Class BondCollection

java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
Direct Known Subclasses:
ModelSet
public abstract class BondCollection extends AtomCollection

  • Field Details

    • 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

    • bsAromatic

      protected BS bsAromatic

    • haveHiddenBonds

      public boolean haveHiddenBonds

    • v1

      protected V3 v1

    • v2

      protected V3 v2

    • BOND_GROWTH_INCREMENT

      protected static final int BOND_GROWTH_INCREMENT
      See Also:

    • MAX_BONDS_LENGTH_TO_CACHE

      protected static final int MAX_BONDS_LENGTH_TO_CACHE
      See Also:

    • MAX_NUM_TO_CACHE

      protected static final int MAX_NUM_TO_CACHE
      See Also:

    • haveAtropicBonds

      protected boolean haveAtropicBonds

  • Constructor Details

    • BondCollection

      public BondCollection()

  • Method Details

    • setupBC

      protected void setupBC()

    • releaseModelSetBC

      protected void releaseModelSetBC()

    • 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)

    • addHBond

      public int addHBond(Atom atom1, Atom atom2, int order, float energy)
      /// bonding methods //////

    • 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)
      Consider the min/max option for CONNECT
      Parameters:
      atom1 -
      atom2 -
      minD -
      maxD -
      minFrac -
      maxfrac -
      isFractional -
      Returns:
      true if in range

    • dBb

      protected void dBb(BS bsBond, boolean isFullModel)
      Delete bonds, but don't shift arrays, just set bond to null, in order to allow for state.
      Parameters:
      bsBond -
      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

    • allowAromaticBond

      protected boolean allowAromaticBond(Bond b)

    • getAtomBitsMDb

      protected BS getAtomBitsMDb(int tokType, Object specInfo)

    • removeUnnecessaryBonds

      public 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)

    • addConnectedHAtoms

      public void addConnectedHAtoms(Atom atom, BS bsAtoms)