public class NucleicPolymer extends BioPolymer
bsSelectedMonomers, hasWingPoints, haveParameters, invalidControl, monomers, sheetSmoothing
bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, 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 vAtoms,
Atom atom1,
Atom atom2) |
protected boolean |
calcEtaThetaAngles() |
void |
calcRasmolHydrogenBonds(Polymer polymer,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.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,
java.util.BitSet bsAtoms,
OutputStringBuffer pdbATOM,
java.lang.StringBuffer pdbCONECT,
java.util.BitSet bsSelected,
boolean addHeader,
boolean bothEnds,
java.util.BitSet bsWritten) |
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
addSecondaryStructure, calculateStructures, calculateStruts, getType, setStructureList
NucleicPolymer(Monomer[] monomers)
Atom getNucleicPhosphorusAtom(int monomerIndex)
protected boolean calcEtaThetaAngles()
calcEtaThetaAngles
in class BioPolymer
public void calcRasmolHydrogenBonds(Polymer polymer, java.util.BitSet bsA, java.util.BitSet bsB, java.util.List vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class Polymer
public void getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, java.util.BitSet bsWritten)
getPdbData
in class Polymer