org.jmol.modelsetbio

Class NucleicPolymer

java.lang.Object

org.jmol.modelsetbio.BioPolymer

org.jmol.modelsetbio.NucleicPolymer

public class NucleicPolymer
extends BioPolymer

Field Summary

Fields inherited from class org.jmol.modelsetbio.BioPolymer

bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, 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 and Description
NucleicPolymer(Monomer[] monomers)

Method Summary

Methods

Modifier and Type	Method and Description
protected static int	addHydrogenBond(JmolList<Bond> vAtoms, Atom atom1, Atom atom2)
protected boolean	calcEtaThetaAngles()
void	calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, JmolList<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
(package private) Atom	getNucleicPhosphorusAtom(int monomerIndex)
void	getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, BS bsAtoms, BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, OutputStringBuilder pdbATOM, SB pdbCONECT, BS bsWritten)

Methods inherited from class org.jmol.modelsetbio.BioPolymer

calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateDssp, calculateRamachandranHelixAngle, calculateStruts, clearStructures, findNearestAtomIndex, getConformation, getControlPoint, getControlPoints, getGroups, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isDna, isMonomerSelected, isRna, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, resetHydrogenPoints, setConformation, setStructureList

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NucleicPolymer

NucleicPolymer(Monomer[] monomers)

Method Detail

getNucleicPhosphorusAtom

Atom getNucleicPhosphorusAtom(int monomerIndex)

calcEtaThetaAngles

protected boolean calcEtaThetaAngles()

Overrides:

calcEtaThetaAngles in class BioPolymer

calcRasmolHydrogenBonds

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

Overrides:

calcRasmolHydrogenBonds in class BioPolymer

addHydrogenBond

protected static int addHydrogenBond(JmolList<Bond> vAtoms,
                  Atom atom1,
                  Atom atom2)

getPdbData

public void getPdbData(Viewer viewer,
              char ctype,
              char qtype,
              int mStep,
              int derivType,
              BS bsAtoms,
              BS bsSelected,
              boolean bothEnds,
              boolean isDraw,
              boolean addHeader,
              LabelToken[] tokens,
              OutputStringBuilder pdbATOM,
              SB pdbCONECT,
              BS bsWritten)

Overrides:

getPdbData in class BioPolymer