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, e:
assert str(e) == 'Unknown cctbx::geometry_restraints::motif::alteration' \
'::action_type: "chnage"\n' \
' Possible action types are: "", "add", "delete", "change"'
def exercise_manipulation():
m = geometry_restraints.motif_manipulation()
assert m.id == ""
assert m.description == ""
assert m.info.size() == 0
assert len(m.alterations_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 list(m.info) == ["c", "d"]
alts = []
a = geometry_restraints.motif_alteration()
a.action = "add"
a.operand = "bond"
alts.append(a)
a = geometry_restraints.motif_alteration()
a.action = "delete"
a.operand = "angle"
alts.append(a)
m.set_alterations(alts)
l = m.alterations_as_list()
assert len(l) == 2
assert l[0].action == "add"
assert l[0].operand == "bond"
assert l[1].action == "delete"
assert l[1].operand == "angle"
#
m = geometry_restraints.motif_manipulation()
m.id = "a"
m.description = "b"
m.info.append("c")
#
alterations = []
a = geometry_restraints.motif_alteration(action="add", operand="atom")
a.motif_ids.append("1")
a.atom.name = "x"
a.atom.scattering_type = "y"
a.atom.nonbonded_type = "z"
a.atom.partial_charge = -0.2
alterations.append(a)
for change_partial_charge in [False, True]:
a = geometry_restraints.motif_alteration(action="change", operand="atom")
a.motif_ids.append("0")
a.motif_atom_name = "p"
a.atom.name = "q"
a.atom.scattering_type = "r"
a.atom.nonbonded_type = "s"
a.atom.partial_charge = 0.3
a.set_change_partial_charge(state=change_partial_charge)
alterations.append(a)
a = geometry_restraints.motif_alteration(action="delete", operand="atom")
a.motif_ids.append("3")
a.motif_atom_name = "d"
alterations.append(a)
#
a = geometry_restraints.motif_alteration(action="add", operand="bond")
a.motif_ids.append("1")
a.motif_ids.append("2")
a.bond.atom_names = ["j", "k"]
a.bond.distance_ideal = 1.2
a.bond.weight = 3.1
a.bond.id = "s"
alterations.append(a)
for change_distance_ideal in [False, True]:
for change_weight in [False, True]:
a = geometry_restraints.motif_alteration(action="change", operand="bond")
a.motif_ids.append("3")
a.motif_ids.append("4")
a.bond.atom_names = ["l", "m"]
a.bond.distance_ideal = 4.5
a.bond.weight = 2.8
a.bond.id = "g"
a.set_change_distance_ideal(state=change_distance_ideal)
a.set_change_weight(state=change_weight)
alterations.append(a)
a = geometry_restraints.motif_alteration(action="delete", operand="bond")
a.motif_ids.append("5")
a.motif_ids.append("6")
a.bond.atom_names = ["t", "n"]
alterations.append(a)
#
a = geometry_restraints.motif_alteration(action="add", operand="angle")
a.motif_ids.append("1")
a.motif_ids.append("2")
a.motif_ids.append("3")
a.angle.atom_names = ["j", "k", "l"]
a.angle.angle_ideal = 1.2
a.angle.weight = 3.1
a.angle.id = "s"
alterations.append(a)
for change_angle_ideal in [False, True]:
for change_weight in [False, True]:
a = geometry_restraints.motif_alteration(
action="change", operand="angle")
a.motif_ids.append("3")
a.motif_ids.append("4")
a.motif_ids.append("5")
a.angle.atom_names = ["l", "m", "g"]
a.angle.angle_ideal = 4.5
a.angle.weight = 2.8
a.angle.id = "g"
a.set_change_angle_ideal(state=change_angle_ideal)
a.set_change_weight(state=change_weight)
alterations.append(a)
a = geometry_restraints.motif_alteration(action="delete", operand="angle")
a.motif_ids.append("6")
a.motif_ids.append("7")
a.motif_ids.append("8")
a.angle.atom_names = ["t", "n", "d"]
alterations.append(a)
#
a = geometry_restraints.motif_alteration(action="add", operand="dihedral")
a.motif_ids.append("1")
a.motif_ids.append("2")
a.motif_ids.append("3")
a.motif_ids.append("4")
a.dihedral.atom_names = ["j", "k", "l", "r"]
a.dihedral.angle_ideal = 1.2
a.dihedral.weight = 3.1
a.dihedral.periodicity = 20
a.dihedral.id = "s"
alterations.append(a)
for change_angle_ideal in [False, True]:
