org.jmol.modelsetbio.NucleicPolymer

All Implemented Interfaces:: Structure

public class NucleicPolymer extends PhosphorusPolymer

Field Summary

Fields

Modifier and Type

Field

Description

static Map<String,String>

htGroup1

boolean

isDssrSet

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
Constructor Summary

Constructors

Constructor

Description

NucleicPolymer(Monomer[] monomers)
Method Summary

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)

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- isDssrSet
  
  public boolean isDssrSet
- htGroup1
  
  public static Map<String,String> htGroup1
Constructor Details
- NucleicPolymer
  
  NucleicPolymer(Monomer[] monomers)
Method Details
- getNucleicPhosphorusAtom
  
  Atom getNucleicPhosphorusAtom(int monomerIndex)
- calcEtaThetaAngles
  
  protected boolean calcEtaThetaAngles()
  
  Overrides:
  
  calcEtaThetaAngles in class BioPolymer
- 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 class BioPolymer
- addHydrogenBond
  
  protected static int addHydrogenBond(javajs.util.Lst<Bond> vAtoms, Atom atom1, Atom atom2)

Class NucleicPolymer

Field Summary

Fields inherited from class org.jmol.modelsetbio.BioPolymer

Constructor Summary

Method Summary

Methods inherited from class org.jmol.modelsetbio.BioPolymer

Methods inherited from class java.lang.Object

Field Details

isDssrSet

htGroup1

Constructor Details

NucleicPolymer

Method Details

getNucleicPhosphorusAtom

calcEtaThetaAngles

calcRasmolHydrogenBonds

addHydrogenBond