def exercise_planarity():
p = geometry_restraints.motif_planarity()
assert p.atom_names.size() == 0
assert p.weights.size() == 0
assert p.id == ""
p = geometry_restraints.motif_planarity(
atom_names=flex.std_string(["a", "b"]),
weights=flex.double([1.5, 2.5]),
id="t")
assert list(p.atom_names) == ["a", "b"]
assert list(p.weights) == [1.5, 2.5]
assert p.id == "t"
p.atom_names = flex.std_string(["x", "y", "z"])
assert list(p.atom_names) == ["x", "y", "z"]
p.weights = flex.double([3.5, 6.5])
assert list(p.weights) == [3.5, 6.5]
p.id = "u"
assert p.id == "u"
def exercise_motif():
m = geometry_restraints.motif()
assert m.id == ""
assert m.description == ""
assert m.info.size() == 0
assert m.manipulation_ids.size() == 0
assert len(m.atoms_as_list()) == 0
assert len(m.bonds_as_list()) == 0
assert len(m.angles_as_list()) == 0
assert len(m.dihedrals_as_list()) == 0
assert len(m.chiralities_as_list()) == 0
assert len(m.planarities_as_list()) == 0
m.id = "a"
assert m.id == "a"
m.description = "b"
assert m.description == "b"
m.info.append("c")
m.info.append("d")
assert m.info.size() == 2
m.manipulation_ids.append("e")
m.manipulation_ids.append("f")
assert m.manipulation_ids.size() == 2
l = [geometry_restraints.motif_atom(*a, **k) for a,k in [
((), {"name": "a", "scattering_type": "b", "nonbonded_type": "c",
"partial_charge": -0.1}),
(("d"),{})]]
m.set_atoms(l)
assert [atom.name for atom in m.atoms_as_list()] == ["a", "d"]
l = [geometry_restraints.motif_bond(*a, **k) for a,k in [
((), {"atom_names": ("a", "b"), "type": "c", "distance_ideal": 2.3,
"weight": 11.5, "id": "d"}),
((("e", "f"),),{})]]
m.set_bonds(l)
assert [bond.atom_names for bond in m.bonds_as_list()] \
== [("a", "b"), ("e", "f")]
l = [geometry_restraints.motif_angle(*a, **k) for a,k in [
((), {"atom_names": ("a", "b", "c"), "angle_ideal": 3.2,
"weight": 15.1, "id": "d"}),
((("e", "f", "g"),),{})]]
m.set_angles(l)
assert [angle.atom_names for angle in m.angles_as_list()] \
== [("a", "b", "c"), ("e", "f", "g")]
l = [geometry_restraints.motif_dihedral(*a, **k) for a,k in [
((), {"atom_names": ("a", "b", "c", "d"), "angle_ideal": 4.3,
"weight": 1.5, "periodicity": 3, "id": "e"}),
((("f", "g", "h", "i"),),{})]]
m.set_dihedrals(l)
assert [dihedral.atom_names for dihedral in m.dihedrals_as_list()] \
== [("a", "b", "c", "d"), ("f", "g", "h", "i")]
l = [geometry_restraints.motif_chirality(*a, **k) for a,k in [
((), {"atom_names": ("a", "b", "c", "d"), "volume_sign": "e",
"both_signs": True, "volume_ideal": 10.3, "weight": 1.5, "id": "f"}),
((("g", "h", "i", "j"),),{})]]
m.set_chiralities(l)
assert [chirality.atom_names for chirality in m.chiralities_as_list()] \
== [("a", "b", "c", "d"), ("g", "h", "i", "j")]
l = [geometry_restraints.motif_planarity(
atom_names=flex.std_string(["a", "b"]),
weights=flex.double([1,2]),
id="c"),
geometry_restraints.motif_planarity(
atom_names=flex.std_string(["d"]),
weights=flex.double([3]))]
m.set_planarities(l)
assert [list(planarity.atom_names)
for planarity in m.planarities_as_list()] \
== [["a", "b"], ["d"]]
out = StringIO()
m.show(out=out, prefix="&*")
assert not show_diff(out.getvalue(), """\
&*geometry_restraints.motif {
&* id = "a"
&* description = "b"
&* info = "c"
&* info = "d"
&* manipulation_id = "e"
&* manipulation_id = "f"
&* atom = [name scattering_type nonbonded_type partial_charge]
&* atom = "a" "b" "c" -0.1
&* atom = "d" "" "" 0
