Example #1
0
    def __init__(self, *args, **kwds):
        super(restrained_crystal_structure_builder,
              self).__init__(*args, **kwds)
        geom = geometry_restraints
        adp = adp_restraints
        self._proxies = {}

        self._proxies = {
            'bond':
            geometry_restraints.shared_bond_simple_proxy(),
            'angle':
            geometry_restraints.shared_angle_proxy(),
            'dihedral':
            geometry_restraints.shared_dihedral_proxy(),
            'planarity':
            geometry_restraints.shared_planarity_proxy(),
            'chirality':
            geometry_restraints.shared_chirality_proxy(),
            'bond_similarity':
            geometry_restraints.shared_bond_similarity_proxy(),
            'adp_similarity':
            adp_restraints.shared_adp_similarity_proxy(),
            'rigid_bond':
            adp_restraints.shared_rigid_bond_proxy(),
            'isotropic_adp':
            adp_restraints.shared_isotropic_adp_proxy(),
            'fixed_u_eq_adp':
            adp_restraints.shared_fixed_u_eq_adp_proxy(),
            'adp_u_eq_similarity':
            adp_restraints.shared_adp_u_eq_similarity_proxy(),
            'adp_volume_similarity':
            adp_restraints.shared_adp_volume_similarity_proxy(),
        }
Example #2
0
  def __init__(self, *args, **kwds):
    super(restrained_crystal_structure_builder, self).__init__(*args, **kwds)
    geom = geometry_restraints
    adp = adp_restraints
    self._proxies = {}

    self._proxies = {
      'bond': geometry_restraints.shared_bond_simple_proxy(),
      'angle': geometry_restraints.shared_angle_proxy(),
      'dihedral': geometry_restraints.shared_dihedral_proxy(),
      'planarity': geometry_restraints.shared_planarity_proxy(),
      'chirality': geometry_restraints.shared_chirality_proxy(),
      'bond_similarity': geometry_restraints.shared_bond_similarity_proxy(),
      'adp_similarity': adp_restraints.shared_adp_similarity_proxy(),
      'rigid_bond': adp_restraints.shared_rigid_bond_proxy(),
      'isotropic_adp': adp_restraints.shared_isotropic_adp_proxy(),
      'fixed_u_eq_adp': adp_restraints.shared_fixed_u_eq_adp_proxy(),
      'adp_u_eq_similarity': adp_restraints.shared_adp_u_eq_similarity_proxy(),
      'adp_volume_similarity': adp_restraints.shared_adp_volume_similarity_proxy(),
    }
Example #3
0
def run(structure_file_path):
    xs = xray.structure.from_shelx(filename=structure_file_path,
                                   strictly_shelxl=False)

    asu_mappings = xs.asu_mappings(buffer_thickness=2)
    bond_table = crystal.pair_asu_table(asu_mappings)
    bond_table.add_covalent_pairs(xs.scattering_types())
    pair_sym_table = bond_table.extract_pair_sym_table()

    rigid_bonds = adp_restraints.shared_rigid_bond_proxy()
    scatterer = xs.scatterers()
    for sym_pair in pair_sym_table.iterator():
        i, j, op = sym_pair.i_seq, sym_pair.j_seq, sym_pair.rt_mx_ji
        if 'H' in [scatterer[idx].scattering_type for idx in (i, j)]: continue
        rigid_bonds.append(adp_restraints.rigid_bond_proxy((i, j), 1.))
    deltas = rigid_bonds.deltas(sites_cart=xs.sites_cart(),
                                u_cart=xs.scatterers().extract_u_cart(
                                    xs.unit_cell()))
    for bond, delta in zip(rigid_bonds, deltas):
        i, j = bond.i_seqs
        sc_1, sc_2 = scatterer[i], scatterer[j]
        print("%s <-> %s: %.3g" % (sc_1.label, sc_2.label, delta))
Example #4
0
def run(structure_file_path):
  xs = xray.structure.from_shelx(filename=structure_file_path,
                                 strictly_shelxl=False)

  asu_mappings = xs.asu_mappings(buffer_thickness=2)
  bond_table = crystal.pair_asu_table(asu_mappings)
  bond_table.add_covalent_pairs(xs.scattering_types())
  pair_sym_table = bond_table.extract_pair_sym_table()

  rigid_bonds = adp_restraints.shared_rigid_bond_proxy()
  scatterer = xs.scatterers()
  for sym_pair in pair_sym_table.iterator():
    i, j, op = sym_pair.i_seq, sym_pair.j_seq, sym_pair.rt_mx_ji
    if 'H' in [ scatterer[idx].scattering_type for idx in (i,j) ]: continue
    rigid_bonds.append(adp_restraints.rigid_bond_proxy((i,j), 1.))
