Uses of Class
javajs.util.BS

fast copy

Performs a logical AND of this target bit set with the argument bit set.

fast copy

Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.

Performs a logical XOR of this bit set with the bit set argument.

remove non-spin atoms and atoms with duplicated spin and set min/max XYZ for the plot

//////// FILTER /////////////////

An attempt to find unique atoms using tensors.

Called when the selected atoms change

////////////////// general post-load processing ////////////////

Adjusts _atoms bitset to account for added hydrogen atoms.

input an array of colixes; returns a Vector for the color list and a HashTable for correlating the colix with a specific color index

assign partial charges ala MMFF94

a bitset indicating the presence of element keys for models; clearing a bit will cause a new key to be produced.

Only for the current model

MODELKIT ADD @3 ...

Delete all atoms that are equivalent to this atom.

Minimize a unit cell with full symmetry constraints.

tracks all presymmetry asymmetric unit atoms; atoms added using the ModelKit will add to this.

these are hydrogens that are being added due to a load 2D command and are therefore not to be flagged as NEW

general unqualified lookup of atom set type

general lookup for integer type -- from Eval

include this frame and all related frames

only some models can be iterated through.

note -- this method returns ALL atoms, including deleted.

return cumulative sum of all atoms in molecules containing these atoms

algorithm discussed above.

a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}.

These are not actual hydrogen bonds.

allows rebuilding of PDB structures; also accessed by ModelManager from Eval

Delete bonds, but don't shift arrays, just set bond to null, in order to allow for state.

////////////////////////////////////////

Get the set of models associated with a set of atoms.

// bio-only methods /////

Set a bitset of the equivalent atoms of an atom.

// super-overloaded methods ///////

Setting and clearing

Set up all the model-related fields in association with a new space group.

///////////////////////////////////////////////

from Trajectory.setAtomPositions base models only; not trajectories

called from state STRUCTURE command

bits in the bitset determines the type

generic renderer -- dots and geosurface

Add hydrogens to a model

Add hydrogens to a model

sets the size of a bond, or sets the selectedBonds set

Returns a vector of bitsets indicating which atoms match the pattern.

Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.

internal to Jmol -- called by org.jmol.Viewer.getSmiles

Returns a vector of bitsets indicating which atoms match the pattern.

Retrieve an array of bit sets that match a given SMARTS

Return a bit set corresponding to a SMARTS

Look for a supercell and adjust lattice down if necessary.

this one slides deleted bits out of a pattern.

a perhaps curious method: b is a reference set, perhaps all atoms in a certain molecule a is the working set, perhaps representing all displayed atoms For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if a is not set, then add to a all set bits of b Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is a subset of a, then --> a not b if a only intersects with b, then --> a or b if a does not intersect with b, then a or b In "toggle" mode, when you click on any atom of the molecule, you want either: (a) all the atoms in the molecule to be displayed if not all are already displayed, or (b) the whole molecule to be hidden if all the atoms of the molecule are already displayed.

Creates an array of JmolMolecules from a set of atoms in the form of simple JmolNodes.