def generate_protein_fragments(
hierarchy,
geometry,
backbone_only=False,
use_capping_hydrogens=False,
verbose=False,
):
from mmtbx.conformation_dependent_library.multi_residue_class import \
ThreeProteinResidues, RestraintsRegistry
registry = RestraintsRegistry()
threes = ThreeProteinResidues(geometry, registry=registry)
for residue in generate_residues_via_conformer(
hierarchy,
backbone_only=backbone_only,
verbose=verbose,
):
list.append(threes, residue)
if verbose: print 'THREE', threes
sub_unit = threes.provide_second_sub_unit_if_unlinked()
if verbose: print 'THREE, SUBUNIT', threes, sub_unit
if sub_unit:
threes.start = True
threes.end = True
yield threes
threes = sub_unit
threes.start = True
threes.end = True
yield threes
def generate_protein_threes(
hierarchy,
geometry,
include_non_linked=False,
omega_cdl=False,
backbone_only=True,
include_non_standard_peptides=False,
verbose=False,
):
peptide_lookup = ['common_amino_acid']
if include_non_standard_peptides:
peptide_lookup.append('modified_amino_acid')
backbone_asc = hierarchy.atom_selection_cache()
backbone_sel = backbone_asc.selection(
"name ca or name c or name n or name o or name cb")
backbone_hierarchy = hierarchy.select(backbone_sel)
get_class = iotbx.pdb.common_residue_names_get_class
threes = ThreeProteinResidues(geometry, registry=registry)
loop_hierarchy = hierarchy
if backbone_only: loop_hierarchy = backbone_hierarchy
for model in loop_hierarchy.models():
if verbose: print 'model: "%s"' % model.id
for chain in model.chains():
if verbose: print 'chain: "%s"' % chain.id
for conformer in chain.conformers():
if verbose:
print ' conformer: altloc="%s"' % (conformer.altloc)
while threes:
del threes[0]
threes.start = None
threes.end = None
list_of_threes = []
for residue in conformer.residues():
if verbose:
if residue.resname not in ["HOH"]:
print ' residue: resname="%s" resid="%s"' % (
residue.resname, residue.resid())
if verbose:
print ' residue class : %s' % get_class(
residue.resname)
if get_class(residue.resname) not in peptide_lookup:
continue
if include_non_linked:
list.append(threes, residue)
if len(threes) > 3: del threes[0]
else:
threes.append(residue)
if len(threes) != 3:
if omega_cdl:
if len(threes) == 2:
threes.insert(0, None)
else:
continue
else:
continue
assert len(threes) <= 3
list_of_threes.append(copy.copy(threes))
# per conformer
for i, threes in enumerate(list_of_threes):
if i == 0:
threes.start = True
if i == len(list_of_threes) - 1:
threes.end = True
else:
if len(threes) != 3:
pass
elif threes[1] != list_of_threes[i + 1][0]:
threes.end = True
list_of_threes[i + 1].start = True
yield threes
threes = ThreeProteinResidues(geometry, registry=registry)
def backrub_move(
prev_res,
cur_res,
next_res,
angle,
move_oxygens=False,
accept_worse_rama=False,
rotamer_manager=None,
rama_manager=None):
import boost.python
ext = boost.python.import_ext("mmtbx_validation_ramachandran_ext")
from mmtbx_validation_ramachandran_ext import rama_eval
from scitbx.matrix import rotate_point_around_axis
from mmtbx.conformation_dependent_library.multi_residue_class import ThreeProteinResidues, \
RestraintsRegistry
if abs(angle) < 1e-4:
return
if prev_res is None or next_res is None:
return
saved_res = [{},{},{}]
for i, r in enumerate([prev_res, cur_res, next_res]):
for a in r.atoms():
saved_res[i][a.name.strip()] = a.xyz
if rotamer_manager is None:
rotamer_manager = RotamerEval()
prev_ca = prev_res.find_atom_by(name=" CA ")
cur_ca = cur_res.find_atom_by(name=" CA ")
next_ca = next_res.find_atom_by(name=" CA ")
if prev_ca is None or next_ca is None or cur_ca is None:
return
atoms_to_move = []
atoms_to_move.append(prev_res.find_atom_by(name=" C "))
atoms_to_move.append(prev_res.find_atom_by(name=" O "))
for atom in cur_res.atoms():
atoms_to_move.append(atom)
atoms_to_move.append(next_res.find_atom_by(name=" N "))
