Field Detail

• atoms

  protected Atom[] atoms

• ac

  private int ac

• minData

  private float minData

• maxData

  private float maxData

• rdVDW

  private static final RadiusData rdVDW

• vZ

  private javajs.util.V3 vZ

• vY

  private javajs.util.V3 vY

• vX

  private javajs.util.V3 vX

• pt1

  private javajs.util.P3 pt1

• pt2

  private javajs.util.P3 pt2

Constructor Detail

• Contact

  public Contact()

Method Detail

• initShape

  public void initShape()

  Overrides:

  initShape in class Isosurface

• setProperty

  public void setProperty​(java.lang.String propertyName,
                          java.lang.Object value,
                          BS bs)

  Overrides:

  setProperty in class Isosurface

• setContacts

  private void setContacts​(java.lang.Object[] value,
                           boolean doEditCpList)

• combineSurfaces

  private float combineSurfaces​(javajs.util.Lst<ContactPair> pairs,
                                int contactType,
                                int displayType,
                                float[] parameters,
                                java.lang.Object func,
                                boolean isColorDensity,
                                boolean colorByType)

  Parameters:

  pairs -

  contactType -

  displayType -

  parameters -

  func -

  isColorDensity -

  colorByType -

  Returns:

  volume

• setColorByScore

  private int setColorByScore​(float score,
                              int nV)

• getPairs

  private javajs.util.Lst<ContactPair> getPairs​(BS bsA,
                                                BS bsB,
                                                RadiusData rd,
                                                int intramolecularMode,
                                                boolean doEditCpList)

  Parameters:

  bsA -

  bsB -

  rd -

  intramolecularMode -

  doEditCpList -

  Returns:

  a list of pairs of atoms to process

• isWithinFourBonds

  private boolean isWithinFourBonds​(Atom atomA,
                                    Atom atomB)

• checkCp

  private static int checkCp​(ContactPair cp1,
                             ContactPair cp2,
                             int i1,
                             int i2)

  Parameters:

  cp1 -

  cp2 -

  i1 -

  i2 -

  Returns:

  0 (no clash); 1 (remove #1); 2 (remove #2)

• newSurface

  private void newSurface​(int displayType,
                          ContactPair cp,
                          BS bs1,
                          BS bs2,
                          RadiusData rd,
                          float[] parameters,
                          java.lang.Object func,
                          boolean isColorDensity,
                          VolumeData volumeData,
                          float sasurfaceRadius)

• setVolumeData

  private void setVolumeData​(int type,
                             VolumeData volumeData,
                             ContactPair cp,
                             float resolution,
                             int nPairs)

• mergeMesh

  private void mergeMesh​(MeshData md)

• addMeshInfo

  protected void addMeshInfo​(IsosurfaceMesh mesh,
                             java.util.Map<java.lang.String,​java.lang.Object> info)

  Overrides:

  addMeshInfo in class Isosurface

• getVdwClashRadius

  private static void getVdwClashRadius​(ContactPair cp,
                                        double x0,
                                        double vdwA,
                                        double vdwB,
                                        double d)

  well, heh, heh... This calculates the VDW extension x at a given distance for a clashing pair that will produce a volume that is equivalent to the volume for the vdw contact at the point of touching (d0 = vdwA + vdwB) and the transition to clash. This will provide the surface that will surround the clash until the clash size is larger than it.

  Parameters:

  cp -

  x0 -

  vdwA -

  vdwB -

  d -