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
pt0
Fields 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
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Method Summary
Modifier and TypeMethodDescriptionprotected boolean
void
calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vHBonds, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) protected float
calculateRamachandranHelixAngle
(int m, char qtype) void
calculateStructures
(boolean alphaOnly) Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.protected void
void
setStructureList
(Map<STR, float[]> structureList) Methods inherited from class org.jmol.modelsetbio.AlphaPolymer
addStructure, addStructureProtected, clearStructures, getControlPoint, getProteinStructure, setStructureBS
Methods 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:
resetHydrogenPoints
in classBioPolymer
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calcPhiPsiAngles
protected boolean calcPhiPsiAngles()- Overrides:
calcPhiPsiAngles
in classBioPolymer
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calculateRamachandranHelixAngle
protected float calculateRamachandranHelixAngle(int m, char qtype) - Overrides:
calculateRamachandranHelixAngle
in classBioPolymer
- 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:
calcRasmolHydrogenBonds
in classBioPolymer
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calculateStructures
public void calculateStructures(boolean alphaOnly) Description copied from class:AlphaPolymer
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
- Overrides:
calculateStructures
in 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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