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, cyclicFlag, 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,
javajs.util.BS bsA,
javajs.util.BS bsB,
javajs.util.Lst<Bond> vAtoms,
int nMaxPerResidue,
int[][][] min,
boolean checkDistances,
boolean dsspIgnoreHydrogens) |
(package private) Atom |
getNucleicPhosphorusAtom(int monomerIndex) |
calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoint, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isCyclic, isMonomerSelected, isNucleic, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, set, setAtomBits, setAtomBitsAndClear, setConformation
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, javajs.util.BS bsA, javajs.util.BS bsB, javajs.util.Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens)
calcRasmolHydrogenBonds
in class BioPolymer