for change_weight in [False, True]:
for change_periodicity in [False, True]:
a = geometry_restraints.motif_alteration(
action="change", operand="dihedral")
a.motif_ids.append("5")
a.motif_ids.append("6")
a.motif_ids.append("7")
a.motif_ids.append("8")
a.dihedral.atom_names = ["l", "m", "g", "e"]
a.dihedral.angle_ideal = 4.5
a.dihedral.weight = 2.8
a.dihedral.periodicity = 13
a.dihedral.id = "g"
a.set_change_angle_ideal(state=change_angle_ideal)
a.set_change_weight(state=change_weight)
a.set_change_periodicity(state=change_periodicity)
alterations.append(a)
a = geometry_restraints.motif_alteration(action="delete", operand="dihedral")
a.motif_ids.append("9")
a.motif_ids.append("10")
a.motif_ids.append("11")
a.motif_ids.append("12")
a.dihedral.atom_names = ["t", "n", "d", "y"]
alterations.append(a)
#
a = geometry_restraints.motif_alteration(action="add", operand="chirality")
a.motif_ids.append("1")
a.motif_ids.append("2")
a.motif_ids.append("3")
a.motif_ids.append("4")
a.chirality.atom_names = ["j", "k", "l", "r"]
a.chirality.volume_sign = "x"
a.chirality.volume_ideal = 1.2
a.chirality.weight = 3.1
a.chirality.id = "w"
alterations.append(a)
for change_volume_ideal in [False, True]:
for change_weight in [False, True]:
a = geometry_restraints.motif_alteration(
action="change", operand="chirality")
a.motif_ids.append("5")
a.motif_ids.append("6")
a.motif_ids.append("7")
a.motif_ids.append("8")
a.chirality.atom_names = ["l", "m", "g", "e"]
a.chirality.volume_sign = "u"
a.chirality.volume_ideal = 4.5
a.chirality.weight = 2.8
a.chirality.id = "g"
a.set_change_volume_ideal(state=change_volume_ideal)
a.set_change_weight(state=change_weight)
alterations.append(a)
a = geometry_restraints.motif_alteration(
action="delete", operand="chirality")
a.motif_ids.append("9")
a.motif_ids.append("10")
a.motif_ids.append("11")
a.motif_ids.append("12")
a.chirality.atom_names = ["t", "n", "d", "y"]
alterations.append(a)
#
a = geometry_restraints.motif_alteration(action="add", operand="planarity")
a.planarity_motif_id = "7"
a.planarity.id = "e"
a.motif_ids.append("1")
a.motif_ids.append("2")
a.motif_ids.append("3")
a.planarity.atom_names.append("s")
a.planarity.atom_names.append("d")
a.planarity.atom_names.append("f")
a.planarity.weights.append(1.2)
a.planarity.weights.append(2.3)
a.planarity.weights.append(3.4)
alterations.append(a)
a = geometry_restraints.motif_alteration(
action="change", operand="planarity")
a.planarity_motif_id = "8"
a.planarity.id = "f"
a.set_planarity_atom_actions(["add", "change", "delete"])
a.motif_ids.append("1")
a.motif_ids.append("2")
a.motif_ids.append("3")
a.planarity.atom_names.append("s")
a.planarity.atom_names.append("d")
a.planarity.atom_names.append("f")
a.planarity.weights.append(1.2)
a.planarity.weights.append(2.3)
a.planarity.weights.append(0)
alterations.append(a)
a = geometry_restraints.motif_alteration(
action="delete", operand="planarity")
a.planarity_motif_id = "4"
a.planarity.id = "n"
alterations.append(a)
#
m.set_alterations(alterations)
out = StringIO()
m.show(out=out, prefix="^")
assert not show_diff(out.getvalue(), """\
^geometry_restraints.motif_manipulation {
^ id = "a"
^ description = "b"
^ info = "c"
^ atom = add [motif_id name scattering_type nonbonded_type partial_charge]
^ atom = add "1" "x" "y" "z" -0.2
^ atom = change [motif_id motif_atom_name \\
^ name scattering_type nonbonded_type partial_charge]
^ atom = change "0" "p" \\
^ "q" "r" "s" None
^ atom = change "0" "p" \\
^ "q" "r" "s" 0.3
^ atom = delete [motif_id motif_atom_name]
^ atom = delete "3" "d"
^ bond = add [(motif_id atom_name)*2 type distance_ideal weight id]
^ bond = add "1" "j" "2" "k" 1.2 3.1 "s"
^ bond = change [(motif_id atom_name)*2 type distance_ideal weight id]
^ bond = change "3" "l" "4" "m" None None "g"
^ bond = change "3" "l" "4" "m" None 2.8 "g"
^ bond = change "3" "l" "4" "m" 4.5 None "g"