  deltas = rigid_bonds.deltas(
    sites_cart=xs.sites_cart(),
    u_cart=xs.scatterers().extract_u_cart(xs.unit_cell()))
  for bond, delta in zip(rigid_bonds, deltas):
    i, j = bond.i_seqs
    sc_1, sc_2 = scatterer[i], scatterer[j]
    print "%s <-> %s: %.3g" % (sc_1.label, sc_2.label, delta)
Example #5
0
    def __init__(self,
                 xray_structure=None,
                 pair_sym_table=None,
                 proxies=None,
                 i_seqs=None,
                 sigma_12=0.01,
                 sigma_13=None,
                 buffer_thickness=3.5):
        """ sigma_12 and sigma_13 are the effective standard deviations used for
        1,2- and 1,3-distances respectively
    """
        assert [xray_structure, pair_sym_table].count(None) == 1
        if i_seqs is not None and len(i_seqs) == 0: i_seqs = None
        if sigma_13 is None: sigma_13 = sigma_12
        if proxies is None:
            proxies = adp_restraints.shared_rigid_bond_proxy()
        if pair_sym_table is None:
            asu_mappings = xray_structure.asu_mappings(
                buffer_thickness=buffer_thickness)
            pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
            scattering_types = xray_structure.scatterers(
            ).extract_scattering_types()
            pair_asu_table.add_covalent_pairs(
                scattering_types,
                exclude_scattering_types=flex.std_string(("H", "D")))
            pair_sym_table = pair_asu_table.extract_pair_sym_table()
        connectivity = pair_sym_table.full_simple_connectivity()
        ij_seqs = set()

        for i_seq, j_seq_dict in enumerate(pair_sym_table):
            if i_seqs is not None and i_seq not in i_seqs: continue
            for j_seq in connectivity[i_seq]:
                if i_seqs is not None and j_seq not in i_seqs: continue
                if i_seq < j_seq:
                    j_sym_ops = pair_sym_table[i_seq][j_seq]
                else:
                    k_sym_ops = pair_sym_table[j_seq][i_seq]
                for sym_op in j_sym_ops:
                    if (sym_op.is_unit_mx() and i_seq < j_seq
                            and (i_seq, j_seq) not in ij_seqs):
                        ij_seqs.add((i_seq, j_seq))
                        weight = 1 / (sigma_12 * sigma_12)
                        proxies.append(
                            adp_restraints.rigid_bond_proxy(i_seqs=(i_seq,
                                                                    j_seq),
                                                            weight=weight))
                        break
                if connectivity[j_seq].size() > 1:
                    for k_seq in connectivity[j_seq]:
                        if i_seqs is not None and k_seq not in i_seqs: continue
                        if k_seq != i_seq:
                            for sym_op in j_sym_ops:
                                if sym_op.is_unit_mx():
                                    if j_seq < k_seq:
                                        k_sym_ops = pair_sym_table[j_seq][
                                            k_seq]
                                    else:
                                        k_sym_ops = pair_sym_table[k_seq][
                                            j_seq]
                                    for sym_op in k_sym_ops:
                                        if (sym_op.is_unit_mx()
                                                and i_seq < k_seq and
                                            (i_seq, k_seq) not in ij_seqs):
                                            ij_seqs.add((i_seq, k_seq))
                                            weight = 1 / (sigma_13 * sigma_13)
                                            proxies.append(
                                                adp_restraints.
