org.jmol.modelsetbio

Class AminoPolymer

public class AminoPolymer extends AlphaPolymer

Field Summary
booleanhasOAtoms
short[]mainchainHbondOffsets
static floatmaxHbondAlphaDistance
static floatmaxHbondAlphaDistance2
short[]min1Energies
short[]min1Indexes
short[]min2Energies
short[]min2Indexes
static floatminimumHbondDistance2
static doubleQConst
Constructor Summary
AminoPolymer(Monomer[] monomers)
Method Summary
voidbondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitSet bsA, BitSet bsB)
intcalcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)
voidcalcHydrogenBonds(BitSet bsA, BitSet bsB)
protected booleancalcPhiPsiAngles()
voidcalcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue)
voidcalcProteinMainchainHydrogenBonds(BitSet bsA, BitSet bsB)
voidcalculateStructures()
booleancheckWingAtoms()
voidcreateResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup, BitSet bsA, BitSet bsB)
voidfreeze()
voidgetPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)
booleanhasWingPoints()
voidinitializeHbondDataStructures()
static booleanisHelix(float psi, float phi)
static booleanisSheet(float psi, float phi)
static booleanisTurn(float psi, float phi)

Field Detail

hasOAtoms

private boolean hasOAtoms

mainchainHbondOffsets

private short[] mainchainHbondOffsets

maxHbondAlphaDistance

private static final float maxHbondAlphaDistance

maxHbondAlphaDistance2

private static final float maxHbondAlphaDistance2

min1Energies

private short[] min1Energies

min1Indexes

private short[] min1Indexes

min2Energies

private short[] min2Energies

min2Indexes

private short[] min2Indexes

minimumHbondDistance2

private static final float minimumHbondDistance2

QConst

private static final double QConst

Constructor Detail

AminoPolymer

AminoPolymer(Monomer[] monomers)

Method Detail

bondAminoHydrogen

private void bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitSet bsA, BitSet bsB)

calcHbondEnergy

private int calcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)

calcHydrogenBonds

public void calcHydrogenBonds(BitSet bsA, BitSet bsB)

calcPhiPsiAngles

protected boolean calcPhiPsiAngles()

calcPhiPsiAngles

private void calcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue)

calcProteinMainchainHydrogenBonds

private void calcProteinMainchainHydrogenBonds(BitSet bsA, BitSet bsB)

calculateStructures

public void calculateStructures()

checkWingAtoms

private boolean checkWingAtoms()

createResidueHydrogenBond

private void createResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup, BitSet bsA, BitSet bsB)

freeze

public void freeze()

getPdbData

public void getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)

hasWingPoints

boolean hasWingPoints()

initializeHbondDataStructures

private void initializeHbondDataStructures()

isHelix

private static boolean isHelix(float psi, float phi)

Parameters: psi N-C-CA-N torsion for NEXT group phi C-CA-N-C torsion for THIS group

Returns: whether this corresponds to a helix

isSheet

private static boolean isSheet(float psi, float phi)

isTurn

private static boolean isTurn(float psi, float phi)