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
Method Summary |
void |
calcHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
(package private) Atom |
getNucleicPhosphorusAtom(int monomerIndex)
|
void |
getPdbData(char ctype,
char qtype,
int mStep,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
java.lang.StringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
java.util.BitSet bsWritten)
|
(package private) boolean |
hasWingPoints()
|
(package private) void |
lookForHbonds(NucleicPolymer other,
java.util.BitSet bsA,
java.util.BitSet bsB)
|
Methods inherited from class org.jmol.modelsetbio.BioPolymer |
allocateBioPolymer, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoints, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getMonomerCount, getMonomers, getPdbData, getPointPoint, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, isMonomerSelected, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, setConformation |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HBOND_MASK
private static final short HBOND_MASK
- See Also:
- Constant Field Values
NucleicPolymer
NucleicPolymer(Monomer[] monomers)
getNucleicPhosphorusAtom
Atom getNucleicPhosphorusAtom(int monomerIndex)
hasWingPoints
boolean hasWingPoints()
- Overrides:
hasWingPoints
in class BioPolymer
calcHydrogenBonds
public void calcHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB)
- Overrides:
calcHydrogenBonds
in class Polymer
lookForHbonds
void lookForHbonds(NucleicPolymer other,
java.util.BitSet bsA,
java.util.BitSet bsB)
getPdbData
public void getPdbData(char ctype,
char qtype,
int mStep,
int derivType,
boolean isDraw,
java.util.BitSet bsAtoms,
java.lang.StringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
java.util.BitSet bsWritten)
- Overrides:
getPdbData
in class Polymer