                                                rigid_bond_proxy(
                                                    i_seqs=(i_seq, k_seq),
                                                    weight=weight))
                                            break
                                    break
        self.proxies = proxies
Example #6
0
def exercise_proxy_show():
  sites_cart = flex.vec3_double((
    (-3.1739,10.8317,7.5653),(-2.5419,9.7567,6.6306),
    (-3.3369,8.8794,4.5191),(-3.4640,9.9882,5.3896)))
  site_labels = ("C1", "C2", "O16", "N8")
  u_cart = flex.sym_mat3_double((
    (0.0153,0.0206,0.0234,0.0035,-0.0052,-0.0051),
    (0.0185,0.0109,0.0206,0.0005,-0.0010,0.0002),
    (0.0295,0.0203,0.0218,-0.0010,-0.0003,-0.0044),
    (0.0159,0.0154,0.0206,-0.0003,0.0004,0.0036)))
  u_iso = flex.double((-1,-1,-1,-1))
  use_u_aniso = flex.bool((True,True,True,True))
  #
  proxies = adp_restraints.shared_adp_similarity_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=flex.sym_mat3_double(),
    u_iso=flex.double(),
    use_u_aniso=flex.bool(),
    f=sio)
  assert not show_diff(sio.getvalue(), """\
ADP similarity restraints: 0
""")
  proxies = adp_restraints.shared_adp_similarity_proxy([
    adp_restraints.adp_similarity_proxy(i_seqs=[0,1],weight=25),
    adp_restraints.adp_similarity_proxy(i_seqs=[2,3],weight=0.3)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix=":")
  assert not show_diff(sio.getvalue(), """\
:ADP similarity restraints: 2
:Sorted by residual:
:scatterers 0
:           1
:          delta    sigma   weight rms_deltas residual
: U11  -3.20e-03 2.00e-01 2.50e+01   4.96e-03 5.54e-03
: U22   9.70e-03 2.00e-01 2.50e+01
: U33   2.80e-03 2.00e-01 2.50e+01
: U12   3.00e-03 2.00e-01 2.50e+01
: U13  -4.20e-03 2.00e-01 2.50e+01
: U23  -5.30e-03 2.00e-01 2.50e+01
:scatterers 2
:           3
:          delta    sigma   weight rms_deltas residual
: U11   1.36e-02 1.83e+00 3.00e-01   6.15e-03 1.02e-04
: U22   4.90e-03 1.83e+00 3.00e-01
: U33   1.20e-03 1.83e+00 3.00e-01
: U12  -7.00e-04 1.83e+00 3.00e-01
: U13  -7.00e-04 1.83e+00 3.00e-01
: U23  -8.00e-03 1.83e+00 3.00e-01
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="rms_deltas",
    site_labels=site_labels,
    u_cart=u_cart,
    u_iso=flex.double((0.024,0.031,0.021,0.028)),
    use_u_aniso=flex.bool((False,False,False,False)),
    f=sio,
    prefix="=")
  assert not show_diff(sio.getvalue(), """\
=ADP similarity restraints: 2
=Sorted by rms_deltas:
=scatterers C1
=           C2
=          delta    sigma   weight residual
= Uiso -7.00e-03 2.00e-01 2.50e+01 1.22e-03
=scatterers O16
=           N8
=          delta    sigma   weight residual
= Uiso -7.00e-03 1.83e+00 3.00e-01 1.47e-05
""")
  #
  proxies = adp_restraints.shared_isotropic_adp_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=flex.sym_mat3_double(),
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio)
  assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 0
""")
  proxies = adp_restraints.shared_isotropic_adp_proxy([
    adp_restraints.isotropic_adp_proxy(i_seqs=(0,),weight=25),
    adp_restraints.isotropic_adp_proxy(i_seqs=(2,),weight=0.3)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    site_labels=site_labels,
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix=" ")
  assert not show_diff(sio.getvalue(), """\
 Isotropic ADP restraints: 2
 Sorted by residual:
 scatterer C1
          delta    sigma   weight rms_deltas residual
  U11 -4.47e-03 2.00e-01 2.50e+01   4.27e-03 4.11e-03
  U22  8.33e-04 2.00e-01 2.50e+01
  U33  3.63e-03 2.00e-01 2.50e+01
  U12  3.50e-03 2.00e-01 2.50e+01
  U13 -5.20e-03 2.00e-01 2.50e+01
  U23 -5.10e-03 2.00e-01 2.50e+01
 scatterer O16
          delta    sigma   weight rms_deltas residual
  U11  5.63e-03 1.83e+00 3.00e-01   3.16e-03 2.69e-05
  U22 -3.57e-03 1.83e+00 3.00e-01
  U33 -2.07e-03 1.83e+00 3.00e-01
  U12 -1.00e-03 1.83e+00 3.00e-01
  U13 -3.00e-04 1.83e+00 3.00e-01
