Package org.jmol.modelsetbio
Class AlphaPolymer
java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
- All Implemented Interfaces:
Structure
- Direct Known Subclasses:
AminoPolymer
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final String[]
int
Specifically for mmTF bitset setting of structuresFields inherited from class org.jmol.modelsetbio.BioPolymer
bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, cyclicFlag, hasStructure, hasWingPoints, haveParameters, invalidControl, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, monomers, reversed, sheetSmoothing, twistedSheets, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addStructure
(STR type, String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, javajs.util.BS bsAssigned) boolean
addStructureProtected
(STR type, String structureID, int serialID, int strandCount, int indexStart, int indexEnd) private void
addStructuresFromTags
(STR[] tags) private float[]
private AlphaPolymer.Code[]
calculateCodes
(float[] angles) private STR[]
calculateRunsFourOrMore
(AlphaPolymer.Code[] codes) void
calculateStructures
(boolean alphaOnly) Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.private void
checkBetaSheetAlphaHelixOverlap
(AlphaPolymer.Code[] codes, float[] angles) void
private void
extendRuns
(STR[] tags) protected javajs.util.P3
getControlPoint
(int i, javajs.util.V3 v) getProteinStructure
(int monomerIndex) private void
searchForTurns
(AlphaPolymer.Code[] codes, float[] angles, STR[] tags) int
setStructureBS
(int count, int dsspType, STR type, javajs.util.BS bs, boolean doOffset) bits in the bitset determines the typeMethods inherited from class org.jmol.modelsetbio.BioPolymer
calcEtaThetaAngles, calcParameters, calcPhiPsiAngles, calcRasmolHydrogenBonds, calcSelectedMonomersCount, calculateRamachandranHelixAngle, findNearestAtomIndex, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isCyclic, isMonomerSelected, isNucleic, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, set, setAtomBits, setAtomBitsAndClear, setConformation, toString
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Field Details
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pt0
public int pt0Specifically for mmTF bitset setting of structures -
dsspTypes
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Constructor Details
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AlphaPolymer
AlphaPolymer(Monomer[] monomers, int pt0)
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Method Details
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getProteinStructure
- Overrides:
getProteinStructure
in classBioPolymer
- Returns:
- "HELIX" "TURN" etc
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getControlPoint
protected javajs.util.P3 getControlPoint(int i, javajs.util.V3 v) - Overrides:
getControlPoint
in classBioPolymer
- Returns:
- the leadPoint unless a protein sheet residue (see AlphaPolymer)
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addStructure
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addStructureProtected
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clearStructures
public void clearStructures()- Overrides:
clearStructures
in classBioPolymer
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calculateStructures
public void calculateStructures(boolean alphaOnly) Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.Levitt and Greer
Automatic Identification of Secondary Structure in Globular Proteins
J.Mol.Biol.(1977) 114, 181-293
http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf
- Parameters:
alphaOnly
- caught by AminoPolymer and discarded if desired
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calculateAnglesInDegrees
private float[] calculateAnglesInDegrees() -
calculateCodes
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checkBetaSheetAlphaHelixOverlap
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calculateRunsFourOrMore
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extendRuns
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searchForTurns
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addStructuresFromTags
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setStructureBS
bits in the bitset determines the type- Parameters:
count
-dsspType
-type
-bs
-doOffset
- allows us to examine just a portion of the- Returns:
- updated count
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