org.jmol.modelsetbio
public class AlphaPolymer extends BioPolymer
Field Summary | |
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static byte | CODE_BETA_SHEET |
static byte | CODE_LEFT_HELIX |
static byte | CODE_LEFT_TURN |
static byte | CODE_NADA |
static byte | CODE_RIGHT_HELIX |
static byte | CODE_RIGHT_TURN |
static byte | TAG_HELIX |
static byte | TAG_NADA |
static byte | TAG_SHEET |
static byte | TAG_TURN |
Constructor Summary | |
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AlphaPolymer(Monomer[] monomers) |
Method Summary | |
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void | addSecondaryStructure(byte type, char startChainID, int startSeqcode, char endChainID, int endSeqcode) |
void | addSecondaryStructure(byte type, int indexStart, int indexEnd) |
void | addStructuresFromTags(byte[] tags) |
void | calcHydrogenBonds() |
float[] | calculateAnglesInDegrees() |
byte[] | calculateCodes(float[] angles) |
byte[] | calculateRunsFourOrMore(byte[] codes) |
void | calculateStructures()
Uses Levitt & Greer algorithm to calculate protien secondary
structures using only alpha-carbon atoms.
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void | checkBetaSheetAlphaHelixOverlap(byte[] codes, float[] angles) |
void | extendRuns(byte[] tags) |
void | searchForTurns(byte[] codes, float[] angles, byte[] tags) |
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