def group_ensembles(self):
groups = []
current_group = last_ensemble = None
for ens in self._ensembles:
# this will check for overlap
if ((last_ensemble is None) or (alt_confs.get_selection_gap(
last_ensemble.selection, ens.selection) > 0)):
current_group = [ens]
groups.append(current_group)
else:
current_group.append(ens)
last_ensemble = ens
return [ensemble_group(ensembles) for ensembles in groups]
def group_ensembles (self) :
groups = []
current_group = last_ensemble = None
for ens in self._ensembles :
# this will check for overlap
if ((last_ensemble is None) or
(alt_confs.get_selection_gap(last_ensemble.selection,
ens.selection) > 0)) :
current_group = [ ens ]
groups.append(current_group)
else :
current_group.append(ens)
last_ensemble = ens
return [ ensemble_group(ensembles) for ensembles in groups ]
def exercise_utils():
#--- coord_stats_with_flips
pdb_1 = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1639 N PHE A 113 18.514 41.994 54.886 1.00 12.36 N
ATOM 1640 CA PHE A 113 19.737 42.742 54.898 1.00 12.97 C
ATOM 1641 C PHE A 113 19.514 44.206 55.111 1.00 11.88 C
ATOM 1642 O PHE A 113 18.442 44.758 54.823 1.00 13.75 O
ATOM 1643 CB PHE A 113 20.587 42.460 53.684 1.00 20.08 C
ATOM 1644 CG PHE A 113 19.893 42.692 52.399 1.00 17.15 C
ATOM 1645 CD1 PHE A 113 19.182 41.689 51.798 1.00 20.34 C
ATOM 1646 CD2 PHE A 113 20.029 43.895 51.745 1.00 21.22 C
ATOM 1647 CE1 PHE A 113 18.577 41.887 50.601 1.00 23.49 C
ATOM 1648 CE2 PHE A 113 19.411 44.105 50.542 1.00 24.87 C
ATOM 1649 CZ PHE A 113 18.675 43.097 49.976 1.00 21.81 C
ATOM 1650 H PHE A 113 17.875 42.342 54.427 1.00 14.83 H
ATOM 1651 HA PHE A 113 20.250 42.435 55.661 1.00 15.57 H
ATOM 1652 HB2 PHE A 113 21.367 43.036 53.708 1.00 24.10 H
ATOM 1653 HB3 PHE A 113 20.865 41.531 53.707 1.00 24.10 H
ATOM 1654 HD1 PHE A 113 19.099 40.866 52.224 1.00 24.40 H
ATOM 1655 HD2 PHE A 113 20.518 44.581 52.138 1.00 25.47 H
ATOM 1656 HE1 PHE A 113 18.077 41.204 50.215 1.00 28.18 H
ATOM 1657 HE2 PHE A 113 19.488 44.927 50.113 1.00 29.84 H
ATOM 1658 HZ PHE A 113 18.261 43.230 49.154 1.00 26.17 H
""")
pdb_2 = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1639 N PHE A 113 18.514 41.994 54.886 1.00 12.36 N
ATOM 1640 CA PHE A 113 19.737 42.742 54.898 1.00 12.97 C
ATOM 1641 C PHE A 113 19.514 44.206 55.111 1.00 11.88 C
ATOM 1642 O PHE A 113 18.442 44.758 54.823 1.00 13.75 O
ATOM 1643 CB PHE A 113 20.587 42.460 53.684 1.00 20.08 C
ATOM 1644 CG PHE A 113 19.893 42.692 52.399 1.00 17.15 C
ATOM 1645 CD1 PHE A 113 20.174 43.797 51.643 1.00 20.34 C
ATOM 1646 CD2 PHE A 113 18.888 41.845 51.991 1.00 21.22 C
ATOM 1647 CE1 PHE A 113 19.512 44.033 50.483 1.00 23.49 C
ATOM 1648 CE2 PHE A 113 18.224 42.071 50.816 1.00 24.87 C
ATOM 1649 CZ PHE A 113 18.548 43.166 50.057 1.00 21.81 C
ATOM 1650 H PHE A 113 17.875 42.342 54.427 1.00 14.83 H
ATOM 1651 HA PHE A 113 20.250 42.435 55.661 1.00 15.57 H
ATOM 1652 HB2 PHE A 113 21.367 43.036 53.708 1.00 24.10 H
ATOM 1653 HB3 PHE A 113 20.865 41.531 53.707 1.00 24.10 H
ATOM 1654 HD1 PHE A 113 20.840 44.386 51.919 1.00 24.40 H