^ bond = change "3" "l" "4" "m" 4.5 2.8 "g"
^ bond = delete [(motif_id atom_name)*2]
^ bond = delete "5" "t" "6" "n"
^ angle = add [(motif_id atom_name)*3 type angle_ideal weight id]
^ angle = add "1" "j" "2" "k" "3" "l" 1.2 3.1 "s"
^ angle = change [(motif_id atom_name)*3 type angle_ideal weight id]
^ angle = change "3" "l" "4" "m" "5" "g" None None "g"
^ angle = change "3" "l" "4" "m" "5" "g" None 2.8 "g"
^ angle = change "3" "l" "4" "m" "5" "g" 4.5 None "g"
^ angle = change "3" "l" "4" "m" "5" "g" 4.5 2.8 "g"
^ angle = delete [(motif_id atom_name)*3]
^ angle = delete "6" "t" "7" "n" "8" "d"
^ dihedral = add [(motif_id atom_name)*4 angle_ideal weight periodicity id]
^ dihedral = add "1" "j" "2" "k" "3" "l" "4" "r" 1.2 3.1 20 "s"
^ dihedral = change [(motif_id atom_name)*4 angle_ideal weight periodicity id]
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" None None None "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" None None 13 "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" None 2.8 None "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" None 2.8 13 "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" 4.5 None None "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" 4.5 None 13 "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" 4.5 2.8 None "g"
^ dihedral = change "5" "l" "6" "m" "7" "g" "8" "e" 4.5 2.8 13 "g"
^ dihedral = delete [(motif_id atom_name)*4]
^ dihedral = delete "9" "t" "10" "n" "11" "d" "12" "y"
^ chirality = add [(motif_id atom_name)*4 \\
^ volume_sign volume_ideal weight id]
^ chirality = add "1" "j" "2" "k" "3" "l" "4" "r" \\
^ "x" 1.2 3.1 "w"
^ chirality = change [(motif_id atom_name)*4 \\
^ volume_sign volume_ideal weight id]
^ chirality = change "5" "l" "6" "m" "7" "g" "8" "e" \\
^ "u" None None "g"
^ chirality = change "5" "l" "6" "m" "7" "g" "8" "e" \\
^ "u" None 2.8 "g"
^ chirality = change "5" "l" "6" "m" "7" "g" "8" "e" \\
^ "u" 4.5 None "g"
^ chirality = change "5" "l" "6" "m" "7" "g" "8" "e" \\
^ "u" 4.5 2.8 "g"
^ chirality = delete [(motif_id atom_name)*4]
^ chirality = delete "9" "t" "10" "n" "11" "d" "12" "y"
^ planarity {
^ action = add
^ motif_id = "7"
^ id = "e"
^ atom = [motif_id name weight]
^ atom = "1" "s" 1.2
^ atom = "2" "d" 2.3
^ atom = "3" "f" 3.4
^ }
^ planarity {
^ action = change
^ motif_id = "8"
^ id = "f"
^ atom = add [motif_id name weight]
^ atom = add "1" "s" 1.2
^ atom = change [motif_id name weight]
^ atom = change "2" "d" 2.3
^ atom = delete [motif_id name]
^ atom = delete "3" "f"
^ }
^ planarity {
^ action = delete
^ motif_id = "4"
^ id = "n"
^ }
^}
""")
out = StringIO()
m.show(out=out)
phil.parse(input_string=out.getvalue())
def as_geometry_restraints_motif_manipulation(self):
result = geometry_restraints.motif_manipulation()
result.id = if_none(self.chem_mod.id, "")
result.description = if_none(self.chem_mod.name, "")
if (self.source_info is not None):
result.info.append(self.source_info)
alts = []
for atom in self.atom_list:
a = geometry_restraints.motif_alteration(
action=if_none(atom.function, ""), operand="atom")
a.motif_ids.append("")
if (a.action != "add"):
a.motif_atom_name = if_none(atom.atom_id, "")
a.atom.name = if_none(atom.new_atom_id, "")
a.atom.scattering_type = if_none(atom.new_type_symbol, "")
a.atom.nonbonded_type = if_none(atom.new_type_energy, "")
a.atom.partial_charge = if_none(atom.new_partial_charge, 0)
if (a.action == "change"):
a.set_change_partial_charge(state=atom.new_partial_charge is not None)
alts.append(a)
for bond in self.bond_list:
a = geometry_restraints.motif_alteration(
action=if_none(bond.function, ""), operand="bond")
a.motif_ids.append("")
a.motif_ids.append("")
a.bond.atom_names = [
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")]
a.bond.type = if_none(bond.new_type, "")
a.bond.distance_ideal = if_none(bond.new_value_dist, 0)
