public static IAtom [ ] findClosestByBond ( IAtomContainer atomContainer , IAtom atom , int max ) { IAtomContainer mol = atomContainer . getBuilder ( ) . newInstance ( IAtomContainer . class ) ; List < IAtom > v = new ArrayList < IAtom > ( ) ; v . add ( atom ) ; breadthFirstSearch ( atomContainer , v , mol , max ) ; IAtom [ ] returnValue = new IAtom [ mol . getAtomCount ( ) - 1 ] ; int k = 0 ; for ( int i = 0 ; i < mol . getAtomCount ( ) ; i ++ ) { if ( ! mol . getAtom ( i ) . equals ( atom ) ) { returnValue [ k ] = mol . getAtom ( i ) ; k ++ ; } } return ( returnValue ) ; }
Returns the atoms which are closest to an atom in an AtomContainer by bonds . If number of atoms in or below sphere x&lt ; max and number of atoms in or below sphere x + 1&gt ; max then atoms in or below sphere x + 1 are returned .