Package org.jmol.modelsetbio
Class AminoMonomer
- java.lang.Object
-
- org.jmol.modelset.Group
-
- org.jmol.modelsetbio.Monomer
-
- org.jmol.modelsetbio.AlphaMonomer
-
- org.jmol.modelsetbio.AminoMonomer
-
- All Implemented Interfaces:
Structure
public class AminoMonomer extends AlphaMonomer
-
-
Field Summary
Fields Modifier and Type Field Description private static float
beta
private static byte
C
private static byte
CA
(package private) static byte[]
interestingAminoAtomIDs
private static byte
N
(package private) boolean
nhChecked
private static byte
O
private static byte
OT
private javajs.util.P3
ptTemp
-
Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets, nitrogenHydrogenPoint, proteinStructure
-
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
-
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
-
-
Constructor Summary
Constructors Modifier Constructor Description protected
AminoMonomer()
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
clear(BS bs, Atom a, boolean andH)
(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.BS
getBSSideChain()
Atom
getCarbonylCarbonAtom()
Atom
getCarbonylOxygenAtom()
Atom
getExplicitNH()
(package private) Atom
getInitiatorAtom()
boolean
getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
Atom
getNitrogenAtom()
(package private) javajs.util.P3
getNitrogenHydrogenPoint()
java.lang.String
getProteinStructureTag()
javajs.util.Quat
getQuaternion(char qType)
(package private) javajs.util.P3
getQuaternionFrameCenter(char qType)
java.lang.String
getStructureId()
(package private) Atom
getTerminatorAtom()
(package private) boolean
hasOAtom()
(package private) boolean
isAminoMonomer()
private static boolean
isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
private static boolean
isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
(package private) boolean
isConnectedAfter(Monomer possiblyPreviousMonomer)
void
resetHydrogenPoint()
(package private) static Monomer
validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
-
Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructureSubType, getProteinStructureType, getQuaternionAlpha, getQuaternionFrameCenterAlpha, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, isWithinStructure, setProteinStructureType, setStrucNo, setStructure, validateAndAllocateA
-
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, updateOffsetsForAlternativeLocations
-
Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, toString
-
-
-
-
Field Detail
-
CA
private static final byte CA
- See Also:
- Constant Field Values
-
O
private static final byte O
- See Also:
- Constant Field Values
-
N
private static final byte N
- See Also:
- Constant Field Values
-
C
private static final byte C
- See Also:
- Constant Field Values
-
OT
private static final byte OT
- See Also:
- Constant Field Values
-
interestingAminoAtomIDs
static final byte[] interestingAminoAtomIDs
-
nhChecked
boolean nhChecked
-
beta
private static final float beta
- See Also:
- Constant Field Values
-
ptTemp
private javajs.util.P3 ptTemp
-
-
Method Detail
-
validateAndAllocate
static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
-
isBondedCorrectlyRange
private static boolean isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
-
isBondedCorrectly
private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
-
isAminoMonomer
boolean isAminoMonomer()
-
getNitrogenAtom
public Atom getNitrogenAtom()
- Overrides:
getNitrogenAtom
in classGroup
-
getCarbonylCarbonAtom
public Atom getCarbonylCarbonAtom()
-
getCarbonylOxygenAtom
public Atom getCarbonylOxygenAtom()
- Overrides:
getCarbonylOxygenAtom
in classGroup
-
getInitiatorAtom
Atom getInitiatorAtom()
- Overrides:
getInitiatorAtom
in classMonomer
-
getTerminatorAtom
Atom getTerminatorAtom()
- Overrides:
getTerminatorAtom
in classMonomer
-
hasOAtom
boolean hasOAtom()
-
isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Overrides:
isConnectedAfter
in classAlphaMonomer
-
findNearestAtomIndex
void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Description copied from class:Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.- Overrides:
findNearestAtomIndex
in classMonomer
-
resetHydrogenPoint
public void resetHydrogenPoint()
-
getNitrogenHydrogenPoint
javajs.util.P3 getNitrogenHydrogenPoint()
-
getExplicitNH
public Atom getExplicitNH()
-
getNHPoint
public boolean getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
-
getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in classAlphaMonomer
- Returns:
- center
-
getQuaternion
public javajs.util.Quat getQuaternion(char qType)
- Overrides:
getQuaternion
in classAlphaMonomer
- Returns:
- quaternion
-
getStructureId
public java.lang.String getStructureId()
- Overrides:
getStructureId
in classMonomer
-
getProteinStructureTag
public java.lang.String getProteinStructureTag()
- Overrides:
getProteinStructureTag
in classGroup
-
getBSSideChain
public BS getBSSideChain()
- Overrides:
getBSSideChain
in classGroup
-
-