a.bond.weight = esd_as_weight(bond.new_value_dist_esd)
if (a.action == "change"):
a.set_change_distance_ideal(state=bond.new_value_dist is not None)
a.set_change_weight(state=bond.new_value_dist_esd is not None)
alts.append(a)
for angle in self.angle_list:
a = geometry_restraints.motif_alteration(
action=if_none(bond.function, ""), operand="angle")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.angle.atom_names = [
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")]
a.angle.angle_ideal = if_none(angle.new_value_angle, 0)
a.angle.weight = esd_as_weight(angle.new_value_angle_esd)
if (a.action == "change"):
a.set_change_angle_ideal(state=angle.new_value_angle is not None)
a.set_change_weight(state=angle.new_value_angle_esd is not None)
alts.append(a)
for tor in self.tor_list:
a = geometry_restraints.motif_alteration(
action=if_none(tor.function, ""), operand="dihedral")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.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, "")]
a.dihedral.angle_ideal = if_none(tor.new_value_angle, 0)
a.dihedral.weight = esd_as_weight(tor.new_value_angle_esd)
a.dihedral.periodicity = if_none(tor.new_period, 0)
a.dihedral.id = if_none(tor.id, "")
if (a.action == "change"):
a.set_change_angle_ideal(state=tor.new_value_angle is not None)
a.set_change_weight(state=tor.new_value_angle_esd is not None)
a.set_change_periodicity(state=tor.new_period is not None)
alts.append(a)
for chir in self.chir_list:
a = geometry_restraints.motif_alteration(
action=if_none(chir.function, ""), operand="chirality")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.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, "")]
a.chirality.volume_sign = if_none(chir.new_volume_sign, 0)
a.chirality.id = if_none(chir.id, "")
alts.append(a)
for plane in self.get_planes():
a = geometry_restraints.motif_alteration(
action="change", operand="planarity")
a.motif_ids.resize(len(plane.plane_atoms))
a.set_planarity_atom_actions([if_none(plane_atom.function, "")
for plane_atom in plane.plane_atoms])
a.planarity.atom_names = flex.std_string([if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms])
a.planarity.weights = flex.double([esd_as_weight(plane_atom.new_dist_esd)
for plane_atom in plane.plane_atoms])
a.planarity.id = plane.plane_id
alts.append(a)
result.set_alterations(alts)
return result
def as_geometry_restraints_motif_manipulation(self):
result = geometry_restraints.motif_manipulation()
result.id = if_none(self.chem_link.id, "")
result.description = if_none(self.chem_link.name, "")
if (self.source_info is not None):
result.info.append(self.source_info)
alts = []
for bond in self.bond_list:
a = geometry_restraints.motif_alteration(
action="add", operand="bond")
a.motif_ids.append(str(if_none(bond.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(bond.atom_2_comp_id, "")))
a.bond.atom_names = [
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")]
a.bond.type = if_none(bond.type, "")
a.bond.distance_ideal = if_none(bond.value_dist, 0)
a.bond.weight = esd_as_weight(bond.value_dist_esd)
alts.append(a)
for angle in self.angle_list:
a = geometry_restraints.motif_alteration(
action="add", operand="angle")
a.motif_ids.append(str(if_none(angle.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(angle.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(angle.atom_3_comp_id, "")))
a.angle.atom_names = [
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")]
a.angle.angle_ideal = if_none(angle.value_angle, 0)
a.angle.weight = esd_as_weight(angle.value_angle_esd)
alts.append(a)
for tor in self.tor_list:
a = geometry_restraints.motif_alteration(
action="add", operand="dihedral")
a.motif_ids.append(str(if_none(tor.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_3_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_4_comp_id, "")))