  U23 -4.40e-03 1.83e+00 3.00e-01
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="rms_deltas",
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix="$")
  assert not show_diff(sio.getvalue(), """\
$Isotropic ADP restraints: 2
$Sorted by rms_deltas:
$scatterer 0
$         delta    sigma   weight rms_deltas residual
$ U11 -4.47e-03 2.00e-01 2.50e+01   4.27e-03 4.11e-03
$ U22  8.33e-04 2.00e-01 2.50e+01
$ U33  3.63e-03 2.00e-01 2.50e+01
$ U12  3.50e-03 2.00e-01 2.50e+01
$ U13 -5.20e-03 2.00e-01 2.50e+01
$ U23 -5.10e-03 2.00e-01 2.50e+01
$scatterer 2
$         delta    sigma   weight rms_deltas residual
$ U11  5.63e-03 1.83e+00 3.00e-01   3.16e-03 2.69e-05
$ U22 -3.57e-03 1.83e+00 3.00e-01
$ U33 -2.07e-03 1.83e+00 3.00e-01
$ U12 -1.00e-03 1.83e+00 3.00e-01
$ U13 -3.00e-04 1.83e+00 3.00e-01
$ U23 -4.40e-03 1.83e+00 3.00e-01
""")
  #
  proxies = adp_restraints.shared_rigid_bond_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    sites_cart=flex.vec3_double(),
    u_cart=flex.sym_mat3_double(),
    f=sio)
  assert not show_diff(sio.getvalue(), """\
Rigid bond restraints: 0
""")
  proxies = adp_restraints.shared_rigid_bond_proxy([
    adp_restraints.rigid_bond_proxy(i_seqs=(0,1),weight=25),
    adp_restraints.rigid_bond_proxy(i_seqs=(0,2),weight=15),
    adp_restraints.rigid_bond_proxy(i_seqs=(2,3),weight=25),
    adp_restraints.rigid_bond_proxy(i_seqs=(3,1),weight=30)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    sites_cart=sites_cart,
    site_labels=site_labels,
    u_cart=u_cart,
    f=sio,
    prefix="*")
  assert not show_diff(sio.getvalue(), """\
*Rigid bond restraints: 4
*Sorted by residual:
*scatterers O16
*           N8
*   delta_z    sigma   weight residual
* -3.96e-03 2.00e-01 2.50e+01 3.92e-04
*scatterers C1
*           C2
*   delta_z    sigma   weight residual
*  1.08e-03 2.00e-01 2.50e+01 2.89e-05
*scatterers C1
*           O16
*   delta_z    sigma   weight residual
*  4.03e-04 2.58e-01 1.50e+01 2.44e-06
*scatterers N8
*           C2
*   delta_z    sigma   weight residual
* -1.54e-04 1.83e-01 3.00e+01 7.16e-07
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="delta",
    sites_cart=sites_cart,
    u_cart=u_cart,
    f=sio,
    prefix="||",
    max_items=2)
  assert not show_diff(sio.getvalue(), """\
||Rigid bond restraints: 4
||Sorted by delta:
||scatterers 2
||           3
||   delta_z    sigma   weight residual
|| -3.96e-03 2.00e-01 2.50e+01 3.92e-04
||scatterers 0
||           1
||   delta_z    sigma   weight residual
||  1.08e-03 2.00e-01 2.50e+01 2.89e-05
||... (remaining 2 not shown)
""")
Example #7
0
def exercise_rigid_bond():
  i_seqs = (1,2)
  weight = 1
  p = adp_restraints.rigid_bond_proxy(i_seqs=i_seqs,weight=weight)
  assert p.i_seqs == i_seqs
  assert p.weight == weight
  sites = ((1,2,3),(2,3,4))
  u_cart = ((1,2,3,4,5,6), (3,4,5,6,7,8))
  expected_gradients = ((-4, -4, -4, -8, -8, -8), (4, 4, 4, 8, 8, 8))
  r = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=weight)
  assert r.weight == weight
  assert approx_equal(r.delta_z(), -6)
  assert approx_equal(r.residual(), 36)
  assert approx_equal(r.gradients(), expected_gradients)
  sites_cart = flex.vec3_double(((1,2,3),(2,5,4),(3,4,5)))
  u_cart = flex.sym_mat3_double(((1,2,3,4,5,6),
                                 (2,3,3,5,7,7),
                                 (3,4,5,3,7,8)))
  r = adp_restraints.rigid_bond(
    adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
    proxy=p)
  assert approx_equal(r.weight, weight)
  unit_cell = uctbx.unit_cell([15,25,30,90,90,90])
  sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
  u_star = flex.sym_mat3_double([
    adptbx.u_cart_as_u_star(unit_cell, u_cart_i)
    for u_cart_i in u_cart])
  pair = adp_restraints.rigid_bond_pair(sites_frac[1],
                                     sites_frac[2],
                                     u_star[1],
                                     u_star[2],
                                     unit_cell)
