org.jmol.modelsetbio
Class AlphaPolymer

java.lang.Object
  extended by org.jmol.modelset.Polymer
      extended by org.jmol.modelsetbio.BioPolymer
          extended by org.jmol.modelsetbio.AlphaPolymer
Direct Known Subclasses:
AminoPolymer

public class AlphaPolymer
extends BioPolymer


Field Summary
(package private) static byte CODE_BETA_SHEET
           
(package private) static byte CODE_LEFT_HELIX
           
(package private) static byte CODE_LEFT_TURN
           
(package private) static byte CODE_NADA
           
(package private) static byte CODE_RIGHT_HELIX
           
(package private) static byte CODE_RIGHT_TURN
           
(package private) static byte TAG_HELIX
           
(package private) static byte TAG_NADA
           
(package private) static byte TAG_SHEET
           
(package private) static byte TAG_TURN
           
 
Fields inherited from class org.jmol.modelsetbio.BioPolymer
bsSelectedMonomers, model, monomerCount, monomers
 
Fields inherited from class org.jmol.modelset.Polymer
leadAtomIndices, leadMidpoints, leadPoints, sheetPoints, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NUCLEIC, TYPE_OTHER, wingVectors
 
Constructor Summary
AlphaPolymer(Monomer[] monomers)
           
 
Method Summary
 void addSecondaryStructure(byte type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
           
(package private)  void addSecondaryStructure(byte type, java.lang.String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
           
(package private)  void addStructuresFromTags(byte[] tags)
           
(package private)  void calcHydrogenBonds()
           
(package private)  float[] calculateAnglesInDegrees()
           
(package private)  byte[] calculateCodes(float[] angles)
           
(package private)  byte[] calculateRunsFourOrMore(byte[] codes)
           
 void calculateStructures()
          Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
(package private)  void checkBetaSheetAlphaHelixOverlap(byte[] codes, float[] angles)
           
(package private)  void extendRuns(byte[] tags)
           
 void getPdbData(char ctype, char qtype, int mStep, int derivType, boolean isDraw, java.util.BitSet bsAtoms, java.lang.StringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, java.util.BitSet bsWritten)
           
(package private)  void searchForTurns(byte[] codes, float[] angles, byte[] tags)
           
 
Methods inherited from class org.jmol.modelsetbio.BioPolymer
allocateBioPolymer, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, clearStructures, findNearestAtomIndex, getControlPoints, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getMonomerCount, getMonomers, getPdbData, getPointPoint, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, hasWingPoints, isMonomerSelected, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, setConformation
 
Methods inherited from class org.jmol.modelset.Polymer
calcHydrogenBonds, freeze, getType
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

CODE_NADA

static final byte CODE_NADA
See Also:
Constant Field Values

CODE_RIGHT_HELIX

static final byte CODE_RIGHT_HELIX
See Also:
Constant Field Values

CODE_BETA_SHEET

static final byte CODE_BETA_SHEET
See Also:
Constant Field Values

CODE_LEFT_HELIX

static final byte CODE_LEFT_HELIX
See Also:
Constant Field Values

CODE_LEFT_TURN

static final byte CODE_LEFT_TURN
See Also:
Constant Field Values

CODE_RIGHT_TURN

static final byte CODE_RIGHT_TURN
See Also:
Constant Field Values

TAG_NADA

static final byte TAG_NADA
See Also:
Constant Field Values

TAG_TURN

static final byte TAG_TURN
See Also:
Constant Field Values

TAG_SHEET

static final byte TAG_SHEET
See Also:
Constant Field Values

TAG_HELIX

static final byte TAG_HELIX
See Also:
Constant Field Values
Constructor Detail

AlphaPolymer

AlphaPolymer(Monomer[] monomers)
Method Detail

addSecondaryStructure

public void addSecondaryStructure(byte type,
                                  java.lang.String structureID,
                                  int serialID,
                                  int strandCount,
                                  char startChainID,
                                  int startSeqcode,
                                  char endChainID,
                                  int endSeqcode)
Overrides:
addSecondaryStructure in class Polymer

addSecondaryStructure

void addSecondaryStructure(byte type,
                           java.lang.String structureID,
                           int serialID,
                           int strandCount,
                           int indexStart,
                           int indexEnd)

calcHydrogenBonds

void calcHydrogenBonds()

calculateStructures

public void calculateStructures()
Uses Levitt & Greer algorithm to calculate protein 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

Overrides:
calculateStructures in class Polymer

calculateAnglesInDegrees

float[] calculateAnglesInDegrees()

calculateCodes

byte[] calculateCodes(float[] angles)

checkBetaSheetAlphaHelixOverlap

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

calculateRunsFourOrMore

byte[] calculateRunsFourOrMore(byte[] codes)

extendRuns

void extendRuns(byte[] tags)

searchForTurns

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

addStructuresFromTags

void addStructuresFromTags(byte[] tags)

getPdbData

public void getPdbData(char ctype,
                       char qtype,
                       int mStep,
                       int derivType,
                       boolean isDraw,
                       java.util.BitSet bsAtoms,
                       java.lang.StringBuffer pdbATOM,
                       java.lang.StringBuffer pdbCONECT,
                       java.util.BitSet bsSelected,
                       boolean addHeader,
                       java.util.BitSet bsWritten)
Overrides:
getPdbData in class Polymer