a.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, "")]
a.dihedral.angle_ideal = if_none(tor.value_angle, 0)
a.dihedral.weight = esd_as_weight(tor.value_angle_esd)
a.dihedral.periodicity = if_none(tor.period, 0)
a.dihedral.id = if_none(tor.id, "")
alts.append(a)
for chir in self.chir_list:
a = geometry_restraints.motif_alteration(
action="add", operand="chirality")
a.motif_ids.append(str(if_none(chir.atom_centre_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_3_comp_id, "")))
a.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, "")]
a.chirality.volume_sign = if_none(chir.volume_sign, 0)
a.chirality.id = if_none(chir.id, "")
alts.append(a)
for plane in self.get_planes():
a = geometry_restraints.motif_alteration(
action="add", operand="planarity")
for plane_atom in plane.plane_atoms:
if (plane_atom.atom_comp_id is None):
a.motif_ids.append("")
else:
a.motif_ids.append(str(plane_atom.atom_comp_id))
a.planarity.atom_names = flex.std_string([if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms])
a.planarity.weights = flex.double([esd_as_weight(plane_atom.dist_esd)
for plane_atom in plane.plane_atoms])
a.planarity.id = plane.plane_id
alts.append(a)
result.set_alterations(alts)
return result
def as_geometry_restraints_motif_manipulation(self):
result = geometry_restraints.motif_manipulation()
result.id = if_none(self.chem_link.id, "")
result.description = if_none(self.chem_link.name, "")
if (self.source_info is not None):
result.info.append(self.source_info)
alts = []
for bond in self.bond_list:
a = geometry_restraints.motif_alteration(action="add",
operand="bond")
a.motif_ids.append(str(if_none(bond.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(bond.atom_2_comp_id, "")))
a.bond.atom_names = [
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")
]
a.bond.type = if_none(bond.type, "")
a.bond.distance_ideal = if_none(bond.value_dist, 0)
a.bond.weight = esd_as_weight(bond.value_dist_esd)
alts.append(a)
for angle in self.angle_list:
a = geometry_restraints.motif_alteration(action="add",
operand="angle")
a.motif_ids.append(str(if_none(angle.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(angle.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(angle.atom_3_comp_id, "")))
a.angle.atom_names = [
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")
]
a.angle.angle_ideal = if_none(angle.value_angle, 0)
a.angle.weight = esd_as_weight(angle.value_angle_esd)
alts.append(a)
for tor in self.tor_list:
a = geometry_restraints.motif_alteration(action="add",
operand="dihedral")
a.motif_ids.append(str(if_none(tor.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_3_comp_id, "")))
a.motif_ids.append(str(if_none(tor.atom_4_comp_id, "")))
a.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, "")
]
a.dihedral.angle_ideal = if_none(tor.value_angle, 0)
a.dihedral.weight = esd_as_weight(tor.value_angle_esd)
a.dihedral.periodicity = if_none(tor.period, 0)
a.dihedral.id = if_none(tor.id, "")
alts.append(a)
for chir in self.chir_list:
a = geometry_restraints.motif_alteration(action="add",
operand="chirality")
a.motif_ids.append(str(if_none(chir.atom_centre_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_1_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_2_comp_id, "")))
a.motif_ids.append(str(if_none(chir.atom_3_comp_id, "")))
a.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, "")
]
a.chirality.volume_sign = if_none(chir.volume_sign, 0)
a.chirality.id = if_none(chir.id, "")
alts.append(a)
for plane in self.get_planes():
a = geometry_restraints.motif_alteration(action="add",
operand="planarity")
for plane_atom in plane.plane_atoms:
if (plane_atom.atom_comp_id is None):
a.motif_ids.append("")
else:
a.motif_ids.append(str(plane_atom.atom_comp_id))
a.planarity.atom_names = flex.std_string([
if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms
])
