org.jmol.modelsetbio

Class AlphaPolymer

java.lang.Object

org.jmol.modelsetbio.BioPolymer

org.jmol.modelsetbio.AlphaPolymer

Direct Known Subclasses:

AminoPolymer

public class AlphaPolymer
extends BioPolymer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	AlphaPolymer.Code

Field Summary

Fields inherited from class org.jmol.modelsetbio.BioPolymer

bioPolymerIndexInModel, bsSelectedMonomers, controlPoints, hasStructure, hasWingPoints, haveParameters, invalidControl, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, monomers, reversed, sheetSmoothing, twistedSheets, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors

Constructor Summary

Constructors

Constructor and Description
AlphaPolymer(Monomer[] monomers)

Method Summary

Modifier and Type	Method and Description
void	addStructure(STR type, java.lang.String structureID, int serialID, int strandCount, int startChainID, int startSeqcode, int endChainID, int endSeqcode, int istart, int iend, BS bsAssigned)
boolean	addStructureProtected(STR type, java.lang.String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
private void	addStructuresFromTags(STR[] tags)
private float[]	calculateAnglesInDegrees()
private AlphaPolymer.Code[]	calculateCodes(float[] angles)
private STR[]	calculateRunsFourOrMore(AlphaPolymer.Code[] codes)
void	calculateStructures(boolean alphaOnly) Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
javajs.util.Lst<Atom[]>	calculateStruts(ModelSet modelSet, BS bs1, BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple) Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous).
private javajs.util.Lst<Atom[]>	calculateStrutsStatic(ModelSet modelSet, BS bs1, BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple)
private void	checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[] codes, float[] angles)
void	clearStructures()
private void	extendRuns(STR[] tags)
protected javajs.util.P3	getControlPoint(int i, javajs.util.V3 v)
ProteinStructure	getProteinStructure(int monomerIndex)
private void	searchForTurns(AlphaPolymer.Code[] codes, float[] angles, STR[] tags)
private static void	setStrut(int i, int j, int n, javajs.util.Lst<Atom> vCA, BS bs1, BS bs2, javajs.util.Lst<Atom[]> vStruts, BS bsStruts, BS bsNotAvailable, BS bsNearbyResidues, int delta)
private static int	strutPoint(int i, int j, int n)

Methods inherited from class org.jmol.modelsetbio.BioPolymer

calcEtaThetaAngles, calcParameters, calcPhiPsiAngles, calcRasmolHydrogenBonds, calcSelectedMonomersCount, calculateRamachandranHelixAngle, drawQuat, findNearestAtomIndex, getConformation, getControlPoints, getIndex, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getType, getWingPoint, getWingVectors, isMonomerSelected, isNucleic, isRna, recalculateLeadMidpointsAndWingVectors, resetHydrogenPoints, set, setConformation, setStructureList

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlphaPolymer

AlphaPolymer(Monomer[] monomers)

Method Detail

getProteinStructure

public ProteinStructure getProteinStructure(int monomerIndex)

Overrides:

getProteinStructure in class BioPolymer

Returns:

"HELIX" "TURN" etc

getControlPoint

protected javajs.util.P3 getControlPoint(int i,
                                         javajs.util.V3 v)

Overrides:

getControlPoint in class BioPolymer

Returns:

the leadPoint unless a protein sheet residue (see AlphaPolymer)

addStructure

public void addStructure(STR type,
                         java.lang.String structureID,
                         int serialID,
                         int strandCount,
                         int startChainID,
                         int startSeqcode,
                         int endChainID,
                         int endSeqcode,
                         int istart,
                         int iend,
                         BS bsAssigned)

addStructureProtected

public boolean addStructureProtected(STR type,
                                     java.lang.String structureID,
                                     int serialID,
                                     int strandCount,
                                     int indexStart,
                                     int indexEnd)

clearStructures

public void clearStructures()

Overrides:

clearStructures in class BioPolymer

calculateStruts

public javajs.util.Lst<Atom[]> calculateStruts(ModelSet modelSet,
                                               BS bs1,
                                               BS bs2,
                                               javajs.util.Lst<Atom> vCA,
                                               float thresh,
                                               int delta,
                                               boolean allowMultiple)

Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous). Like George, we go from thresh-4 to thresh in units of 1 Angstrom, but we do not require this threshold to be an integer. In addition, we prevent double-creation of struts by tracking where struts are, and we do not look for any addtional end struts if there is a strut already to an atom at a particular biopolymer end. The three parameters are: set strutDefaultRadius 0.3 set strutSpacingMinimum 6 set strutLengthMaximum 7.0 Struts will be introduced by: calculate struts {atom set A} {atom set B} where the two atom sets are optional and default to the currently selected set. They can be manipulated using the STRUTS command much like any "bond" struts 0.3 color struts opaque pink connect {atomno=3} {atomno=4} strut struts only command

Overrides:

calculateStruts in class BioPolymer

Parameters:

modelSet -

bs1 -

bs2 -

vCA -

thresh -

delta -

allowMultiple -

Returns:

vector of pairs of atoms

calculateStrutsStatic

private javajs.util.Lst<Atom[]> calculateStrutsStatic(ModelSet modelSet,
                                                      BS bs1,
                                                      BS bs2,
                                                      javajs.util.Lst<Atom> vCA,
                                                      float thresh,
                                                      int delta,
                                                      boolean allowMultiple)

strutPoint

private static int strutPoint(int i,
                              int j,
                              int n)

setStrut

private static void setStrut(int i,
                             int j,
                             int n,
                             javajs.util.Lst<Atom> vCA,
                             BS bs1,
                             BS bs2,
                             javajs.util.Lst<Atom[]> vStruts,
                             BS bsStruts,
                             BS bsNotAvailable,
                             BS bsNearbyResidues,
                             int delta)

calculateStructures

public void calculateStructures(boolean alphaOnly)

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

Parameters:

alphaOnly - caught by AminoPolymer and discarded if desired

calculateAnglesInDegrees

private float[] calculateAnglesInDegrees()

calculateCodes

private AlphaPolymer.Code[] calculateCodes(float[] angles)

checkBetaSheetAlphaHelixOverlap

private void checkBetaSheetAlphaHelixOverlap(AlphaPolymer.Code[] codes,
                                             float[] angles)

calculateRunsFourOrMore

private STR[] calculateRunsFourOrMore(AlphaPolymer.Code[] codes)

extendRuns

private void extendRuns(STR[] tags)

searchForTurns

private void searchForTurns(AlphaPolymer.Code[] codes,
                            float[] angles,
                            STR[] tags)

addStructuresFromTags

private void addStructuresFromTags(STR[] tags)