for atom in atoms_to_move:
assert atom is not None
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = next_ca.xyz,
point = atom.xyz,
angle = angle,
deg = True)
atom.xyz = new_xyz
if move_oxygens:
registry = RestraintsRegistry()
if rama_manager is None:
rama_manager = rama_eval()
tpr = ThreeProteinResidues(geometry=None, registry=registry)
tpr.append(prev_res)
tpr.append(cur_res)
tpr.append(next_res)
phi_psi_angles = tpr.get_phi_psi_angles()
rama_key = tpr.get_ramalyze_key()
ev_before = rama_manager.evaluate_angles(rama_key, phi_psi_angles[0], phi_psi_angles[1])
theta1 = _find_theta(
ap1 = prev_ca.xyz,
ap2 = cur_ca.xyz,
cur_xyz = prev_res.find_atom_by(name=" O ").xyz,
needed_xyz = saved_res[0]["O"])
theta2 = _find_theta(
ap1 = cur_ca.xyz,
ap2 = next_ca.xyz,
cur_xyz = cur_res.find_atom_by(name=" O ").xyz,
needed_xyz = saved_res[1]["O"])
for a in [prev_res.find_atom_by(name=" C "),
prev_res.find_atom_by(name=" O "),
cur_res.find_atom_by(name=" C ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = cur_ca.xyz,
point = a.xyz,
angle = theta1,
deg = True)
a.xyz = new_xyz
for a in [cur_res.find_atom_by(name=" C "),
cur_res.find_atom_by(name=" O "),
next_res.find_atom_by(name=" N ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = cur_ca.xyz,
axis_point_2 = next_ca.xyz,
point = a.xyz,
angle = theta2,
deg = True)
a.xyz = new_xyz
phi_psi_angles = tpr.get_phi_psi_angles()
rama_key = tpr.get_ramalyze_key()
ev_after = rama_manager.evaluate_angles(rama_key, phi_psi_angles[0], phi_psi_angles[1])
if ev_before > ev_after and not accept_worse_rama:
for a in [prev_res.find_atom_by(name=" C "),
prev_res.find_atom_by(name=" O "),
cur_res.find_atom_by(name=" C ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = prev_ca.xyz,
axis_point_2 = cur_ca.xyz,
point = a.xyz,
angle = -theta1,
deg = True)
a.xyz = new_xyz
for a in [cur_res.find_atom_by(name=" C "),
cur_res.find_atom_by(name=" O "),
next_res.find_atom_by(name=" N ")]:
new_xyz = rotate_point_around_axis(
axis_point_1 = cur_ca.xyz,
axis_point_2 = next_ca.xyz,
point = a.xyz,
angle = -theta2,
deg = True)
a.xyz = new_xyz
def generate_protein_threes(hierarchy,
geometry,
include_non_linked=False,
omega_cdl=False,
backbone_only=True,
verbose=False,
):
backbone_asc = hierarchy.atom_selection_cache()
backbone_sel = backbone_asc.selection("name ca or name c or name n or name o or name cb")
backbone_hierarchy = hierarchy.select(backbone_sel)
get_class = iotbx.pdb.common_residue_names_get_class
threes = ThreeProteinResidues(geometry, registry=registry)
loop_hierarchy=hierarchy
if backbone_only: loop_hierarchy=backbone_hierarchy
for model in loop_hierarchy.models():
if verbose: print 'model: "%s"' % model.id
for chain in model.chains():
if verbose: print 'chain: "%s"' % chain.id
for conformer in chain.conformers():
if verbose: print ' conformer: altloc="%s"' % (
conformer.altloc)
while threes: del threes[0]
threes.start=None
threes.end=None
list_of_threes = []
for residue in conformer.residues():
if verbose:
if residue.resname not in ["HOH"]:
print ' residue: resname="%s" resid="%s"' % (
residue.resname, residue.resid())
if verbose: print ' residue class : %s' % get_class(residue.resname)
if get_class(residue.resname) not in ["common_amino_acid"]:
continue
if include_non_linked:
list.append(threes, residue)
if len(threes)>3: del threes[0]
else:
threes.append(residue)
if len(threes)!=3:
if omega_cdl:
if len(threes)==2:
threes.insert(0,None)
else: continue
else: continue
assert len(threes)<=3
list_of_threes.append(copy.copy(threes))
# per conformer
for i, threes in enumerate(list_of_threes):
if i==0:
threes.start = True
if i==len(list_of_threes)-1:
threes.end = True
else:
if len(threes)!=3:
pass
elif threes[1] != list_of_threes[i+1][0]:
threes.end = True
list_of_threes[i+1].start = True
yield threes
threes = ThreeProteinResidues(geometry, registry=registry)