a.planarity.weights = flex.double([
esd_as_weight(plane_atom.dist_esd)
for plane_atom in plane.plane_atoms
])
a.planarity.id = plane.plane_id
alts.append(a)
result.set_alterations(alts)
return result
def as_geometry_restraints_motif_manipulation(self):
result = geometry_restraints.motif_manipulation()
result.id = if_none(self.chem_mod.id, "")
result.description = if_none(self.chem_mod.name, "")
if (self.source_info is not None):
result.info.append(self.source_info)
alts = []
for atom in self.atom_list:
a = geometry_restraints.motif_alteration(action=if_none(
atom.function, ""),
operand="atom")
a.motif_ids.append("")
if (a.action != "add"):
a.motif_atom_name = if_none(atom.atom_id, "")
a.atom.name = if_none(atom.new_atom_id, "")
a.atom.scattering_type = if_none(atom.new_type_symbol, "")
a.atom.nonbonded_type = if_none(atom.new_type_energy, "")
a.atom.partial_charge = if_none(atom.new_partial_charge, 0)
if (a.action == "change"):
a.set_change_partial_charge(
state=atom.new_partial_charge is not None)
alts.append(a)
for bond in self.bond_list:
a = geometry_restraints.motif_alteration(action=if_none(
bond.function, ""),
operand="bond")
a.motif_ids.append("")
a.motif_ids.append("")
a.bond.atom_names = [
if_none(bond.atom_id_1, ""),
if_none(bond.atom_id_2, "")
]
a.bond.type = if_none(bond.new_type, "")
a.bond.distance_ideal = if_none(bond.new_value_dist, 0)
a.bond.weight = esd_as_weight(bond.new_value_dist_esd)
if (a.action == "change"):
a.set_change_distance_ideal(
state=bond.new_value_dist is not None)
a.set_change_weight(state=bond.new_value_dist_esd is not None)
alts.append(a)
for angle in self.angle_list:
a = geometry_restraints.motif_alteration(action=if_none(
bond.function, ""),
operand="angle")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.angle.atom_names = [
if_none(angle.atom_id_1, ""),
if_none(angle.atom_id_2, ""),
if_none(angle.atom_id_3, "")
]
a.angle.angle_ideal = if_none(angle.new_value_angle, 0)
a.angle.weight = esd_as_weight(angle.new_value_angle_esd)
if (a.action == "change"):
a.set_change_angle_ideal(
state=angle.new_value_angle is not None)
a.set_change_weight(
state=angle.new_value_angle_esd is not None)
alts.append(a)
for tor in self.tor_list:
a = geometry_restraints.motif_alteration(action=if_none(
tor.function, ""),
operand="dihedral")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.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, "")
]
a.dihedral.angle_ideal = if_none(tor.new_value_angle, 0)
a.dihedral.weight = esd_as_weight(tor.new_value_angle_esd)
a.dihedral.periodicity = if_none(tor.new_period, 0)
a.dihedral.id = if_none(tor.id, "")
if (a.action == "change"):
a.set_change_angle_ideal(state=tor.new_value_angle is not None)
a.set_change_weight(state=tor.new_value_angle_esd is not None)
a.set_change_periodicity(state=tor.new_period is not None)
alts.append(a)
for chir in self.chir_list:
a = geometry_restraints.motif_alteration(action=if_none(
chir.function, ""),
operand="chirality")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.motif_ids.append("")
a.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, "")
]
a.chirality.volume_sign = if_none(chir.new_volume_sign, 0)
a.chirality.id = if_none(chir.id, "")
alts.append(a)
for plane in self.get_planes():
a = geometry_restraints.motif_alteration(action="change",
operand="planarity")
a.motif_ids.resize(len(plane.plane_atoms))
a.set_planarity_atom_actions([
if_none(plane_atom.function, "")
for plane_atom in plane.plane_atoms
])
a.planarity.atom_names = flex.std_string([
if_none(plane_atom.atom_id, "")
for plane_atom in plane.plane_atoms
])
a.planarity.weights = flex.double([
esd_as_weight(plane_atom.new_dist_esd)
for plane_atom in plane.plane_atoms
])
a.planarity.id = plane.plane_id
alts.append(a)
result.set_alterations(alts)
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()