Package org.jmol.modelsetbio
Class AminoPolymer
java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
org.jmol.modelsetbio.AminoPolymer
- All Implemented Interfaces:
Structure
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Field Summary
Fields inherited from class org.jmol.modelsetbio.AlphaPolymer
pt0Fields inherited from class org.jmol.modelsetbio.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 booleanvoidcalcRasmolHydrogenBonds(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) Uses Levitt invalid input: '&' Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.protected voidvoidsetStructureList(Map<STR, float[]> structureList) Methods inherited from class org.jmol.modelsetbio.AlphaPolymer
addStructure, addStructureProtected, clearStructures, getControlPoint, getProteinStructure, setStructureBSMethods inherited from class org.jmol.modelsetbio.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) Description copied from class:AlphaPolymerUses Levitt invalid input: '&' 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
- Overrides:
calculateStructuresin classAlphaPolymer- Parameters:
alphaOnly- caught by AminoPolymer and discarded if desired
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setStructureList
- Parameters:
structureList- protein only -- helix, sheet, turn definitions
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