Package org.jmol.modelsetbio
Class NucleicPolymer
- java.lang.Object
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- org.jmol.modelsetbio.BioPolymer
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- org.jmol.modelsetbio.PhosphorusPolymer
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- org.jmol.modelsetbio.NucleicPolymer
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- All Implemented Interfaces:
Structure
public class NucleicPolymer extends PhosphorusPolymer
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Field Summary
Fields Modifier and Type Field Description static Map<String,String>
htGroup1
boolean
isDssrSet
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Fields 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 Constructor Description NucleicPolymer(Monomer[] monomers)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static int
addHydrogenBond(javajs.util.Lst<Bond> vAtoms, Atom atom1, Atom atom2)
protected boolean
calcEtaThetaAngles()
void
calcRasmolHydrogenBonds(BioPolymer polymer, javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
(package private) Atom
getNucleicPhosphorusAtom(int monomerIndex)
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Methods inherited from class org.jmol.modelsetbio.BioPolymer
calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoint, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isCyclic, isMonomerSelected, isNucleic, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, set, setAtomBits, setAtomBitsAndClear, setConformation, toString
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Constructor Detail
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NucleicPolymer
NucleicPolymer(Monomer[] monomers)
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Method Detail
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getNucleicPhosphorusAtom
Atom getNucleicPhosphorusAtom(int monomerIndex)
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calcEtaThetaAngles
protected boolean calcEtaThetaAngles()
- Overrides:
calcEtaThetaAngles
in classBioPolymer
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calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(BioPolymer polymer, javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
- Overrides:
calcRasmolHydrogenBonds
in classBioPolymer
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