&* bond = [atom_name*2 type distance_ideal weight id]
&* bond = "a" "b" "c" 2.3 11.5 "d"
&* bond = "e" "f" "" 0 0 ""
&* angle = [atom_name*3 angle_ideal weight id]
&* angle = "a" "b" "c" 3.2 15.1 "d"
&* angle = "e" "f" "g" 0 0 ""
&* dihedral = [atom_name*4 angle_ideal weight periodicity id]
&* dihedral = "a" "b" "c" "d" 4.3 1.5 3 "e"
&* dihedral = "f" "g" "h" "i" 0 0 0 ""
&* chirality = [atom_name*4 volume_sign both_signs volume_ideal weight id]
&* chirality = "a" "b" "c" "d" "e" True 10.3 1.5 "f"
&* chirality = "g" "h" "i" "j" "" False 0 0 ""
&* planarity {
&* id = "c"
&* atom = [name weight]
&* atom = "a" 1
&* atom = "b" 2
&* }
&* planarity {
&* id = ""
&* atom = [name weight]
&* atom = "d" 3
&* }
&*}
""")
out = StringIO()
m.show(out=out)
phil.parse(input_string=out.getvalue())
assert list(a.motif_ids) == ["-", "+"]
a.atom = geometry_restraints.motif_atom(name="a")
assert a.atom.name == "a"
a.motif_atom_name = "x"
assert a.motif_atom_name == "x"
a.bond = geometry_restraints.motif_bond(atom_names=["b", "c"])
assert a.bond.atom_names == ("b", "c")
a.angle = geometry_restraints.motif_angle(atom_names=["d", "e", "f"])
assert a.angle.atom_names == ("d", "e", "f")
a.dihedral = geometry_restraints.motif_dihedral(atom_names=["h","i","j","k"])
assert a.dihedral.atom_names == ("h", "i", "j", "k")
a.chirality = geometry_restraints.motif_chirality(
atom_names=["l","m","n","o"])
assert a.chirality.atom_names == ("l", "m", "n", "o")
a.planarity = geometry_restraints.motif_planarity(
atom_names=flex.std_string(["p", "q"]),
weights=flex.double([1,2]))
a.planarity_motif_id = "h"
assert a.planarity_motif_id == "h"
a.set_planarity_atom_actions(["add", "change", "delete"])
assert a.planarity_atom_actions_as_list() == ["add", "change", "delete"]
try: a.set_planarity_atom_actions(["add", "chnage", "delete"])
except RuntimeError, e:
assert str(e) == 'Unknown cctbx::geometry_restraints::motif::alteration' \
'::action_type: "chnage"\n' \
' Possible action types are: "", "add", "delete", "change"'
else: raise Exception_expected
assert a.planarity_atom_actions_as_list() == []
assert list(a.planarity.atom_names) == ["p", "q"]
assert a.set_change_partial_charge(state=True) is a
assert a.change_partial_charge()
def as_geometry_restraints_motif(self):
result = geometry_restraints.motif()
result.id = if_none(self.chem_comp.id, "")
result.description = if_none(self.chem_comp.name, "").strip()
if (self.source_info is not None):
result.info.append(self.source_info)
result.set_atoms([
geometry_restraints.motif_atom(
name=if_none(atom.atom_id, ""),
scattering_type=if_none(atom.type_symbol, ""),
nonbonded_type=if_none(atom.type_energy, ""),
partial_charge=if_none(atom.partial_charge, 0))
for atom in self.atom_list])
result.set_bonds([
geometry_restraints.motif_bond(
atom_names=[
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")],
type=if_none(bond.type, ""),
distance_ideal=if_none(bond.value_dist, 0),
weight=esd_as_weight(bond.value_dist_esd))
for bond in self.bond_list])
result.set_angles([
geometry_restraints.motif_angle(
atom_names=[
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")],
angle_ideal=if_none(angle.value_angle, 0),
weight=esd_as_weight(angle.value_angle_esd))
for angle in self.angle_list])
result.set_dihedrals([
geometry_restraints.motif_dihedral(
atom_names=[
if_none(tor.atom_id_1, ""),
if_none(tor.atom_id_2, ""),
if_none(tor.atom_id_3, ""),
