public class AlphaPolymer extends BioPolymer
Modifier and Type | Class and Description |
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private static class |
AlphaPolymer.Code |
Modifier and Type | Field and Description |
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private static java.lang.String[] |
dsspTypes |
int |
pt0 |
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
Constructor and Description |
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AlphaPolymer(Monomer[] monomers,
int pt0) |
Modifier and Type | Method and Description |
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void |
addStructure(STR type,
java.lang.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,
java.lang.String structureID,
int serialID,
int strandCount,
int indexStart,
int indexEnd) |
private void |
addStructuresFromTags(STR[] tags) |
private float[] |
calculateAnglesInDegrees() |
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 |
clearStructures() |
private void |
extendRuns(STR[] tags) |
protected javajs.util.P3 |
getControlPoint(int i,
javajs.util.V3 v) |
ProteinStructure |
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 type
|
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
AlphaPolymer(Monomer[] monomers, int pt0)
public ProteinStructure getProteinStructure(int monomerIndex)
getProteinStructure
in class BioPolymer
protected javajs.util.P3 getControlPoint(int i, javajs.util.V3 v)
getControlPoint
in class BioPolymer
public void addStructure(STR type, java.lang.String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, javajs.util.BS bsAssigned)
public boolean addStructureProtected(STR type, java.lang.String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
public void clearStructures()
clearStructures
in class BioPolymer
public void calculateStructures(boolean alphaOnly)
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
alphaOnly
- caught by AminoPolymer and discarded if desiredprivate float[] calculateAnglesInDegrees()
private AlphaPolymer.Code[] calculateCodes(float[] angles)
private void checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[] codes, float[] angles)
private STR[] calculateRunsFourOrMore(AlphaPolymer.Code[] codes)
private void extendRuns(STR[] tags)
private void searchForTurns(AlphaPolymer.Code[] codes, float[] angles, STR[] tags)
private void addStructuresFromTags(STR[] tags)
public int setStructureBS(int count, int dsspType, STR type, javajs.util.BS bs, boolean doOffset)
count
- dsspType
- type
- bs
- doOffset
- allows us to examine just a portion of the