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(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_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(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_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