if_none(tor.atom_id_4, "")],
angle_ideal=if_none(tor.value_angle, 0),
weight=esd_as_weight(tor.value_angle_esd),
periodicity=if_none(tor.period, 0),
id=tor.id)
for tor in self.tor_list])
result.set_chiralities([
geometry_restraints.motif_chirality(
atom_names=[
if_none(chir.atom_id_centre, ""),
if_none(chir.atom_id_1, ""),
if_none(chir.atom_id_2, ""),
if_none(chir.atom_id_3, "")],
volume_sign=chir.volume_sign,
id=chir.id)
for chir in self.chir_list])
planarities = []
for plane in self.get_planes():
atom_names = flex.std_string([if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms])
weights = flex.double([esd_as_weight(plane_atom.dist_esd)
for plane_atom in plane.plane_atoms])
planarities.append(
geometry_restraints.motif_planarity(
atom_names=atom_names,
weights=weights,
id=plane.plane_id))
result.set_planarities(planarities)
return result
def as_geometry_restraints_motif(self):
result = geometry_restraints.motif()
result.id = if_none(self.chem_comp.id, "")
result.description = if_none(self.chem_comp.name, "").strip()
if (self.source_info is not None):
result.info.append(self.source_info)
result.set_atoms([
geometry_restraints.motif_atom(
name=if_none(atom.atom_id, ""),
scattering_type=if_none(atom.type_symbol, ""),
nonbonded_type=if_none(atom.type_energy, ""),
partial_charge=if_none(atom.partial_charge, 0))
for atom in self.atom_list
])
result.set_bonds([
geometry_restraints.motif_bond(
atom_names=[
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")
],
type=if_none(bond.type, ""),
distance_ideal=if_none(bond.value_dist, 0),
weight=esd_as_weight(bond.value_dist_esd))
for bond in self.bond_list
])
result.set_angles([
geometry_restraints.motif_angle(
atom_names=[
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")
],
angle_ideal=if_none(angle.value_angle, 0),
weight=esd_as_weight(angle.value_angle_esd))
for angle in self.angle_list
])
result.set_dihedrals([
geometry_restraints.motif_dihedral(
atom_names=[
if_none(tor.atom_id_1, ""),
if_none(tor.atom_id_2, ""),
if_none(tor.atom_id_3, ""),
if_none(tor.atom_id_4, "")
],
angle_ideal=if_none(tor.value_angle, 0),
weight=esd_as_weight(tor.value_angle_esd),
periodicity=if_none(tor.period, 0),
id=tor.id) for tor in self.tor_list
])
result.set_chiralities([
geometry_restraints.motif_chirality(atom_names=[
if_none(chir.atom_id_centre, ""),
if_none(chir.atom_id_1, ""),
if_none(chir.atom_id_2, ""),
if_none(chir.atom_id_3, "")
],
volume_sign=chir.volume_sign,
id=chir.id)
for chir in self.chir_list
])
planarities = []
for plane in self.get_planes():
atom_names = flex.std_string([
if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms
])
weights = flex.double([
esd_as_weight(plane_atom.dist_esd)
for plane_atom in plane.plane_atoms
])
planarities.append(
geometry_restraints.motif_planarity(atom_names=atom_names,
weights=weights,
id=plane.plane_id))
result.set_planarities(planarities)
return result
def exercise_alteration():
a = geometry_restraints.motif_alteration()
assert a.action == ""
assert a.operand == ""
a = geometry_restraints.motif_alteration(action="add")
assert a.action == "add"
assert a.operand == ""
a = geometry_restraints.motif_alteration(action="change", operand="bond")
assert a.action == "change"
assert a.operand == "bond"
assert a.motif_ids.size() == 0
assert a.atom.name == ""
assert a.motif_atom_name == ""
assert a.bond.atom_names == ("", "")
assert a.angle.atom_names == ("", "", "")
