public class NucleicPolymer extends 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 and Description |
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NucleicPolymer(Monomer[] monomers) |
Modifier and Type | Method and Description |
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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) |
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
NucleicPolymer(Monomer[] monomers)
Atom getNucleicPhosphorusAtom(int monomerIndex)
protected boolean calcEtaThetaAngles()
calcEtaThetaAngles
in class BioPolymer
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, JmolList<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class BioPolymer
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)
getPdbData
in class BioPolymer