Class AminoPolymer
java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
org.jmol.modelsetbio.AminoPolymer
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Structure
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Field Summary
Fields inherited from class AlphaPolymer
pt0Fields inherited from class BioPolymer
bioPolymerIndexInModel, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean//////////////////////////////////////////////voidcalcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) ///////////////////////////////////////////////protected floatcalculateRamachandranHelixAngle(int m, char qtype) voidcalculateStructures(boolean alphaOnly) /////////////////////////////////////////////////////protected voidvoidsetStructureList(Map<STR, float[]> structureList) Methods inherited from class AlphaPolymer
addStructure, addStructureProtected, clearStructures, getControlPoint, getProteinStructure, setStructureBSMethods inherited from class BioPolymer
calcEtaThetaAngles, calcParameters, calcSelectedMonomersCount, findNearestAtomIndex, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidpoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getRange, getRangeGroups, getSequence, getType, getWingVectors, isCyclic, isNucleic, recalculateLeadMidpointsAndWingVectors, setAtomBits, setAtomBitsAndClear, setConformation, toString
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Method Details
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resetHydrogenPoints
protected void resetHydrogenPoints()- Overrides:
resetHydrogenPointsin classBioPolymer
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calcPhiPsiAngles
protected boolean calcPhiPsiAngles()//////////////////////////////////////////////- Overrides:
calcPhiPsiAnglesin classBioPolymer
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calculateRamachandranHelixAngle
protected float calculateRamachandranHelixAngle(int m, char qtype) - Overrides:
calculateRamachandranHelixAnglein classBioPolymer- Parameters:
m-qtype-- Returns:
- calculated value
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calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) ///////////////////////////////////////////////- Overrides:
calcRasmolHydrogenBondsin classBioPolymer- Parameters:
polymer-bsA-bsB-vHBonds-nMaxPerResidue-min-checkDistances-dsspIgnoreHydrogens-
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calculateStructures
public void calculateStructures(boolean alphaOnly) /////////////////////////////////////////////////////- Overrides:
calculateStructuresin classAlphaPolymer- Parameters:
alphaOnly- caught by AminoPolymer and discarded if desired
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setStructureList
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