public class NucleicPolymer extends PhosphorusPolymer
Modifier and Type | Field and Description |
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static java.util.Map<java.lang.String,java.lang.String> |
htGroup1 |
boolean |
isDssrSet |
bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, hasStructure, 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(javajs.util.Lst<Bond> vAtoms,
Atom atom1,
Atom atom2) |
protected boolean |
calcEtaThetaAngles() |
void |
calcRasmolHydrogenBonds(BioPolymer polymer,
BS bsA,
BS bsB,
javajs.util.Lst<Bond> vAtoms,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
(package private) Atom |
getNucleicPhosphorusAtom(int monomerIndex) |
setP
calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, calculateStruts, clearStructures, drawQuat, findNearestAtomIndex, getConformation, getControlPoint, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isMonomerSelected, isNucleic, isRna, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, set, setConformation, setStructureList
public boolean isDssrSet
public static java.util.Map<java.lang.String,java.lang.String> htGroup1
NucleicPolymer(Monomer[] monomers)
Atom getNucleicPhosphorusAtom(int monomerIndex)
protected boolean calcEtaThetaAngles()
calcEtaThetaAngles
in class BioPolymer
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, javajs.util.Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class BioPolymer