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(java.util.List<Bond> vAtoms,
Atom atom1,
Atom atom2)
|
protected boolean |
calcEtaThetaAngles()
|
void |
calcRasmolHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.List<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,
java.util.BitSet bsAtoms,
java.util.BitSet bsSelected,
boolean bothEnds,
boolean isDraw,
boolean addHeader,
LabelToken[] tokens,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
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 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,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.List<Bond> vAtoms,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens)
- Overrides:
calcRasmolHydrogenBonds
in class Polymer
addHydrogenBond
protected static int addHydrogenBond(java.util.List<Bond> vAtoms,
Atom atom1,
Atom atom2)
getPdbData
public void getPdbData(Viewer viewer,
char ctype,
char qtype,
int mStep,
int derivType,
java.util.BitSet bsAtoms,
java.util.BitSet bsSelected,
boolean bothEnds,
boolean isDraw,
boolean addHeader,
LabelToken[] tokens,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsWritten)
- Overrides:
getPdbData
in class Polymer