org.jmol.modelsetbio

Class AlphaPolymer

public class AlphaPolymer extends BioPolymer

Field Summary
static byteCODE_BETA_SHEET
static byteCODE_LEFT_HELIX
static byteCODE_LEFT_TURN
static byteCODE_NADA
static byteCODE_RIGHT_HELIX
static byteCODE_RIGHT_TURN
static byteTAG_HELIX
static byteTAG_NADA
static byteTAG_SHEET
static byteTAG_TURN
Constructor Summary
AlphaPolymer(Monomer[] monomers)
Method Summary
voidaddSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
voidaddSecondaryStructure(byte type, int indexStart, int indexEnd)
voidaddStructuresFromTags(byte[] tags)
voidcalcHydrogenBonds()
float[]calculateAnglesInDegrees()
byte[]calculateCodes(float[] angles)
byte[]calculateRunsFourOrMore(byte[] codes)
voidcalculateStructures()
Uses Levitt & Greer algorithm to calculate protien secondary structures using only alpha-carbon atoms.
voidcheckBetaSheetAlphaHelixOverlap(byte[] codes, float[] angles)
voidextendRuns(byte[] tags)
voidsearchForTurns(byte[] codes, float[] angles, byte[] tags)

Field Detail

CODE_BETA_SHEET

static final byte CODE_BETA_SHEET

CODE_LEFT_HELIX

static final byte CODE_LEFT_HELIX

CODE_LEFT_TURN

static final byte CODE_LEFT_TURN

CODE_NADA

static final byte CODE_NADA

CODE_RIGHT_HELIX

static final byte CODE_RIGHT_HELIX

CODE_RIGHT_TURN

static final byte CODE_RIGHT_TURN

TAG_HELIX

static final byte TAG_HELIX

TAG_NADA

static final byte TAG_NADA

TAG_SHEET

static final byte TAG_SHEET

TAG_TURN

static final byte TAG_TURN

Constructor Detail

AlphaPolymer

AlphaPolymer(Monomer[] monomers)

Method Detail

addSecondaryStructure

public void addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode)

addSecondaryStructure

void addSecondaryStructure(byte type, int indexStart, int indexEnd)

addStructuresFromTags

void addStructuresFromTags(byte[] tags)

calcHydrogenBonds

void calcHydrogenBonds()

calculateAnglesInDegrees

float[] calculateAnglesInDegrees()

calculateCodes

byte[] calculateCodes(float[] angles)

calculateRunsFourOrMore

byte[] calculateRunsFourOrMore(byte[] codes)

calculateStructures

public void calculateStructures()
Uses Levitt & Greer algorithm to calculate protien secondary structures using only alpha-carbon atoms.

Levitt and Greer
Automatic Identification of Secondary Structure in Globular Proteins
J.Mol.Biol.(1977) 114, 181-293

http://csb.stanford.edu/levitt/Levitt_JMB77_Secondary_structure.pdf

checkBetaSheetAlphaHelixOverlap

void checkBetaSheetAlphaHelixOverlap(byte[] codes, float[] angles)

extendRuns

void extendRuns(byte[] tags)

searchForTurns

void searchForTurns(byte[] codes, float[] angles, byte[] tags)