Field Detail

• bo

  public Bond[] bo

• bondCount

  public int bondCount

• numCached

  protected int[] numCached

• freeBonds

  protected Bond[][][] freeBonds

• molecules

  protected JmolMolecule[] molecules

• moleculeCount

  protected int moleculeCount

• defaultCovalentMad

  protected short defaultCovalentMad

• bsAromaticSingle

  private BS bsAromaticSingle

• bsAromaticDouble

  private BS bsAromaticDouble

• bsAromatic

  protected BS bsAromatic

• haveHiddenBonds

  public boolean haveHiddenBonds

• BOND_GROWTH_INCREMENT

  protected static final int BOND_GROWTH_INCREMENT

  See Also:

  Constant Field Values

• MAX_BONDS_LENGTH_TO_CACHE

  protected static final int MAX_BONDS_LENGTH_TO_CACHE

  See Also:

  Constant Field Values

• MAX_NUM_TO_CACHE

  protected static final int MAX_NUM_TO_CACHE

  See Also:

  Constant Field Values

Constructor Detail

• BondCollection

  public BondCollection()

Method Detail

• setupBC

  protected void setupBC()

• releaseModelSetBC

  protected void releaseModelSetBC()

• resetMolecules

  public void resetMolecules()

• getBondIteratorForType

  public BondIterator getBondIteratorForType​(int bondType,
                                             BS bsAtoms)

• getBondIterator

  public BondIterator getBondIterator​(BS bsBonds)

• getBondColix1

  public short getBondColix1​(int i)

• getBondColix2

  public short getBondColix2​(int i)

• getBondCountInModel

  protected int getBondCountInModel​(int modelIndex)

  for general use

  Parameters:

  modelIndex - the model of interest or -1 for all

  Returns:

  the actual number of connections

• getBondsForSelectedAtoms

  public BS getBondsForSelectedAtoms​(BS bsAtoms,
                                     boolean bondSelectionModeOr)

• bondAtoms

  public Bond bondAtoms​(Atom atom1,
                        Atom atom2,
                        int order,
                        short mad,
                        BS bsBonds,
                        float energy,
                        boolean addGroup,
                        boolean isNew)

• getOrAddBond

  protected Bond getOrAddBond​(Atom atom,
                              Atom atomOther,
                              int order,
                              short mad,
                              BS bsBonds,
                              float energy,
                              boolean overrideBonding)

• setBond

  protected Bond setBond​(int index,
                         Bond bond)

• bondMutually

  protected Bond bondMutually​(Atom atom,
                              Atom atomOther,
                              int order,
                              short mad,
                              float energy)

• addBondToAtom

  private void addBondToAtom​(Atom atom,
                             Bond bond)

• addToBonds

  private Bond[] addToBonds​(Bond newBond,
                            Bond[] oldBonds)

• addHBond

  public int addHBond​(Atom atom1,
                      Atom atom2,
                      int order,
                      float energy)

• deleteAllBonds2

  protected void deleteAllBonds2()

• getDefaultMadFromOrder

  public short getDefaultMadFromOrder​(int order)

  When creating a new bond, determine bond diameter from order

  Parameters:

  order -

  Returns:

  if hydrogen bond, default to 1; otherwise 0 (general default)

• deleteConnections

  protected int[] deleteConnections​(float minD,
                                    float maxD,
                                    int order,
                                    BS bsA,
                                    BS bsB,
                                    boolean isBonds,
                                    boolean matchNull)

• fixD

  protected float fixD​(float d,
                       boolean isF)

• isInRange

  protected boolean isInRange​(Atom atom1,
                              Atom atom2,
                              float minD,
                              float maxD,
                              boolean minFrac,
                              boolean maxfrac,
                              boolean isFractional)

• dBm

  protected void dBm​(BS bsBonds,
                     boolean isFullModel)

  send request up to ModelCollection level. Done this way to avoid JavaScript super call

  Parameters:

  bsBonds -

  isFullModel -

• dBb

  protected void dBb​(BS bsBond,
                     boolean isFullModel)

• resetAromatic

  public void resetAromatic()

• assignAromaticBondsBs

  public void assignAromaticBondsBs​(boolean isUserCalculation,
                                    BS bsBonds)

  algorithm discussed above.

  Parameters:

  isUserCalculation - if set, don't reset the base aromatic bitset and do report changes to STICKS as though this were a bondOrder command.

  bsBonds - passed to us by autoBond routine

• assignAromaticDouble

  private boolean assignAromaticDouble​(Bond bond)

  try to assign AROMATICDOUBLE to this bond. Each atom needs to be have all single bonds except for this one.

  Parameters:

  bond -

  Returns:

  true if successful; false otherwise

• assignAromaticSingle

  private boolean assignAromaticSingle​(Bond bond)

  try to assign AROMATICSINGLE to this bond. Each atom needs to be able to have one aromatic double bond attached.

  Parameters:

  bond -

  Returns:

  true if successful; false otherwise

• assignAromaticSingleForAtom

  private boolean assignAromaticSingleForAtom​(Atom atom,
                                              int notBondIndex)

  N atoms with 3 bonds cannot also have a double bond; other atoms needs all single bonds, because the bond leading up to it is double.

  Parameters:

  atom -

  notBondIndex - that index of the bond leading to this atom --- to be ignored

  Returns:

  true if successful, false if not

• assignAromaticDoubleForAtom

  private boolean assignAromaticDoubleForAtom​(Atom atom)

  N atoms with 3 bonds cannot also have a double bond; other atoms need one and only one double bond; the rest must be single bonds.

  Parameters:

  atom -

  Returns:

  true if successful, false if not

• allowAromaticBond

  protected boolean allowAromaticBond​(Bond b)

• assignAromaticMustBeSingle

  private boolean assignAromaticMustBeSingle​(Atom atom)

• assignAromaticNandO

  private void assignAromaticNandO​(BS bsSelected)

• getAtomBitsMDb

  protected BS getAtomBitsMDb​(int tokType,
                              java.lang.Object specInfo)

• assignBond

  public BS assignBond​(int bondIndex,
                       char type)

• removeUnnecessaryBonds

  protected void removeUnnecessaryBonds​(Atom atom,
                                        boolean deleteAtom)

• displayBonds

  public void displayBonds​(BondSet bs,
                           boolean isDisplay)

• getAtomsConnected

  public BS getAtomsConnected​(float min,
                              float max,
                              int intType,
                              BS bs)