Package org.jmol.modelsetbio
Class NucleicPolymer
java.lang.Object
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.PhosphorusPolymer
org.jmol.modelsetbio.NucleicPolymer
- All Implemented Interfaces:
Structure
-
Field Summary
FieldsFields inherited from class org.jmol.modelsetbio.BioPolymer
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 Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected static int
addHydrogenBond
(javajs.util.Lst<Bond> vAtoms, Atom atom1, Atom atom2) protected boolean
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) Methods inherited from class org.jmol.modelsetbio.BioPolymer
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, toString
-
Field Details
-
isDssrSet
public boolean isDssrSet -
htGroup1
-
-
Constructor Details
-
NucleicPolymer
NucleicPolymer(Monomer[] monomers)
-
-
Method Details
-
getNucleicPhosphorusAtom
-
calcEtaThetaAngles
protected boolean calcEtaThetaAngles()- Overrides:
calcEtaThetaAngles
in classBioPolymer
-
calcRasmolHydrogenBonds
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) - Overrides:
calcRasmolHydrogenBonds
in classBioPolymer
-
addHydrogenBond
-