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        $atom -> type($type);
        $atom -> number($anum);
        $atom -> name($aname);
        $atom -> residue_name($rname);
        $atom -> chain($chain);
        $atom -> residue_number($rnum);
        $atom ->x($xx);
        $atom ->y($yy);
        $atom ->z($zz);
        $atom -> occupancy($coor);
        $atom -> beta($beta);
        #since alterate location and insertion code are seldomly used only include them for atoms that have them
        $atom -> alt($altloc) if ( $altloc  ne " ");
        $atom -> insertion_code($icode) if ( $icode ne " ");
        $self-> push($atom);
        }
    close FPDB;
    return;
    }

#print out a molecule to stdout or to a file
sub print
    {

    #names of all the pdb atoms with correct justification for pdb print out
    #these are set by convention and are important for some programs to work correctly
    my %atom_name = (
    'C'    => ' C  ',
    'C1'   => ' C1 ',
    'C1A'  => ' C1A',
    'C1B'  => ' C1B',
    'C1C'  => ' C1C',
    'C1D'  => ' C1D',
    'C2'   => ' C2 ',
    'C2A'  => ' C2A',
    'C2B'  => ' C2B',
    'C2C'  => ' C2C',
    'C2D'  => ' C2D',
    'C3'   => ' C3 ',
    'C3A'  => ' C3A',
    'C3B'  => ' C3B',
    'C3C'  => ' C3C',
    'C3D'  => ' C3D',
    'C4'   => ' C4 ',
    'C4A'  => ' C4A',
    'C4A'  => ' C4A',
    'C4B'  => ' C4B',
    'C4C'  => ' C4C',
    'C4D'  => ' C4D',
    'C5'   => ' C5 ',
    'C6'   => ' C6 ',
    'CA'   => ' CA ',
    'CAA'  => ' CAA',
    'CAB'  => ' CAB',
    'CAC'  => ' CAC',
    'CAD'  => ' CAD',
    'CB'   => ' CB ',
    'CBA'  => ' CBA',
    'CBB'  => ' CBB',
    'CBC'  => ' CBC',
    'CBD'  => ' CBD',
    'CD'   => ' CD ',
    'CD1'  => ' CD1',
    'CD2'  => ' CD2',
    'CE'   => ' CE ',
    'CE1'  => ' CE1',
    'CE2'  => ' CE2',
    'CE3'  => ' CE3',
    'CG'   => ' CG ',
    'CG1'  => ' CG1',
    'CG2'  => ' CG2',
    'CGA'  => ' CGA',
    'CGD'  => ' CGD',
    'CH2'  => ' CH2',
    'CHA'  => ' CHA',
    'CHB'  => ' CHB',
    'CHC'  => ' CHC',
    'CHD'  => ' CHD',
    'CMA'  => ' CMA',
    'CMB'  => ' CMB',
    'CMC'  => ' CMC',
    'CMD'  => ' CMD',
    'CZ'   => ' CZ ',
    'CZ2'  => ' CZ2',
    'CZ3'  => ' CZ3',
    'FE'   => 'FE  ',
    'H'    => ' H  ',
    'HA'   => ' HA ',
    'HB'   => ' HB ',
    'HG'   => ' HG ',
    'HE'   => ' HE ',
    'HZ'   => ' HZ ',
    'HH'   => ' HH ',
    '1H'   => '1H  ',
    '2H'   => '2H  ',
    '3H'   => '3H  ',
    '1HA'  => '1HA ',
    '1HB'  => '1HB ',
    '1HD'  => '1HD ',
    '1HE'  => '1HE ',
    '1HG'  => '1HG ',
    '1HZ'  => '1HZ ',
    '2HA'  => '2HA ',
    '2HB'  => '2HB ',
    '2HD'  => '2HD ',
    '2HE'  => '2HE ',
    '2HG'  => '2HG ',
    '1HZ'  => '1HZ ',
    '2HZ'  => '2HZ ',
    '3HB'  => '3HB ',
    '3HE'  => '3HE ',
    '3HZ'  => '3HZ ',
    'N'    => ' N  ',
    'NA'   => ' NA ',
    'NB'   => ' NB ',
    'NC'   => ' NC ',
    'ND'   => ' ND ',
    'N A'  => ' N A',
    'N B'  => ' N B',
    'N C'  => ' N C',