  assert approx_equal(pair.delta_z(), abs(r.delta_z()))
  assert approx_equal(pair.z_12(), r.z_12())
  assert approx_equal(pair.z_21(), r.z_21())
  #
  gradients_aniso_cart = flex.sym_mat3_double(sites_cart.size(), (0,0,0,0,0,0))
  gradients_iso = flex.double(sites_cart.size(), 0)
  proxies = adp_restraints.shared_rigid_bond_proxy([p,p])
  params = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
  residuals = adp_restraints.rigid_bond_residuals(params, proxies=proxies)
  assert approx_equal(residuals, (r.residual(),r.residual()))
  deltas = adp_restraints.rigid_bond_deltas(params, proxies=proxies)
  assert approx_equal(deltas, (r.delta_z(),r.delta_z()))
  residual_sum = adp_restraints.rigid_bond_residual_sum(
    params=params,
    proxies=proxies,
    gradients_aniso_cart=gradients_aniso_cart)
  assert approx_equal(residual_sum, 2 * r.residual())
  for g,e in zip(gradients_aniso_cart[1:3], r.gradients()):
    assert approx_equal(g, matrix.col(e)*2)
  fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
    restraint_type=adp_restraints.rigid_bond,
    proxy=p,
    sites_cart=sites_cart,
    u_cart=u_cart)
  for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
    assert approx_equal(g, matrix.col(e)*2)
  #
  # check frame invariance of residual
  #
  u_cart_1 = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
  u_cart_2 = matrix.sym(sym_mat3=(0.21,0.32,0.11,0.02,0.02,0.07))
  u_cart = (u_cart_1.as_sym_mat3(),u_cart_2.as_sym_mat3())
  site_cart_1 = matrix.col((1,2,3))
  site_cart_2 = matrix.col((3,1,4.2))
  sites = (tuple(site_cart_1),tuple(site_cart_2))
  a = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=1)
  expected_residual = a.residual()
  gen = flex.mersenne_twister()
  for i in range(20):
    R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
    u_cart_1_rot = R * u_cart_1 * R.transpose()
    u_cart_2_rot = R * u_cart_2 * R.transpose()
    u_cart = (u_cart_1_rot.as_sym_mat3(),u_cart_2_rot.as_sym_mat3())
    site_cart_1_rot = R * site_cart_1
    site_cart_2_rot = R * site_cart_2
    sites = (tuple(site_cart_1_rot),tuple(site_cart_2_rot))
    a = adp_restraints.rigid_bond(
      sites=sites, u_cart=u_cart,
      weight=1)
    assert approx_equal(a.residual(), expected_residual)
Example #8
0
def exercise_proxy_show():
  if sys.platform.startswith("win") and sys.version_info[:2] < (2,6):
    # This appears to be a windows-specific bug with string formatting
    # for python versions prior to 2.6, where the exponent is printed
    # with 3 digits rather than 2.
    print "Skipping exercise_proxy_show()"
    return
  sites_cart = flex.vec3_double((
    (-3.1739,10.8317,7.5653),(-2.5419,9.7567,6.6306),
    (-3.3369,8.8794,4.5191),(-3.4640,9.9882,5.3896)))
  site_labels = ("C1", "C2", "O16", "N8")
  u_cart = flex.sym_mat3_double((
    (0.0153,0.0206,0.0234,0.0035,-0.0052,-0.0051),
    (0.0185,0.0109,0.0206,0.0005,-0.0010,0.0002),
    (0.0295,0.0203,0.0218,-0.0010,-0.0003,-0.0044),
    (0.0159,0.0154,0.0206,-0.0003,0.0004,0.0036)))
  u_iso = flex.double((-1,-1,-1,-1))
  use_u_aniso = flex.bool((True,True,True,True))
  #
  proxies = adp_restraints.shared_adp_similarity_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=flex.sym_mat3_double(),
    u_iso=flex.double(),
    use_u_aniso=flex.bool(),
    f=sio)
  assert not show_diff(sio.getvalue(), """\
ADP similarity restraints: 0
""")
  proxies = adp_restraints.shared_adp_similarity_proxy([
    adp_restraints.adp_similarity_proxy(i_seqs=[0,1],weight=25),
    adp_restraints.adp_similarity_proxy(i_seqs=[2,3],weight=0.3)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix=":")
  assert not show_diff(sio.getvalue(), """\
:ADP similarity restraints: 2
:Sorted by residual:
:scatterers 0
:           1
:          delta    sigma   weight rms_deltas residual
: U11  -3.20e-03 2.00e-01 2.50e+01   4.96e-03 5.54e-03
: U22   9.70e-03 2.00e-01 2.50e+01
: U33   2.80e-03 2.00e-01 2.50e+01
: U12   3.00e-03 2.00e-01 2.50e+01
