NucleicPolymer (Jmol 16.3.55 API)

java.lang.Object

org.jmol.modelsetbio.BioPolymer

org.jmol.modelsetbio.PhosphorusPolymer

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 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 Type

Method

Description

protected static int

addHydrogenBond(Lst<Bond> vAtoms, Atom atom1, Atom atom2)

protected boolean

calcEtaThetaAngles()

void

calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)

Methods inherited from class BioPolymer
calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoint, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidpoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSequence, getType, getWingVectors, isCyclic, isNucleic, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, setAtomBits, setAtomBitsAndClear, setConformation, toString

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

Field Details
- isDssrSet
  
  public boolean isDssrSet
- htGroup1
  
  public static Map<String,String> htGroup1
Method Details
- calcEtaThetaAngles
  
  protected boolean calcEtaThetaAngles()
  
  Overrides:
  
  calcEtaThetaAngles in class BioPolymer
- calcRasmolHydrogenBonds
  
  public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
  
  Overrides:
  
  calcRasmolHydrogenBonds in class BioPolymer
  
  Parameters:
  
  polymer -
  
  bsA -
  
  bsB -
  
  vAtoms -
  
  nMaxPerResidue -
  
  min -
  
  checkDistances -
  
  dsspIgnoreHydrogens -
- addHydrogenBond
  
  protected static int addHydrogenBond(Lst<Bond> vAtoms, Atom atom1, Atom atom2)