ATOM 1655 HD2 PHE A 113 18.681 41.096 52.501 1.00 25.47 H
ATOM 1656 HE1 PHE A 113 19.730 44.776 49.967 1.00 28.18 H
ATOM 1657 HE2 PHE A 113 17.560 41.484 50.533 1.00 29.84 H
ATOM 1658 HZ PHE A 113 18.093 43.330 49.263 1.00 26.17 H
""")
hierarchy_1 = pdb_1.hierarchy
hierarchy_2 = pdb_2.hierarchy
pdb_atoms_1 = hierarchy_1.atoms()
sites_1 = pdb_atoms_1.extract_xyz()
sites_2 = hierarchy_2.atoms().extract_xyz()
result = alternate_conformations.coord_stats_with_flips(
sites_1, sites_2, pdb_atoms_1)
assert (approx_equal(result.rmsd, 0.2, eps=0.001))
assert (approx_equal(result.max_dev, 0.452427, eps=0.00001))
#--- get_selection_gap
assert (alternate_conformations.get_selection_gap([1, 2, 3, 4, 5],
[6, 7, 8, 9]) == 0)
assert (alternate_conformations.get_selection_gap([6, 7],
[1, 2, 3, 4, 5]) == 0)
assert (alternate_conformations.get_selection_gap([1, 2, 3, 4, 5],
[7, 8, 9]) == 1)
assert (alternate_conformations.get_selection_gap([1, 2, 3, 4, 5],
[4, 5, 7, 8, 9]) == -2)
assert (alternate_conformations.get_selection_gap([4, 5, 7, 8, 9],
[1, 2, 3, 4]) == -1)
#--- score_rotamers
n_outliers = alternate_conformations.score_rotamers(
hierarchy_2, flex.bool(sites_2.size(), True))
assert (n_outliers == 0)
#--- get_partial_omit_map
xrs = pdb_1.input.xray_structure_simple()
f_calc = abs(xrs.structure_factors(d_min=1.5).f_calc())
f_calc.set_observation_type_xray_amplitude()
flags = f_calc.generate_r_free_flags()
fmodel = mmtbx.utils.fmodel_simple(xray_structures=[xrs],
f_obs=f_calc,
r_free_flags=flags,
scattering_table="n_gaussian",
bulk_solvent_and_scaling=False,
skip_twin_detection=True)
sel = pdb_1.hierarchy.atom_selection_cache().selection("name CZ")
assert (sel.count(True) == 1)
two_fofc_map, fofc_map = alternate_conformations.get_partial_omit_map(
fmodel=fmodel, selection=sel)
site = xrs.sites_frac()[sel.iselection()[0]] # CZ coordinate
assert (fofc_map.tricubic_interpolation(site) > 20)
def exercise_utils () :
#--- coord_stats_with_flips
pdb_1 = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1639 N PHE A 113 18.514 41.994 54.886 1.00 12.36 N
ATOM 1640 CA PHE A 113 19.737 42.742 54.898 1.00 12.97 C
ATOM 1641 C PHE A 113 19.514 44.206 55.111 1.00 11.88 C
ATOM 1642 O PHE A 113 18.442 44.758 54.823 1.00 13.75 O
ATOM 1643 CB PHE A 113 20.587 42.460 53.684 1.00 20.08 C
ATOM 1644 CG PHE A 113 19.893 42.692 52.399 1.00 17.15 C
ATOM 1645 CD1 PHE A 113 19.182 41.689 51.798 1.00 20.34 C
ATOM 1646 CD2 PHE A 113 20.029 43.895 51.745 1.00 21.22 C
ATOM 1647 CE1 PHE A 113 18.577 41.887 50.601 1.00 23.49 C
ATOM 1648 CE2 PHE A 113 19.411 44.105 50.542 1.00 24.87 C
ATOM 1649 CZ PHE A 113 18.675 43.097 49.976 1.00 21.81 C
ATOM 1650 H PHE A 113 17.875 42.342 54.427 1.00 14.83 H
ATOM 1651 HA PHE A 113 20.250 42.435 55.661 1.00 15.57 H
ATOM 1652 HB2 PHE A 113 21.367 43.036 53.708 1.00 24.10 H
ATOM 1653 HB3 PHE A 113 20.865 41.531 53.707 1.00 24.10 H
ATOM 1654 HD1 PHE A 113 19.099 40.866 52.224 1.00 24.40 H
ATOM 1655 HD2 PHE A 113 20.518 44.581 52.138 1.00 25.47 H
