public class NucleicPolymer extends BioPolymer
bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, hasWingPoints, haveParameters, invalidControl, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, monomers, sheetSmoothing, 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(java.util.List<Bond> vAtoms,
Atom atom1,
Atom atom2) |
protected boolean |
calcEtaThetaAngles() |
void |
calcRasmolHydrogenBonds(BioPolymer 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) |
addSecondaryStructure, allocateBioPolymer, calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, calculateStructures, calculateStructures, calculateStruts, 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, 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, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class BioPolymer
protected static int addHydrogenBond(java.util.List<Bond> vAtoms, Atom atom1, Atom atom2)
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)
getPdbData
in class BioPolymer