public AtomContactSet getAtomContacts ( ) { AtomContactSet contacts = new AtomContactSet ( cutoff ) ; List < Contact > list = getIndicesContacts ( ) ; if ( jAtomObjects == null ) { for ( Contact cont : list ) { contacts . add ( new AtomContact ( new Pair < Atom > ( iAtomObjects [ cont . getI ( ) ] , iAtomObjects [ cont . getJ ( ) ] ) , cont . getDistance ( ) ) ) ; } } else { for ( Contact cont : list ) { contacts . add ( new AtomContact ( new Pair < Atom > ( iAtomObjects [ cont . getI ( ) ] , jAtomObjects [ cont . getJ ( ) ] ) , cont . getDistance ( ) ) ) ; } } return contacts ; }
Returns all contacts i . e . all atoms that are within the cutoff distance . If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms if jAtoms is null then contacts are within the iAtoms .