org.jmol.modelsetbio

Class NucleicPolymer

java.lang.Object

org.jmol.modelset.Polymer

org.jmol.modelsetbio.BioPolymer

org.jmol.modelsetbio.NucleicPolymer

public class NucleicPolymer
extends BioPolymer

Field Summary

Fields inherited from class org.jmol.modelsetbio.BioPolymer

bsSelectedMonomers, hasWingPoints, haveParameters, invalidControl, monomers, sheetSmoothing

Fields inherited from class org.jmol.modelset.Polymer

bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, 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(java.util.List vAtoms, Atom atom1, Atom atom2)
protected boolean	calcEtaThetaAngles()
void	calcRasmolHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List 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, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, java.util.BitSet bsWritten)

Methods inherited from class org.jmol.modelsetbio.BioPolymer

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

Methods inherited from class org.jmol.modelset.Polymer

addSecondaryStructure, calculateStructures, calculateStruts, getType, 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(Polymer polymer,
                           java.util.BitSet bsA,
                           java.util.BitSet bsB,
                           java.util.List vAtoms,
                           int nMaxPerResidue,
                           int[][][] min,
                           boolean checkDistances,
                           boolean dsspIgnoreHydrogens)

Overrides:

calcRasmolHydrogenBonds in class Polymer

addHydrogenBond

protected static int addHydrogenBond(java.util.List vAtoms,
                  Atom atom1,
                  Atom atom2)

getPdbData

public void getPdbData(Viewer viewer,
              char ctype,
              char qtype,
              int mStep,
              int derivType,
              boolean isDraw,
              java.util.BitSet bsAtoms,
              OutputStringBuffer pdbATOM,
              java.lang.StringBuffer pdbCONECT,
              java.util.BitSet bsSelected,
              boolean addHeader,
              boolean bothEnds,
              java.util.BitSet bsWritten)

Overrides:

getPdbData in class Polymer