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
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Field Summary
FieldsFields inherited from class org.jmol.modelsetbio.BioPolymer
bioPolymerIndexInModel, 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
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Method Summary
Modifier and TypeMethodDescriptionprotected static int
addHydrogenBond
(Lst<Bond> vAtoms, Atom atom1, Atom atom2) protected boolean
void
calcRasmolHydrogenBonds
(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) Methods inherited from class org.jmol.modelsetbio.BioPolymer
calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoint, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidpoints, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSequence, getType, getWingVectors, isCyclic, isNucleic, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, setAtomBits, setAtomBitsAndClear, setConformation, toString
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Field Details
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isDssrSet
public boolean isDssrSet -
htGroup1
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Method Details
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calcEtaThetaAngles
protected boolean calcEtaThetaAngles()- Overrides:
calcEtaThetaAngles
in classBioPolymer
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calcRasmolHydrogenBonds
public void calcRasmolHydrogenBonds(BioPolymer polymer, BS bsA, BS bsB, Lst<Bond> vAtoms, int nMaxPerResidue, int[][][] min, boolean checkDistances, boolean dsspIgnoreHydrogens) - Overrides:
calcRasmolHydrogenBonds
in classBioPolymer
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addHydrogenBond
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