org.jmol.modelsetbio
Class AlphaPolymer
java.lang.Object
org.jmol.modelset.Polymer
org.jmol.modelsetbio.BioPolymer
org.jmol.modelsetbio.AlphaPolymer
- Direct Known Subclasses:
- AminoPolymer
public class AlphaPolymer
- extends BioPolymer
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
AlphaPolymer
AlphaPolymer(Monomer[] monomers)
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