Field Detail

• type

  STR type

• subtype

  STR subtype

• structureID

  java.lang.String structureID

• strucNo

  int strucNo

• serialID

  int serialID

• strandCount

  int strandCount

• nRes

  public int nRes

• apolymer

  public AlphaPolymer apolymer

• monomerIndexFirst

  protected int monomerIndexFirst

• monomerIndexLast

  int monomerIndexLast

• axisA

  protected javajs.util.P3 axisA

• axisB

  protected javajs.util.P3 axisB

• axisUnitVector

  protected javajs.util.V3 axisUnitVector

• vectorProjection

  protected javajs.util.V3 vectorProjection

• globalStrucNo

  private static int globalStrucNo

• segments

  private javajs.util.P3[] segments

• resMap

  private java.util.Map<Monomer,​java.lang.Integer> resMap

Constructor Detail

• ProteinStructure

  public ProteinStructure()

Method Detail

• setupPS

  protected void setupPS​(AlphaPolymer apolymer,
                         STR type,
                         int monomerIndex,
                         int monomerCount)

  Parameters:

  apolymer -

  type -

  monomerIndex -

  monomerCount -

• addMonomer

  void addMonomer​(int index)

  Note that this method does not check to see that there are no overlapping protein structures.

  Parameters:

  index -

• removeMonomer

  void removeMonomer​(int index)

  should be OK here to remove the first -- we just get a monomerCount of 0; but we don't remove monomers that aren't part of this structure.

  Parameters:

  index -

• calcAxis

  public void calcAxis()

• isWithin

  public boolean isWithin​(int monomerIndex)

• getIndex

  public int getIndex​(Monomer monomer)

• getSegments

  public javajs.util.P3[] getSegments()

  Returns:

  points for rocket segment rendering

• getStructureMidPoint

  javajs.util.P3 getStructureMidPoint​(int index)

• calcSegments

  private void calcSegments()

• getAxisStartPoint

  public javajs.util.P3 getAxisStartPoint()

• getAxisEndPoint

  public javajs.util.P3 getAxisEndPoint()

• resetAxes

  void resetAxes()

• setAtomBits

  public void setAtomBits​(BS bs)

  Specified by:

  setAtomBits in interface Structure

• setAtomBitsAndClear

  public void setAtomBitsAndClear​(BS bs,
                                  BS bsOut)

  Specified by:

  setAtomBitsAndClear in interface Structure

• findMonomer

  public Monomer findMonomer​(BS bsAtoms,
                             boolean isFirst)