: U13  -4.20e-03 2.00e-01 2.50e+01
: U23  -5.30e-03 2.00e-01 2.50e+01
:scatterers 2
:           3
:          delta    sigma   weight rms_deltas residual
: U11   1.36e-02 1.83e+00 3.00e-01   6.15e-03 1.02e-04
: U22   4.90e-03 1.83e+00 3.00e-01
: U33   1.20e-03 1.83e+00 3.00e-01
: U12  -7.00e-04 1.83e+00 3.00e-01
: U13  -7.00e-04 1.83e+00 3.00e-01
: U23  -8.00e-03 1.83e+00 3.00e-01
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="rms_deltas",
    site_labels=site_labels,
    u_cart=u_cart,
    u_iso=flex.double((0.024,0.031,0.021,0.028)),
    use_u_aniso=flex.bool((False,False,False,False)),
    f=sio,
    prefix="=")
  assert not show_diff(sio.getvalue(), """\
=ADP similarity restraints: 2
=Sorted by rms_deltas:
=scatterers C1
=           C2
=          delta    sigma   weight residual
= Uiso -7.00e-03 2.00e-01 2.50e+01 1.22e-03
=scatterers O16
=           N8
=          delta    sigma   weight residual
= Uiso -7.00e-03 1.83e+00 3.00e-01 1.47e-05
""")
  #
  proxies = adp_restraints.shared_isotropic_adp_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    u_cart=flex.sym_mat3_double(),
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio)
  assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 0
""")
  proxies = adp_restraints.shared_isotropic_adp_proxy([
    adp_restraints.isotropic_adp_proxy(i_seqs=(0,),weight=25),
    adp_restraints.isotropic_adp_proxy(i_seqs=(2,),weight=0.3)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    site_labels=site_labels,
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix=" ")
  assert not show_diff(sio.getvalue(), """\
 Isotropic ADP restraints: 2
 Sorted by residual:
 scatterer C1
          delta    sigma   weight rms_deltas residual
  U11 -4.47e-03 2.00e-01 2.50e+01   4.27e-03 4.11e-03
  U22  8.33e-04 2.00e-01 2.50e+01
  U33  3.63e-03 2.00e-01 2.50e+01
  U12  3.50e-03 2.00e-01 2.50e+01
  U13 -5.20e-03 2.00e-01 2.50e+01
  U23 -5.10e-03 2.00e-01 2.50e+01
 scatterer O16
          delta    sigma   weight rms_deltas residual
  U11  5.63e-03 1.83e+00 3.00e-01   3.16e-03 2.69e-05
  U22 -3.57e-03 1.83e+00 3.00e-01
  U33 -2.07e-03 1.83e+00 3.00e-01
  U12 -1.00e-03 1.83e+00 3.00e-01
  U13 -3.00e-04 1.83e+00 3.00e-01
  U23 -4.40e-03 1.83e+00 3.00e-01
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="rms_deltas",
    u_cart=u_cart,
    u_iso=u_iso,
    use_u_aniso=use_u_aniso,
    f=sio,
    prefix="$")
  assert not show_diff(sio.getvalue(), """\
$Isotropic ADP restraints: 2
$Sorted by rms_deltas:
$scatterer 0
$         delta    sigma   weight rms_deltas residual
$ U11 -4.47e-03 2.00e-01 2.50e+01   4.27e-03 4.11e-03
$ U22  8.33e-04 2.00e-01 2.50e+01
$ U33  3.63e-03 2.00e-01 2.50e+01
$ U12  3.50e-03 2.00e-01 2.50e+01
$ U13 -5.20e-03 2.00e-01 2.50e+01
$ U23 -5.10e-03 2.00e-01 2.50e+01
$scatterer 2
$         delta    sigma   weight rms_deltas residual
$ U11  5.63e-03 1.83e+00 3.00e-01   3.16e-03 2.69e-05
$ U22 -3.57e-03 1.83e+00 3.00e-01
$ U33 -2.07e-03 1.83e+00 3.00e-01
$ U12 -1.00e-03 1.83e+00 3.00e-01
$ U13 -3.00e-04 1.83e+00 3.00e-01
$ U23 -4.40e-03 1.83e+00 3.00e-01
""")
  #
  proxies = adp_restraints.shared_rigid_bond_proxy()
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    sites_cart=flex.vec3_double(),
    u_cart=flex.sym_mat3_double(),
    f=sio)
  assert not show_diff(sio.getvalue(), """\
Rigid bond restraints: 0
""")
  proxies = adp_restraints.shared_rigid_bond_proxy([
    adp_restraints.rigid_bond_proxy(i_seqs=(0,1),weight=25),
    adp_restraints.rigid_bond_proxy(i_seqs=(0,2),weight=15),
    adp_restraints.rigid_bond_proxy(i_seqs=(2,3),weight=25),
    adp_restraints.rigid_bond_proxy(i_seqs=(3,1),weight=30)])
  sio = StringIO()
  proxies.show_sorted(
    by_value="residual",
    sites_cart=sites_cart,
    site_labels=site_labels,
    u_cart=u_cart,
    f=sio,
    prefix="*")
  assert not show_diff(sio.getvalue(), """\
*Rigid bond restraints: 4
*Sorted by residual:
*scatterers O16
*           N8