ATOM 1656 HE1 PHE A 113 18.077 41.204 50.215 1.00 28.18 H
ATOM 1657 HE2 PHE A 113 19.488 44.927 50.113 1.00 29.84 H
ATOM 1658 HZ PHE A 113 18.261 43.230 49.154 1.00 26.17 H
""")
pdb_2 = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1639 N PHE A 113 18.514 41.994 54.886 1.00 12.36 N
ATOM 1640 CA PHE A 113 19.737 42.742 54.898 1.00 12.97 C
ATOM 1641 C PHE A 113 19.514 44.206 55.111 1.00 11.88 C
ATOM 1642 O PHE A 113 18.442 44.758 54.823 1.00 13.75 O
ATOM 1643 CB PHE A 113 20.587 42.460 53.684 1.00 20.08 C
ATOM 1644 CG PHE A 113 19.893 42.692 52.399 1.00 17.15 C
ATOM 1645 CD1 PHE A 113 20.174 43.797 51.643 1.00 20.34 C
ATOM 1646 CD2 PHE A 113 18.888 41.845 51.991 1.00 21.22 C
ATOM 1647 CE1 PHE A 113 19.512 44.033 50.483 1.00 23.49 C
ATOM 1648 CE2 PHE A 113 18.224 42.071 50.816 1.00 24.87 C
ATOM 1649 CZ PHE A 113 18.548 43.166 50.057 1.00 21.81 C
ATOM 1650 H PHE A 113 17.875 42.342 54.427 1.00 14.83 H
ATOM 1651 HA PHE A 113 20.250 42.435 55.661 1.00 15.57 H
ATOM 1652 HB2 PHE A 113 21.367 43.036 53.708 1.00 24.10 H
ATOM 1653 HB3 PHE A 113 20.865 41.531 53.707 1.00 24.10 H
ATOM 1654 HD1 PHE A 113 20.840 44.386 51.919 1.00 24.40 H
ATOM 1655 HD2 PHE A 113 18.681 41.096 52.501 1.00 25.47 H
ATOM 1656 HE1 PHE A 113 19.730 44.776 49.967 1.00 28.18 H
ATOM 1657 HE2 PHE A 113 17.560 41.484 50.533 1.00 29.84 H
ATOM 1658 HZ PHE A 113 18.093 43.330 49.263 1.00 26.17 H
""")
hierarchy_1 = pdb_1.hierarchy
hierarchy_2 = pdb_2.hierarchy
pdb_atoms_1 = hierarchy_1.atoms()
sites_1 = pdb_atoms_1.extract_xyz()
sites_2 = hierarchy_2.atoms().extract_xyz()
result = alternate_conformations.coord_stats_with_flips(sites_1, sites_2, pdb_atoms_1)
assert (approx_equal(result.rmsd, 0.2, eps=0.001))
assert (approx_equal(result.max_dev, 0.452427, eps=0.00001))
#--- get_selection_gap
assert (alternate_conformations.get_selection_gap([1,2,3,4,5],[6,7,8,9]) == 0)
assert (alternate_conformations.get_selection_gap([6,7], [1,2,3,4,5]) == 0)
assert (alternate_conformations.get_selection_gap([1,2,3,4,5],[7,8,9]) == 1)
assert (alternate_conformations.get_selection_gap([1,2,3,4,5],[4,5,7,8,9]) == -2)
assert (alternate_conformations.get_selection_gap([4,5,7,8,9],[1,2,3,4]) == -1)
#--- score_rotamers
n_outliers = alternate_conformations.score_rotamers(hierarchy_2,
flex.bool(sites_2.size(), True))
assert (n_outliers == 0)
#--- get_partial_omit_map
xrs = pdb_1.input.xray_structure_simple()
f_calc = abs(xrs.structure_factors(d_min=1.5).f_calc())
f_calc.set_observation_type_xray_amplitude()
flags = f_calc.generate_r_free_flags()
fmodel = mmtbx.utils.fmodel_simple(
xray_structures=[xrs],
f_obs=f_calc,
r_free_flags=flags,
scattering_table="n_gaussian",
bulk_solvent_and_scaling=False,
skip_twin_detection=True)
sel = pdb_1.hierarchy.atom_selection_cache().selection("name CZ")
assert (sel.count(True) == 1)
two_fofc_map, fofc_map = alternate_conformations.get_partial_omit_map(
fmodel=fmodel,
selection=sel)
site = xrs.sites_frac()[sel.iselection()[0]] # CZ coordinate
assert (fofc_map.tricubic_interpolation(site) > 20)