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
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 |
Method Summary |
protected static int |
addHydrogenBond(List vAtoms,
Atom atom1,
Atom atom2)
|
protected boolean |
calcEtaThetaAngles()
|
void |
calcRasmolHydrogenBonds(Polymer polymer,
BitSet bsA,
BitSet bsB,
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,
BitSet bsAtoms,
OutputStringBuffer pdbATOM,
StringBuffer pdbCONECT,
BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
NucleicPolymer
NucleicPolymer(Monomer[] monomers)
getNucleicPhosphorusAtom
Atom getNucleicPhosphorusAtom(int monomerIndex)
calcEtaThetaAngles
protected boolean calcEtaThetaAngles()
- Overrides:
calcEtaThetaAngles
in class BioPolymer
calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(Polymer polymer,
BitSet bsA,
BitSet bsB,
List vAtoms,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens)
- Overrides:
calcRasmolHydrogenBonds
in class Polymer
addHydrogenBond
protected static int addHydrogenBond(List vAtoms,
Atom atom1,
Atom atom2)
getPdbData
public void getPdbData(Viewer viewer,
char ctype,
char qtype,
int mStep,
int derivType,
boolean isDraw,
BitSet bsAtoms,
OutputStringBuffer pdbATOM,
StringBuffer pdbCONECT,
BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
BitSet bsWritten)
- Overrides:
getPdbData
in class Polymer