*   delta_z    sigma   weight residual
* -3.96e-03 2.00e-01 2.50e+01 3.92e-04
*scatterers C1
*           C2
*   delta_z    sigma   weight residual
*  1.08e-03 2.00e-01 2.50e+01 2.89e-05
*scatterers C1
*           O16
*   delta_z    sigma   weight residual
*  4.03e-04 2.58e-01 1.50e+01 2.44e-06
*scatterers N8
*           C2
*   delta_z    sigma   weight residual
* -1.54e-04 1.83e-01 3.00e+01 7.16e-07
""")
  sio = StringIO()
  proxies.show_sorted(
    by_value="delta",
    sites_cart=sites_cart,
    u_cart=u_cart,
    f=sio,
    prefix="||",
    max_items=2)
  assert not show_diff(sio.getvalue(), """\
||Rigid bond restraints: 4
||Sorted by delta:
||scatterers 2
||           3
||   delta_z    sigma   weight residual
|| -3.96e-03 2.00e-01 2.50e+01 3.92e-04
||scatterers 0
||           1
||   delta_z    sigma   weight residual
||  1.08e-03 2.00e-01 2.50e+01 2.89e-05
||... (remaining 2 not shown)
""")
Example #9
0
def exercise_rigid_bond():
  i_seqs = (1,2)
  weight = 1
  p = adp_restraints.rigid_bond_proxy(i_seqs=i_seqs,weight=weight)
  assert p.i_seqs == i_seqs
  assert p.weight == weight
  sites = ((1,2,3),(2,3,4))
  u_cart = ((1,2,3,4,5,6), (3,4,5,6,7,8))
  expected_gradients = ((-4, -4, -4, -8, -8, -8), (4, 4, 4, 8, 8, 8))
  r = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=weight)
  assert r.weight == weight
  assert approx_equal(r.delta_z(), -6)
  assert approx_equal(r.residual(), 36)
  assert approx_equal(r.gradients(), expected_gradients)
  sites_cart = flex.vec3_double(((1,2,3),(2,5,4),(3,4,5)))
  u_cart = flex.sym_mat3_double(((1,2,3,4,5,6),
                                 (2,3,3,5,7,7),
                                 (3,4,5,3,7,8)))
  r = adp_restraints.rigid_bond(
    adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
    proxy=p)
  assert approx_equal(r.weight, weight)
  unit_cell = uctbx.unit_cell([15,25,30,90,90,90])
  sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
  u_star = flex.sym_mat3_double([
    adptbx.u_cart_as_u_star(unit_cell, u_cart_i)
    for u_cart_i in u_cart])
  pair = adp_restraints.rigid_bond_pair(sites_frac[1],
                                     sites_frac[2],
                                     u_star[1],
                                     u_star[2],
                                     unit_cell)
  assert approx_equal(pair.delta_z(), abs(r.delta_z()))
  assert approx_equal(pair.z_12(), r.z_12())
  assert approx_equal(pair.z_21(), r.z_21())
  #
  gradients_aniso_cart = flex.sym_mat3_double(sites_cart.size(), (0,0,0,0,0,0))
  gradients_iso = flex.double(sites_cart.size(), 0)
  proxies = adp_restraints.shared_rigid_bond_proxy([p,p])
  params = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
  residuals = adp_restraints.rigid_bond_residuals(params, proxies=proxies)
  assert approx_equal(residuals, (r.residual(),r.residual()))
  deltas = adp_restraints.rigid_bond_deltas(params, proxies=proxies)
  assert approx_equal(deltas, (r.delta_z(),r.delta_z()))
  residual_sum = adp_restraints.rigid_bond_residual_sum(
    params=params,
    proxies=proxies,
    gradients_aniso_cart=gradients_aniso_cart)
  assert approx_equal(residual_sum, 2 * r.residual())
  for g,e in zip(gradients_aniso_cart[1:3], r.gradients()):
    assert approx_equal(g, matrix.col(e)*2)
  fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
    restraint_type=adp_restraints.rigid_bond,
    proxy=p,
    sites_cart=sites_cart,
    u_cart=u_cart)
  for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
    assert approx_equal(g, matrix.col(e)*2)
  #
  # check frame invariance of residual
  #
  u_cart_1 = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
  u_cart_2 = matrix.sym(sym_mat3=(0.21,0.32,0.11,0.02,0.02,0.07))
  u_cart = (u_cart_1.as_sym_mat3(),u_cart_2.as_sym_mat3())
  site_cart_1 = matrix.col((1,2,3))
  site_cart_2 = matrix.col((3,1,4.2))
  sites = (tuple(site_cart_1),tuple(site_cart_2))
  a = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=1)
