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

Field Summary

Fields

Modifier and Type	Field and Description
private static byte	CODE_BETA_SHEET
private static byte	CODE_LEFT_HELIX
private static byte	CODE_LEFT_TURN
private static byte	CODE_NADA
private static byte	CODE_RIGHT_HELIX
private static byte	CODE_RIGHT_TURN
private static byte	TAG_HELIX
private static byte	TAG_NADA
private static byte	TAG_SHEET
private static byte	TAG_TURN

Fields inherited from class org.jmol.modelsetbio.BioPolymer

bsSelectedMonomers, hasWingPoints, haveParameters, invalidControl, monomers, sheetSmoothing

Fields inherited from class org.jmol.modelset.Polymer

bioPolymerIndexInModel, controlPoints, leadAtomIndices, leadMidpoints, leadPoints, model, monomerCount, type, TYPE_AMINO, TYPE_CARBOHYDRATE, TYPE_NOBONDING, TYPE_NUCLEIC, wingVectors

Constructor Summary

Constructors

Constructor and Description
AlphaPolymer(Monomer[] monomers)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSecondaryStructure(byte type, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSeqcode, char endChainID, int endSeqcode)
protected void	addSecondaryStructure(byte type, java.lang.String structureID, int serialID, int strandCount, int indexStart, int indexEnd)
private void	addStructuresFromTags(byte[] tags)
private float[]	calculateAnglesInDegrees()
private byte[]	calculateCodes(float[] angles)
private byte[]	calculateRunsFourOrMore(byte[] codes)
void	calculateStructures(boolean alphaOnly) Uses Levitt & Greer algorithm to calculate protein secondary structures using only alpha-carbon atoms.
java.util.List	calculateStruts(ModelSet modelSet, Atom[] atoms, java.util.BitSet bs1, java.util.BitSet bs2, java.util.List 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 void	checkBetaSheetAlphaHelixOverlap(byte[] codes, float[] angles)
private void	extendRuns(byte[] tags)
protected javax.vecmath.Point3f	getControlPoint(int i, javax.vecmath.Vector3f v)
void	getPdbData(Viewer viewer, char ctype, char qtype, int mStep, int derivType, boolean isDraw, java.util.BitSet bsAtoms, OutputStringBuffer pdbATOM, java.lang.StringBuffer pdbCONECT, java.util.BitSet bsSelected, boolean addHeader, boolean bothEnds, java.util.BitSet bsWritten)
private void	searchForTurns(byte[] codes, float[] angles, byte[] tags)
private void	setStrut(int i, int j, int n, java.util.List vCA, java.util.BitSet bs1, java.util.BitSet bs2, java.util.List vStruts, java.util.BitSet bsStruts, java.util.BitSet bsNotAvailable, java.util.BitSet bsNearbyResidues, int delta)
private int	strutPoint(int i, int j, int n)

Methods inherited from class org.jmol.modelsetbio.BioPolymer

allocateBioPolymer, calcEtaThetaAngles, calcParameters, calcPhiPsiAngles, calcSelectedMonomersCount, calculateRamachandranHelixAngle, calculateStructures, clearStructures, findNearestAtomIndex, getConformation, getControlPoints, getControlPoints, getGroups, getIndex, getInitiatorPoint, getLeadAtomIndices, getLeadMidPoint, getLeadMidpoints, getLeadPoint, getLeadPoint, getLeadPoints, getPdbData, getPolymerInfo, getPolymerPointsAndVectors, getPolymerSequenceAtoms, getProteinStructure, getRange, getRangeGroups, getSelectedMonomerCount, getSequence, getTerminatorPoint, getWingPoint, getWingVectors, isDna, isMonomerSelected, isRna, recalculateLeadMidpointsAndWingVectors, removeProteinStructure, resetHydrogenPoints, setConformation

Methods inherited from class org.jmol.modelset.Polymer

calcRasmolHydrogenBonds, getType, setStructureList

Methods inherited from class java.lang.Object

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

Field Detail

CODE_NADA

private static final byte CODE_NADA

See Also:

Constant Field Values

CODE_RIGHT_HELIX

private static final byte CODE_RIGHT_HELIX

See Also:

Constant Field Values

CODE_BETA_SHEET

private static final byte CODE_BETA_SHEET

See Also:

Constant Field Values

CODE_LEFT_HELIX

private static final byte CODE_LEFT_HELIX

See Also:

Constant Field Values

CODE_LEFT_TURN

private static final byte CODE_LEFT_TURN

See Also:

Constant Field Values

CODE_RIGHT_TURN

private static final byte CODE_RIGHT_TURN

See Also:

Constant Field Values

TAG_NADA

private static final byte TAG_NADA

See Also:

Constant Field Values

TAG_TURN

private static final byte TAG_TURN

See Also:

Constant Field Values

TAG_SHEET

private static final byte TAG_SHEET

See Also:

Constant Field Values

TAG_HELIX

private static final byte TAG_HELIX

See Also:

Constant Field Values

Constructor Detail

AlphaPolymer

AlphaPolymer(Monomer[] monomers)

Method Detail

getControlPoint

protected javax.vecmath.Point3f getControlPoint(int i,
                                    javax.vecmath.Vector3f v)

Overrides:

getControlPoint in class BioPolymer

Returns:

the leadPoint unless a protein sheet residue (see AlphaPolymer)

getPdbData

public void getPdbData(Viewer viewer,
              char ctype,
              char qtype,
              int mStep,
              int derivType,
              boolean isDraw,
              java.util.BitSet bsAtoms,
              OutputStringBuffer pdbATOM,
              java.lang.StringBuffer pdbCONECT,
              java.util.BitSet bsSelected,
              boolean addHeader,
              boolean bothEnds,
              java.util.BitSet bsWritten)

Overrides:

getPdbData in class Polymer

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

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

calculateStruts

public java.util.List calculateStruts(ModelSet modelSet,
                             Atom[] atoms,
                             java.util.BitSet bs1,
                             java.util.BitSet bs2,
                             java.util.List 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 structs only command

Overrides:

calculateStruts in class Polymer

Parameters:

modelSet -

atoms -

bs1 -

bs2 -

vCA -

thresh -

delta -

allowMultiple -

Returns:

vector of pairs of atoms

strutPoint

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

setStrut

private void setStrut(int i,
            int j,
            int n,
            java.util.List vCA,
            java.util.BitSet bs1,
            java.util.BitSet bs2,
            java.util.List vStruts,
            java.util.BitSet bsStruts,
            java.util.BitSet bsNotAvailable,
            java.util.BitSet 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

Overrides:

calculateStructures in class Polymer

Parameters:

alphaOnly -

calculateAnglesInDegrees

private float[] calculateAnglesInDegrees()

calculateCodes

private byte[] calculateCodes(float[] angles)

checkBetaSheetAlphaHelixOverlap

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

calculateRunsFourOrMore

private byte[] calculateRunsFourOrMore(byte[] codes)

extendRuns

private void extendRuns(byte[] tags)

searchForTurns

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

addStructuresFromTags

private void addStructuresFromTags(byte[] tags)