org.jmol.modelsetbio

Class AminoPolymer

public class AminoPolymer extends AlphaPolymer

Field Summary
boolean	hasOAtoms
short[]	mainchainHbondOffsets
static float	maxHbondAlphaDistance
static float	maxHbondAlphaDistance2
short[]	min1Energies
short[]	min1Indexes
short[]	min2Energies
short[]	min2Indexes
static float	minimumHbondDistance2
static double	QConst

Constructor Summary
	AminoPolymer(Monomer[] monomers)

Method Summary
void	bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint, BitSet bsA, BitSet bsB)
int	calcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint, Point3f hydrogenPoint, AminoMonomer target)
void	calcHydrogenBonds(BitSet bsA, BitSet bsB)
protected boolean	calcPhiPsiAngles()
void	calcPhiPsiAngles(AminoMonomer leadingResidue, AminoMonomer trailingResidue)
void	calcProteinMainchainHydrogenBonds(BitSet bsA, BitSet bsB)
void	calculateStructures()
boolean	checkWingAtoms()
void	createResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup, BitSet bsA, BitSet bsB)
void	freeze()
void	getPdbData(char ctype, char qtype, int derivType, boolean isDraw, BitSet bsAtoms, StringBuffer pdbATOM, StringBuffer pdbCONECT, BitSet bsSelected, boolean addHeader, BitSet bsWritten)
boolean	hasWingPoints()
void	initializeHbondDataStructures()
static boolean	isHelix(float psi, float phi)
static boolean	isSheet(float psi, float phi)
static boolean	isTurn(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)