)
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getAtomPoint
public final javajs.util.P3 getAtomPoint(byte specialAtomID)
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Specified by:
isConnectedAfter
in classMonomer
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getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in classMonomer
- Returns:
- center
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isWithinStructure
public boolean isWithinStructure(STR type)
- Overrides:
isWithinStructure
in classGroup
- Returns:
- T/F
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getQuaternionFrameCenterAlpha
protected javajs.util.P3 getQuaternionFrameCenterAlpha(char qType)
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getHelixData
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
- Overrides:
getHelixData
in classGroup
- Returns:
- helix data of some sort
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getQuaternion
public javajs.util.Quat getQuaternion(char qType)
- Overrides:
getQuaternion
in classGroup
- Returns:
- quaternion
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getQuaternionAlpha
protected javajs.util.Quat getQuaternionAlpha(char qType)
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