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is( $bonds[0]->name,      'N1_CA1',           "bond name1" );
is( $bonds[1]->name,      'CA1_C1',           "bond name2" );
is( $bonds[2]->name,      'C1_N2',            "bond name3" );
is( $angles[1]->name,     'CA1_C1_N2',        "second angle name" );
is( $dihedrals[-1]->name, 'C19_N20_CA20_C20', "last dihedral name" );
is( $bonds[-1]->name,     'CA20_C20',         "last bond name1" );
is( $angles[-1]->name,    'N20_CA20_C20',     "last angle name1" );

dies_ok { $hack->build_dihedrals( @bb[ 0 .. 2 ] ) } "build_dihedrals croak";
dies_ok { $hack->build_bonds( $bb[0] ) } "build_bonds croak";
dies_ok { $hack->build_angles( @bb[ 0, 1 ] ) } "build_angles croak";

{
    $_->clear_name foreach @bb;
    my @bonds     = $hack->build_bonds(@bb);
    my @angles    = $hack->build_angles(@bb);
    my @dihedrals = $hack->build_dihedrals(@bb);

    is( $dihedrals[0]->name, 'D1_D1_D1_D2', "dihedral noname default" );
    is( $angles[0]->name,    'A1_A1_A1',    "angle noname default" );
    is( $bonds[0]->name,     'B1_B1',       "bond noname default" );
}

{
    $_->name("foo") foreach @bb;
    $_->resid foreach @bb;
    my @bonds     = $hack->build_bonds(@bb);
    my @angles    = $hack->build_angles(@bb);
    my @dihedrals = $hack->build_dihedrals(@bb);

    is( $dihedrals[0]->name, 'foo1_foo1_foo1_foo2',
        "dihedral name foo resid default" );
    is( $angles[0]->name, 'foo1_foo1_foo1', "angle name foo resid default" );
    is( $bonds[0]->name,  'foo1_foo1',      "bond name foo resid default" );

}

{    #find_disulfide_bonds
    my $mol = $hack->read_file_mol("t/lib/1V0Z_A.pdb");
    my @ss  = $hack->find_disulfide_bonds( $mol->all_atoms );
    is( scalar(@ss), 9, "found 9  disulfides in 1V0Z" );
    my @ss_atoms = map { $_->all_atoms } @ss;
    is( scalar(@ss_atoms), 18, "9  disulfides have 18 atoms" );
    is( ( grep { $_->symbol eq "S" } @ss_atoms ), 18, "18 Sulfur atoms" );
    my $bc = 0;
    $bc += $_->bond_count foreach @ss_atoms;
    is( $bc, 0, "0 bonds for 9 disulfides with no molecule" );
    my $mol2 = HackaMol::Molecule->new(
        name  => "1voz.ss",
        atoms => [@ss_atoms],
        bonds => [@ss]
    );

    $bc += $_->bond_count foreach @ss_atoms;
    is( $bc, 18, "18 bonds for 9  disulfides (1/atom) in molecule" );


    my @ss_2 = $hack->mol_disulfide_bonds($mol,0.15);
    is_deeply([@ss],[@ss_2],'mol_disulfide gives same as find_disulfide');

    # checks out by viz xyz and pdb overlay
    # $mol2->print_xyz;
}

{    # guess element from name make them dirty if don't exist in lookup
    my @atoms;
    warning_is { @atoms = $hack->read_file_atoms("t/lib/1L2Y_noelem.pdb") }
    "MolReadRole> found 2 dirty atoms. Check symbols and lookup names PeriodicTable.pm: DIRTY: index 34 name HXYY element H     -5.592      8.445     -1.281; DIRTY: index 35 name HXXX element H      0.000      0.000      0.000;",
      "warning for dirty atoms";

    # no warning...
    is( $hack->hush_read, 0, 'hush_read off' );
    $hack->hush_read(1);
    is( $hack->hush_read, 1, 'hush_read on' );

    my @watoms = $hack->read_file_atoms("t/lib/1L2Y_noelem.pdb");

    my @lsymbols = map { $_->symbol } @atoms;

    my @dirty = grep { $_->is_dirty } @atoms;
    is( scalar(@dirty), 2, "2 dirty atoms" );
    my @esymbols = qw(N C C O C C O N H H H H H H H H N C C O C C
      C C H H H H H H H H H H H H);
    is_deeply( \@lsymbols, \@esymbols, "symbols set from names" );

}

{    # pdbqt reading tests
    my @atoms;
    my $hack = HackaMol->new;
    warning_is { @atoms = $hack->read_file_atoms("t/lib/test.pdbqt") }
    "MolReadRole> found 27 dirty atoms. Check symbols and lookup names",
      "warning for dirty atoms";
    my $mol = HackaMol::Molecule->new( name => "drugs", atoms => [@atoms] );
    is( $mol->tmax, 8, "9 models in  test.pdbqt" )
}

{ # superpose tests... 
  my $g1 = HackaMol::AtomGroup->new(atoms => [
      HackaMol::Atom->new(Z => 80, coords => [V(1,1,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(2,1,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(1,2,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(1,1,2)]),
      HackaMol::Atom->new(Z => 80, coords => [V( 0,1,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(1, 0,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(1,1, 0)]),
  ]);

  my $g2 = HackaMol::AtomGroup->new(atoms => [
      HackaMol::Atom->new(Z => 80, coords => [V(0,0,0)]),
      HackaMol::Atom->new(Z => 80, coords => [V(1,0,0)]),
      HackaMol::Atom->new(Z => 80, coords => [V(0,1,0)]),
      HackaMol::Atom->new(Z => 80, coords => [V(0,0,1)]),
      HackaMol::Atom->new(Z => 80, coords => [V(-1,0,0)]),
      HackaMol::Atom->new(Z => 80, coords => [V(0,-1,0)]),
      HackaMol::Atom->new(Z => 80, coords => [V(0,0,-1)]),
  ]);

  # superpose has been checked against VMD, but more tests are needed

  my $hack = HackaMol->new;