assert a.dihedral.atom_names == ("", "", "", "")
assert a.chirality.atom_names == ("", "", "", "")
assert a.planarity.atom_names.size() == 0
assert a.planarity_motif_id == ""
assert a.planarity_atom_actions_as_list() == []
assert not a.change_partial_charge()
assert not a.change_distance_ideal()
assert not a.change_weight()
assert not a.change_angle_ideal()
assert not a.change_periodicity()
assert not a.change_both_signs()
assert not a.change_volume_ideal()
for action in ["", "add", "delete", "change"]:
a.action = action
assert a.action == action
try:
a.action = "chnage"
except RuntimeError as e:
assert str(e) == 'Unknown cctbx::geometry_restraints::motif::alteration' \
'::action_type: "chnage"\n' \
' Possible action types are: "", "add", "delete", "change"'
else:
raise Exception_expected
for operand in [
"", "atom", "bond", "angle", "dihedral", "chirality", "planarity"
]:
a.operand = operand
assert a.operand == operand
try:
a.operand = "diehdral"
except RuntimeError as e:
assert str(e) == 'Unknown cctbx::geometry_restraints::motif::alteration' \
'::operand_type: "diehdral"\n' \
' Possible operand types are: "", "atom", "bond", "angle",' \
' "dihedral", "chirality", "planarity"'
else:
raise Exception_expected
a.motif_ids = flex.std_string(["-", "+"])
assert list(a.motif_ids) == ["-", "+"]
a.atom = geometry_restraints.motif_atom(name="a")
assert a.atom.name == "a"
a.motif_atom_name = "x"
assert a.motif_atom_name == "x"
a.bond = geometry_restraints.motif_bond(atom_names=["b", "c"])
assert a.bond.atom_names == ("b", "c")
a.angle = geometry_restraints.motif_angle(atom_names=["d", "e", "f"])
assert a.angle.atom_names == ("d", "e", "f")
a.dihedral = geometry_restraints.motif_dihedral(
atom_names=["h", "i", "j", "k"])
assert a.dihedral.atom_names == ("h", "i", "j", "k")
a.chirality = geometry_restraints.motif_chirality(
atom_names=["l", "m", "n", "o"])
assert a.chirality.atom_names == ("l", "m", "n", "o")
a.planarity = geometry_restraints.motif_planarity(
atom_names=flex.std_string(["p", "q"]), weights=flex.double([1, 2]))
a.planarity_motif_id = "h"
assert a.planarity_motif_id == "h"
a.set_planarity_atom_actions(["add", "change", "delete"])
assert a.planarity_atom_actions_as_list() == ["add", "change", "delete"]
try:
a.set_planarity_atom_actions(["add", "chnage", "delete"])
except RuntimeError as e:
assert str(e) == 'Unknown cctbx::geometry_restraints::motif::alteration' \
'::action_type: "chnage"\n' \
' Possible action types are: "", "add", "delete", "change"'
else:
raise Exception_expected
assert a.planarity_atom_actions_as_list() == []
assert list(a.planarity.atom_names) == ["p", "q"]
assert a.set_change_partial_charge(state=True) is a
assert a.change_partial_charge()
assert not a.change_distance_ideal()
assert a.set_change_distance_ideal(state=True) is a
assert a.change_distance_ideal()
assert not a.change_weight()
assert a.set_change_weight(state=True) is a
assert a.change_weight()
assert not a.change_angle_ideal()
assert a.set_change_angle_ideal(state=True) is a
assert a.change_angle_ideal()
assert not a.change_periodicity()
assert a.set_change_periodicity(state=True) is a
assert a.change_periodicity()
assert not a.change_both_signs()
assert a.set_change_both_signs(state=True) is a
assert a.change_both_signs()
assert not a.change_volume_ideal()
assert a.set_change_volume_ideal(state=True) is a
assert a.change_volume_ideal()