  expected_residual = a.residual()
  gen = flex.mersenne_twister()
  for i in range(20):
    R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
    u_cart_1_rot = R * u_cart_1 * R.transpose()
    u_cart_2_rot = R * u_cart_2 * R.transpose()
    u_cart = (u_cart_1_rot.as_sym_mat3(),u_cart_2_rot.as_sym_mat3())
    site_cart_1_rot = R * site_cart_1
    site_cart_2_rot = R * site_cart_2
    sites = (tuple(site_cart_1_rot),tuple(site_cart_2_rot))
    a = adp_restraints.rigid_bond(
      sites=sites, u_cart=u_cart,
      weight=1)
    assert approx_equal(a.residual(), expected_residual)
Example #10
0
    def __init__(
        self,
        xray_structure=None,
        pair_sym_table=None,
        proxies=None,
        i_seqs=None,
        sigma_12=0.01,
        sigma_13=None,
        buffer_thickness=3.5,
    ):
        """ sigma_12 and sigma_13 are the effective standard deviations used for
        1,2- and 1,3-distances respectively
    """
        assert [xray_structure, pair_sym_table].count(None) == 1
        if i_seqs is not None and len(i_seqs) == 0:
            i_seqs = None
        if sigma_13 is None:
            sigma_13 = sigma_12
        if proxies is None:
            proxies = adp_restraints.shared_rigid_bond_proxy()
        if pair_sym_table is None:
            asu_mappings = xray_structure.asu_mappings(buffer_thickness=buffer_thickness)
            pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
            scattering_types = xray_structure.scatterers().extract_scattering_types()
            pair_asu_table.add_covalent_pairs(scattering_types, exclude_scattering_types=flex.std_string(("H", "D")))
            pair_sym_table = pair_asu_table.extract_pair_sym_table()
        connectivity = pair_sym_table.full_simple_connectivity()
        ij_seqs = set()

        for i_seq, j_seq_dict in enumerate(pair_sym_table):
            if i_seqs is not None and i_seq not in i_seqs:
                continue
            for j_seq in connectivity[i_seq]:
                if i_seqs is not None and j_seq not in i_seqs:
                    continue
                if i_seq < j_seq:
                    j_sym_ops = pair_sym_table[i_seq][j_seq]
                else:
                    k_sym_ops = pair_sym_table[j_seq][i_seq]
                for sym_op in j_sym_ops:
                    if sym_op.is_unit_mx() and i_seq < j_seq and (i_seq, j_seq) not in ij_seqs:
                        ij_seqs.add((i_seq, j_seq))
                        weight = 1 / (sigma_12 * sigma_12)
                        proxies.append(adp_restraints.rigid_bond_proxy(i_seqs=(i_seq, j_seq), weight=weight))
                        break
                if connectivity[j_seq].size() > 1:
                    for k_seq in connectivity[j_seq]:
                        if i_seqs is not None and k_seq not in i_seqs:
                            continue
                        if k_seq != i_seq:
                            for sym_op in j_sym_ops:
                                if sym_op.is_unit_mx():
                                    if j_seq < k_seq:
                                        k_sym_ops = pair_sym_table[j_seq][k_seq]
                                    else:
                                        k_sym_ops = pair_sym_table[k_seq][j_seq]
                                    for sym_op in k_sym_ops:
                                        if sym_op.is_unit_mx() and i_seq < k_seq and (i_seq, k_seq) not in ij_seqs:
                                            ij_seqs.add((i_seq, k_seq))
                                            weight = 1 / (sigma_13 * sigma_13)
                                            proxies.append(
                                                adp_restraints.rigid_bond_proxy(i_seqs=(i_seq, k_seq), weight=weight)
                                            )
                                            break
                                    break
        self.proxies = proxies